PDB Short entry for 1BPY HEADER TRANSFERASE/DNA 15-APR-97 1BPY TITLE HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*DOC)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: PROTEIN (DNA POLYMERASE BETA); COMPND 16 CHAIN: A; COMPND 17 SYNONYM: POL BETA, BETA-POL; COMPND 18 EC: 2.7.7.7; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 CELLULAR_LOCATION: NUCLEUS; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDYLTRANSFERASE, DNA REPAIR, BASE EXCISION REPAIR PATHWAY, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,H.PELLETIER,R.PRASAD,S.H.WILSON,J.KRAUT REVDAT 4 02-AUG-23 1BPY 1 REMARK LINK REVDAT 3 15-FEB-17 1BPY 1 AUTHOR VERSN SOURCE REVDAT 2 24-FEB-09 1BPY 1 VERSN REVDAT 1 16-JUN-97 1BPY 0 JRNL AUTH M.R.SAWAYA,R.PRASAD,S.H.WILSON,J.KRAUT,H.PELLETIER JRNL TITL CRYSTAL STRUCTURES OF HUMAN DNA POLYMERASE BETA COMPLEXED JRNL TITL 2 WITH GAPPED AND NICKED DNA: EVIDENCE FOR AN INDUCED FIT JRNL TITL 3 MECHANISM. JRNL REF BIOCHEMISTRY V. 36 11205 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9287163 JRNL DOI 10.1021/BI9703812 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA REMARK 1 TITL CHARACTERIZATION OF THE METAL ION BINDING REMARK 1 TITL 2 HELIX-HAIRPIN-HELIX MOTIFS IN HUMAN DNA POLYMERASE BETA BY REMARK 1 TITL 3 X-RAY STRUCTURAL ANALYSIS REMARK 1 REF BIOCHEMISTRY V. 35 12778 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,W.WOLFLE,S.H.WILSON,J.KRAUT REMARK 1 TITL A STRUCTURAL BASIS FOR METAL ION MUTAGENICITY AND NUCLEOTIDE REMARK 1 TITL 2 SELECTIVITY IN HUMAN DNA POLYMERASE BETA REMARK 1 REF BIOCHEMISTRY V. 35 12762 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,W.WOLFLE,S.H.WILSON,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF HUMAN DNA POLYMERASE BETA COMPLEXED REMARK 1 TITL 2 WITH DNA: IMPLICATIONS FOR CATALYTIC MECHANISM, REMARK 1 TITL 3 PROCESSIVITY, AND FIDELITY REMARK 1 REF BIOCHEMISTRY V. 35 12742 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A REMARK 1 TITL 2 COMMON POLYMERASE MECHANISM REMARK 1 REF SCIENCE V. 264 1930 1994 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 5 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,A.KUMAR,S.H.WILSON,J.KRAUT REMARK 1 TITL STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, REMARK 1 TITL 2 A DNA TEMPLATE- PRIMER, AND DDCTP REMARK 1 REF SCIENCE V. 264 1891 1994 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5D REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 21036 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2079 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2270 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2320 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2079 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2614 REMARK 3 NUCLEIC ACID ATOMS : 631 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.020 ; 0.390 ; 3407 REMARK 3 BOND ANGLES (DEGREES) : 3.000 ; 0.970 ; 4709 REMARK 3 TORSION ANGLES (DEGREES) : 22.100; 1.000 ; 1995 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.015 ; 1.000 ; 73 REMARK 3 GENERAL PLANES (A) : 0.006 ; 10.000; 414 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 6.500 ; 0.015 ; 3407 REMARK 3 NON-BONDED CONTACTS (A) : 0.016 ; 10.000; 171 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MOEWS REMARK 3 KSOL : 0.91 REMARK 3 BSOL : 23.80 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000171992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-96 REMARK 200 TEMPERATURE (KELVIN) : 100.00 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21036 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 9ICW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN-DNA COMPLEX WAS CRYSTALLIZED REMARK 280 USING A RESERVOIR CONTAINING 16.0% PEG 3350, 180 MM SODIUM REMARK 280 ACETATE, AND 50 MM HEPES, PH 7.5., VAPOR DIFFUSION 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 39.90850 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 APPLY THE FOLLOWING TO CHAINS: T, P, D, A 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 400 REMARK 400 COMPOUND REMARK 400 THE 3'-TERMINUS OF C P 10 IS 2'3'-DIDEOXYCYTIDINE. REMARK 400 THE 5'-TERMINUS OF G D 1 IS PHOSPHORYLATED. 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 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 DC T 1 O3' DC T 1 C3' -0.038 REMARK 500 DC T 1 N1 DC T 1 C6 -0.037 REMARK 500 DG T 3 O3' DG T 3 C3' -0.040 REMARK 500 DG T 3 N9 DG T 3 C4 0.053 REMARK 500 DC T 8 P DC T 8 O5' 0.064 REMARK 500 DC T 8 C5' DC T 8 C4' 0.043 REMARK 500 DG T 9 O3' DG T 9 C3' -0.067 REMARK 500 DA T 14 N3 DA T 14 C4 -0.038 REMARK 500 DC P 2 N3 DC P 2 C4 0.044 REMARK 500 DT P 3 O3' DT P 3 C3' -0.052 REMARK 500 DA P 5 N9 DA P 5 C4 -0.061 REMARK 500 DT P 6 C1' DT P 6 N1 -0.090 REMARK 500 DG P 9 O3' DG P 9 C3' -0.082 REMARK 500 DG D 1 P DG D 1 OP3 -0.102 REMARK 500 DG D 1 O3' DG D 1 C3' -0.041 REMARK 500 GLU A 21 CD GLU A 21 OE2 0.079 REMARK 500 GLU A 26 CD GLU A 26 OE1 0.085 REMARK 500 GLU A 75 CD GLU A 75 OE1 0.069 REMARK 500 GLU A 117 CD GLU A 117 OE2 0.083 REMARK 500 GLU A 123 CD GLU A 123 OE1 0.078 REMARK 500 GLU A 147 CD GLU A 147 OE2 0.077 REMARK 500 GLU A 153 CD GLU A 153 OE2 0.078 REMARK 500 GLU A 154 CD GLU A 154 OE2 0.083 REMARK 500 GLU A 232 CD GLU A 232 OE2 0.087 REMARK 500 GLU A 247 CD GLU A 247 OE2 0.069 REMARK 500 GLU A 288 CD GLU A 288 OE2 0.077 REMARK 500 GLU A 295 CD GLU A 295 OE2 0.078 REMARK 500 GLU A 335 CD GLU A 335 OE2 0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DC T 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC T 1 C3' - O3' - P ANGL. DEV. = -9.5 DEGREES REMARK 500 DC T 2 P - O5' - C5' ANGL. DEV. = -10.0 DEGREES REMARK 500 DC T 2 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG T 3 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG T 3 N9 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = -7.4 DEGREES REMARK 500 DG T 3 N3 - C4 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA T 4 C8 - N9 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC T 5 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA T 11 C8 - N9 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA T 14 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG T 15 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC T 16 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC T 16 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG P 1 C8 - N9 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC P 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT P 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA P 5 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 DA P 5 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA P 5 C8 - N9 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG P 7 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 DC P 8 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG D 1 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG D 1 N3 - C4 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 2 C5' - C4' - C3' ANGL. DEV. = -12.2 DEGREES REMARK 500 DT D 2 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG D 4 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 17 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 17 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 LYS A 41 N - CA - CB ANGL. DEV. = 12.0 DEGREES REMARK 500 TYR A 49 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 74 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 91 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 91 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 116 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 LYS A 120 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 ASP A 124 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 79 ANGLE DEVIATIONS. 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 LEU A 11 -51.28 -175.35 REMARK 500 ALA A 32 77.11 -117.63 REMARK 500 LYS A 61 -7.73 -59.33 REMARK 500 LYS A 120 15.67 -150.46 REMARK 500 ASN A 128 39.82 -143.85 REMARK 500 PHE A 143 -52.58 -25.08 REMARK 500 ASP A 170 110.78 -163.10 REMARK 500 CYS A 178 -136.21 -98.10 REMARK 500 SER A 202 -11.09 -42.64 REMARK 500 GLU A 203 53.86 -147.97 REMARK 500 LYS A 230 115.98 -165.80 REMARK 500 ASP A 246 -4.91 67.19 REMARK 500 GLU A 249 149.41 -39.28 REMARK 500 SER A 275 176.77 -56.51 REMARK 500 GLN A 324 45.23 75.71 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 341 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 766 O 89.2 REMARK 620 3 THR A 101 O 171.6 83.8 REMARK 620 4 VAL A 103 O 90.3 174.0 97.2 REMARK 620 5 ILE A 106 O 96.9 102.1 89.0 72.0 REMARK 620 6 HOH A 617 O 86.1 97.7 90.4 88.3 160.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 342 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 587 O 82.8 REMARK 620 3 HOH D 588 O 85.9 73.0 REMARK 620 4 LYS A 60 O 166.2 89.9 103.3 REMARK 620 5 LEU A 62 O 94.7 92.6 165.4 73.8 REMARK 620 6 VAL A 65 O 86.9 166.6 97.7 101.8 96.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 339 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 89.8 REMARK 620 3 DCT A 338 O1A 90.3 90.6 REMARK 620 4 DCT A 338 O1G 88.3 178.1 89.4 REMARK 620 5 DCT A 338 O2B 176.8 93.3 90.6 88.6 REMARK 620 6 HOH A 530 O 92.8 86.7 175.9 93.4 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 340 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 190 OD1 51.3 REMARK 620 3 ASP A 192 OD1 135.4 86.3 REMARK 620 4 ASP A 256 OD2 106.1 132.3 92.4 REMARK 620 5 DCT A 338 O1A 85.6 66.1 88.7 161.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A 338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BPX RELATED DB: PDB REMARK 900 RELATED ID: 1BPZ RELATED DB: PDB DBREF 1BPY A 2 335 UNP P06746 DPOB_HUMAN 1 334 DBREF 1BPY T 1 16 PDB 1BPY 1BPY 1 16 DBREF 1BPY P 1 10 PDB 1BPY 1BPY 1 10 DBREF 1BPY D 1 5 PDB 1BPY 1BPY 1 5 SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DOC SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU MODRES 1BPY DOC P 10 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC P 10 18 HET MG A 339 1 HET MG A 340 1 HET NA A 341 1 HET NA A 342 1 HET DCT A 338 27 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 5 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 DCT C9 H16 N3 O12 P3 FORMUL 10 HOH *321(H2 O) HELIX 1 A GLY A 13 SER A 30 1 18 HELIX 2 B ILE A 33 LYS A 48 1 16 HELIX 3 C GLY A 56 LYS A 61 1 6 HELIX 4 D THR A 67 THR A 79 1SEE REMARK 650 13 HELIX 5 E ARG A 83 GLN A 90 1 8 HELIX 6 F ASP A 92 ARG A 102 1 11 HELIX 7 G PRO A 108 ASP A 116 1SEE REMARK 650 9 HELIX 8 H LEU A 122 LYS A 127 1 6 HELIX 9 I HIS A 134 GLU A 147 1 14 HELIX 10 J ARG A 152 VAL A 169 1 18 HELIX 11 K SER A 180 ARG A 183 1 4 HELIX 12 L PRO A 208 LYS A 220 1 13 HELIX 13 M LYS A 262 THR A 273 1 12 HELIX 14 N ASP A 276 GLU A 288 1 13 HELIX 15 O GLU A 316 ILE A 323 1 8 HELIX 16 P PRO A 330 ASP A 332 5 3 SHEET 1 S1 2 ILE A 150 PRO A 151 0 SHEET 2 S1 2 SER A 187 SER A 188 -1 N SER A 188 O ILE A 150 SHEET 1 S2 5 ILE A 174 CYS A 178 0 SHEET 2 S2 5 MET A 191 THR A 196 -1 N THR A 196 O ILE A 174 SHEET 3 S2 5 ARG A 253 ARG A 258 1 N ASP A 256 O MET A 191 SHEET 4 S2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 S2 5 SER A 229 GLY A 231 -1 O SER A 229 N MET A 236 SHEET 1 S3 2 PHE A 291 ASN A 294 0 SHEET 2 S3 2 THR A 297 PRO A 300 -1 N ARG A 299 O THR A 292 LINK O3' DG P 9 P DOC P 10 1555 1555 1.57 LINK OP1 DG P 9 NA NA A 341 1555 1555 2.86 LINK O HOH P 766 NA NA A 341 1555 1555 3.02 LINK OP1 DC D 3 NA NA A 342 1555 1555 2.41 LINK O HOH D 587 NA NA A 342 1555 1555 2.96 LINK O HOH D 588 NA NA A 342 1555 1555 2.92 LINK O LYS A 60 NA NA A 342 1555 1555 2.47 LINK O LEU A 62 NA NA A 342 1555 1555 2.17 LINK O VAL A 65 NA NA A 342 1555 1555 2.30 LINK O THR A 101 NA NA A 341 1555 1555 2.32 LINK O VAL A 103 NA NA A 341 1555 1555 2.87 LINK O ILE A 106 NA NA A 341 1555 1555 2.29 LINK OD1 ASP A 190 MG MG A 339 1555 1555 1.96 LINK OD2 ASP A 190 MG MG A 340 1555 1555 2.22 LINK OD1 ASP A 190 MG MG A 340 1555 1555 2.68 LINK OD2 ASP A 192 MG MG A 339 1555 1555 1.97 LINK OD1 ASP A 192 MG MG A 340 1555 1555 2.20 LINK OD2 ASP A 256 MG MG A 340 1555 1555 2.63 LINK O1A DCT A 338 MG MG A 339 1555 1555 1.94 LINK O1G DCT A 338 MG MG A 339 1555 1555 1.98 LINK O2B DCT A 338 MG MG A 339 1555 1555 2.09 LINK O1A DCT A 338 MG MG A 340 1555 1555 2.37 LINK MG MG A 339 O HOH A 530 1555 1555 1.98 LINK NA NA A 341 O HOH A 617 1555 1555 3.01 CISPEP 1 GLY A 274 SER A 275 0 1.30 SITE 1 ACT 5 ASP A 190 ASP A 192 ASP A 256 MG A 339 SITE 2 ACT 5 MG A 340 SITE 1 AC1 5 ASP A 190 ASP A 192 DCT A 338 MG A 340 SITE 2 AC1 5 HOH A 530 SITE 1 AC2 6 ASP A 190 ASP A 192 ASP A 256 DCT A 338 SITE 2 AC2 6 MG A 339 DOC P 10 SITE 1 AC3 6 THR A 101 VAL A 103 ILE A 106 HOH A 617 SITE 2 AC3 6 DG P 9 HOH P 766 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 2 AC4 6 HOH D 587 HOH D 588 SITE 1 AC5 23 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC5 23 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC5 23 PHE A 272 GLY A 274 ASP A 276 MG A 339 SITE 4 AC5 23 MG A 340 HOH A 509 HOH A 530 HOH A 545 SITE 5 AC5 23 HOH A 546 HOH A 609 HOH A 636 HOH A 645 SITE 6 AC5 23 HOH A 648 DOC P 10 DG T 6 CRYST1 50.543 79.817 54.942 90.00 107.11 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 0.019785 0.000000 0.006090 0.00000 SCALE2 0.000000 0.012529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019044 0.00000