HEADER TRANSFERASE/DNA 30-NOV-16 5U2S
TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED
TITLE 2 DNA SUBSTRATE INCOMING (-)3TC-TP AND CA2+.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE BETA;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.7.7,4.2.99.-;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER;
COMPND 8 CHAIN: D;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: 10- MER PRIMER;
COMPND 12 CHAIN: P;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 4;
COMPND 15 MOLECULE: 16- MER TEMPLATE;
COMPND 16 CHAIN: T;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLB;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 14 ORGANISM_TAXID: 32630;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 18 ORGANISM_TAXID: 32630;
SOURCE 19 MOL_ID: 4;
SOURCE 20 SYNTHETIC: YES;
SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 22 ORGANISM_TAXID: 32630
KEYWDS X-FAMILY, POL BETA, DNA POLYMERASE BETA, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR R.VYAS,Z.SUO
REVDAT 6 04-OCT-23 5U2S 1 LINK
REVDAT 5 27-NOV-19 5U2S 1 REMARK
REVDAT 4 17-JUL-19 5U2S 1 COMPND HETNAM HETSYN
REVDAT 3 13-SEP-17 5U2S 1 REMARK
REVDAT 2 14-JUN-17 5U2S 1 JRNL
REVDAT 1 24-MAY-17 5U2S 0
JRNL AUTH R.VYAS,A.J.REED,A.T.RAPER,W.J.ZAHURANCIK,P.C.WALLENMEYER,
JRNL AUTH 2 Z.SUO
JRNL TITL STRUCTURAL BASIS FOR THE D-STEREOSELECTIVITY OF HUMAN DNA
JRNL TITL 2 POLYMERASE BETA.
JRNL REF NUCLEIC ACIDS RES. V. 45 6228 2017
JRNL REFN ESSN 1362-4962
JRNL PMID 28402499
JRNL DOI 10.1093/NAR/GKX252
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 19157
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.233
REMARK 3 R VALUE (WORKING SET) : 0.230
REMARK 3 FREE R VALUE : 0.284
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 997
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1386
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.3070
REMARK 3 BIN FREE R VALUE SET COUNT : 83
REMARK 3 BIN FREE R VALUE : 0.3920
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2612
REMARK 3 NUCLEIC ACID ATOMS : 632
REMARK 3 HETEROGEN ATOMS : 56
REMARK 3 SOLVENT ATOMS : 94
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.93
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.09000
REMARK 3 B22 (A**2) : 0.03000
REMARK 3 B33 (A**2) : -0.09000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.03000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.420
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.275
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.856
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3414 ; 0.010 ; 0.018
REMARK 3 BOND LENGTHS OTHERS (A): 2964 ; 0.007 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4725 ; 1.476 ; 1.799
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6864 ; 0.946 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 6.257 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;36.845 ;24.286
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 507 ;16.390 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.520 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.079 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3378 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 761 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1308 ; 2.695 ; 4.008
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1301 ; 2.664 ; 4.003
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1624 ; 4.404 ; 5.990
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1625 ; 4.404 ; 5.992
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2106 ; 2.493 ; 4.010
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2105 ; 2.492 ; 4.010
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3101 ; 3.975 ; 5.927
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4118 ; 7.219 ;32.201
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4102 ; 7.208 ;32.208
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5U2S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-16.
REMARK 100 THE DEPOSITION ID IS D_1000225222.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-DEC-14
REMARK 200 TEMPERATURE (KELVIN) : 295
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 31-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23005
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 44.030
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.16000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.44200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 4RQ7
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.75
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM
REMARK 280 ACETATE, 17% PEG3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.72500
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6020 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21320 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A -1
REMARK 465 GLY A 0
REMARK 465 MET A 1
REMARK 465 SER A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 4
REMARK 465 LYS A 5
REMARK 465 THR A 205
REMARK 465 LYS A 206
REMARK 465 SER A 334
REMARK 465 GLU A 335
REMARK 465 HIS A 336
REMARK 465 HIS A 337
REMARK 465 HIS A 338
REMARK 465 HIS A 339
REMARK 465 HIS A 340
REMARK 465 HIS A 341
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NE2 HIS A 212 OE2 GLU A 216 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 DG D 1 P DG D 1 OP3 -0.125
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 PRO A 50 41.49 -82.17
REMARK 500 ASP A 170 117.82 -161.37
REMARK 500 CYS A 178 -140.06 -110.41
REMARK 500 ASP A 190 -167.13 -168.18
REMARK 500 ASP A 276 -17.15 99.83
REMARK 500 VAL A 303 -1.28 80.74
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 405 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 24 OD1
REMARK 620 2 HOH A 521 O 154.3
REMARK 620 3 HOH A 568 O 106.2 60.4
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 403 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 84.2
REMARK 620 3 VAL A 65 O 87.0 79.5
REMARK 620 4 DC D 3 OP1 166.9 82.8 89.3
REMARK 620 5 HOH D 102 O 99.8 174.7 104.1 93.3
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 404 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 101 O
REMARK 620 2 VAL A 103 O 94.3
REMARK 620 3 ILE A 106 O 98.9 85.7
REMARK 620 4 ACT A 406 OXT 86.5 85.2 169.7
REMARK 620 5 DG P 9 OP1 166.1 95.5 91.5 84.7
REMARK 620 6 HOH P 104 O 84.9 173.1 87.6 101.6 86.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 402 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD1
REMARK 620 2 ASP A 192 OD1 71.0
REMARK 620 3 ASP A 192 OD2 106.6 43.8
REMARK 620 4 1RZ A 401 O3G 80.5 139.1 172.0
REMARK 620 5 1RZ A 401 O2A 126.4 89.0 87.9 84.8
REMARK 620 6 1RZ A 401 O3B 125.9 162.9 120.9 54.7 82.0
REMARK 620 7 HOH A 507 O 68.2 52.2 88.9 90.5 60.6 131.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 412 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 1RZ A 401 O1A
REMARK 620 2 1RZ A 401 O2A 55.6
REMARK 620 3 HOH A 507 O 104.8 55.6
REMARK 620 4 DC P 10 O3' 85.7 107.3 88.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 1RZ A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 411
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 412
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5U2R RELATED DB: PDB
REMARK 900 RELATED ID: 5U2T RELATED DB: PDB
DBREF 5U2S A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 5U2S D 1 5 PDB 5U2S 5U2S 1 5
DBREF 5U2S P 1 10 PDB 5U2S 5U2S 1 10
DBREF 5U2S T 1 16 PDB 5U2S 5U2S 1 16
SEQADV 5U2S MET A -1 UNP P06746 INITIATING METHIONINE
SEQADV 5U2S GLY A 0 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 336 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 337 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 338 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 339 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 340 UNP P06746 EXPRESSION TAG
SEQADV 5U2S HIS A 341 UNP P06746 EXPRESSION TAG
SEQRES 1 A 343 MET GLY MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU
SEQRES 2 A 343 ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN
SEQRES 3 A 343 PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN
SEQRES 4 A 343 ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO
SEQRES 5 A 343 HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO
SEQRES 6 A 343 GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE
SEQRES 7 A 343 LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG
SEQRES 8 A 343 GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR ARG
SEQRES 9 A 343 VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL
SEQRES 10 A 343 ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN
SEQRES 11 A 343 GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS
SEQRES 12 A 343 TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU
SEQRES 13 A 343 MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS
SEQRES 14 A 343 LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER
SEQRES 15 A 343 PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL
SEQRES 16 A 343 LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR LYS
SEQRES 17 A 343 GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN
SEQRES 18 A 343 LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU
SEQRES 19 A 343 THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN
SEQRES 20 A 343 ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG
SEQRES 21 A 343 LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR
SEQRES 22 A 343 PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA
SEQRES 23 A 343 HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR
SEQRES 24 A 343 ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO
SEQRES 25 A 343 LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE
SEQRES 26 A 343 GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HIS
SEQRES 27 A 343 HIS HIS HIS HIS HIS
SEQRES 1 D 5 DG DT DC DG DG
SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC
SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC
SEQRES 2 T 16 DA DG DC
HET 1RZ A 401 27
HET CA A 402 1
HET NA A 403 1
HET NA A 404 1
HET NA A 405 1
HET ACT A 406 4
HET ACT A 407 4
HET ACT A 408 4
HET ACT A 409 4
HET ACT A 410 4
HET ACT A 411 4
HET NA A 412 1
HETNAM 1RZ LAMIVUDINE TRIPHOSPHATE
HETNAM CA CALCIUM ION
HETNAM NA SODIUM ION
HETNAM ACT ACETATE ION
HETSYN 1RZ LAMIVUDINE-5'-TRIPHOSPHATE; 3TC TRIPHOSPHATE; [[(2R,
HETSYN 2 1RZ 5S)-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-
HETSYN 3 1RZ OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO
HETSYN 4 1RZ HYDROGEN PHOSPHATE
FORMUL 5 1RZ C8 H14 N3 O12 P3 S
FORMUL 6 CA CA 2+
FORMUL 7 NA 4(NA 1+)
FORMUL 10 ACT 6(C2 H3 O2 1-)
FORMUL 17 HOH *94(H2 O)
HELIX 1 AA1 ASN A 12 VAL A 29 1 18
HELIX 2 AA2 ALA A 32 LYS A 48 1 17
HELIX 3 AA3 SER A 55 LYS A 60 1 6
HELIX 4 AA4 GLY A 66 GLY A 80 1 15
HELIX 5 AA5 LEU A 82 ASP A 91 1 10
HELIX 6 AA6 ASP A 91 THR A 101 1 11
HELIX 7 AA7 GLY A 107 GLU A 117 1 11
HELIX 8 AA8 THR A 121 ASN A 128 1 8
HELIX 9 AA9 GLU A 129 LEU A 132 5 4
HELIX 10 AB1 ASN A 133 TYR A 142 1 10
HELIX 11 AB2 GLY A 144 LYS A 148 5 5
HELIX 12 AB3 ARG A 152 ASP A 170 1 19
HELIX 13 AB4 CYS A 178 ARG A 183 1 6
HELIX 14 AB5 LYS A 209 VAL A 221 1 13
HELIX 15 AB6 PRO A 261 ASP A 263 5 3
HELIX 16 AB7 GLN A 264 GLY A 274 1 11
HELIX 17 AB8 ASP A 276 LYS A 289 1 14
HELIX 18 AB9 LYS A 317 TYR A 322 1 6
SHEET 1 AA1 2 ILE A 150 PRO A 151 0
SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150
SHEET 1 AA2 5 ILE A 174 VAL A 177 0
SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176
SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195
SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N GLY A 237 O ILE A 255
SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236
SHEET 1 AA3 2 PHE A 291 ILE A 293 0
SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK OD1 ASN A 24 NA NA A 405 1555 1555 2.57
LINK O LYS A 60 NA NA A 403 1555 1555 2.42
LINK O LEU A 62 NA NA A 403 1555 1555 2.92
LINK O VAL A 65 NA NA A 403 1555 1555 2.39
LINK O THR A 101 NA NA A 404 1555 1555 2.27
LINK O VAL A 103 NA NA A 404 1555 1555 2.48
LINK O ILE A 106 NA NA A 404 1555 1555 2.26
LINK OD1 ASP A 190 CA CA A 402 1555 1555 2.37
LINK OD1 ASP A 192 CA CA A 402 1555 1555 3.13
LINK OD2 ASP A 192 CA CA A 402 1555 1555 2.45
LINK O3G 1RZ A 401 CA CA A 402 1555 1555 2.41
LINK O2A 1RZ A 401 CA CA A 402 1555 1555 2.24
LINK O3B 1RZ A 401 CA CA A 402 1555 1555 2.86
LINK O1A 1RZ A 401 NA NA A 412 1555 1555 2.75
LINK O2A 1RZ A 401 NA NA A 412 1555 1555 2.83
LINK CA CA A 402 O HOH A 507 1555 1555 2.76
LINK NA NA A 403 OP1 DC D 3 1555 1555 2.73
LINK NA NA A 403 O HOH D 102 1555 1555 2.20
LINK NA NA A 404 OXT ACT A 406 1555 1555 2.33
LINK NA NA A 404 OP1 DG P 9 1555 1555 2.35
LINK NA NA A 404 O HOH P 104 1555 1555 2.42
LINK NA NA A 405 O HOH A 521 1555 1555 2.90
LINK NA NA A 405 O HOH A 568 1555 1555 2.24
LINK NA NA A 412 O HOH A 507 1555 1555 2.65
LINK NA NA A 412 O3' DC P 10 1555 1555 2.79
CISPEP 1 GLY A 274 SER A 275 0 14.14
CISPEP 2 THR A 304 GLY A 305 0 5.86
SITE 1 AC1 19 ARG A 149 GLY A 179 SER A 180 ARG A 183
SITE 2 AC1 19 SER A 188 GLY A 189 ASP A 190 ASP A 192
SITE 3 AC1 19 TYR A 271 ASP A 276 ASN A 279 ARG A 283
SITE 4 AC1 19 CA A 402 NA A 412 HOH A 507 HOH A 537
SITE 5 AC1 19 HOH A 556 HOH P 101 DG T 6
SITE 1 AC2 4 ASP A 190 ASP A 192 1RZ A 401 HOH A 507
SITE 1 AC3 5 LYS A 60 LEU A 62 VAL A 65 DC D 3
SITE 2 AC3 5 HOH D 102
SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 ACT A 406
SITE 2 AC4 6 DG P 9 HOH P 104
SITE 1 AC5 5 ASN A 24 LYS A 27 ASN A 28 HOH A 521
SITE 2 AC5 5 HOH A 568
SITE 1 AC6 7 THR A 101 ARG A 102 VAL A 103 SER A 104
SITE 2 AC6 7 NA A 404 DG P 9 DC P 10
SITE 1 AC7 5 HIS A 34 ASN A 37 HOH A 508 DG D 1
SITE 2 AC7 5 DC T 5
SITE 1 AC8 3 ASP A 130 LEU A 132 ARG A 137
SITE 1 AC9 1 ALA A 110
SITE 1 AD1 1 PRO A 63
SITE 1 AD2 3 ARG A 89 GLN A 90 SER A 95
SITE 1 AD3 3 1RZ A 401 HOH A 507 DC P 10
CRYST1 54.630 79.450 55.170 90.00 106.66 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.018305 0.000000 0.005478 0.00000
SCALE2 0.000000 0.012587 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018920 0.00000
(ATOM LINES ARE NOT SHOWN.)
END