PDB Short entry for 2PFO HEADER TRANSFERASE, LYASE/DNA 05-APR-07 2PFO TITLE DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND DUPNPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEMPLATE; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PRIMER; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DOWNSTREAM PRIMER; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL COMPND 17 BETA2; COMPND 18 EC: 2.7.7.7, 4.2.99.-; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2; SOURCE 3 SYNTHETIC: YES; SOURCE 4 MOL_ID: 3; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 4; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: POLL; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, DNA REPAIR, PHOSPHORYL TRANSFER REACTION, MANGANESE, KEYWDS 2 TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.C.PEDERSEN,T.A.KUNKEL REVDAT 6 30-AUG-23 2PFO 1 REMARK REVDAT 5 20-OCT-21 2PFO 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2PFO 1 REMARK REVDAT 3 24-FEB-09 2PFO 1 VERSN REVDAT 2 04-SEP-07 2PFO 1 JRNL REVDAT 1 15-MAY-07 2PFO 0 JRNL AUTH M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.C.PEDERSEN,T.A.KUNKEL JRNL TITL ROLE OF THE CATALYTIC METAL DURING POLYMERIZATION BY DNA JRNL TITL 2 POLYMERASE LAMBDA. JRNL REF DNA REPAIR V. 6 1333 2007 JRNL REFN ISSN 1568-7864 JRNL PMID 17475573 JRNL DOI 10.1016/J.DNAREP.2007.03.005 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 31224 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1556 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2431 REMARK 3 NUCLEIC ACID ATOMS : 426 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.96000 REMARK 3 B22 (A**2) : -11.89200 REMARK 3 B33 (A**2) : 2.93200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.303 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.154 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.948 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.723 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 52.33 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : LDUMPB.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33210 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 1XSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% 2-PROPANOL, 0.2 M SODIUM REMARK 280 CITRATE AND 0.1M SODIUM CACODYLATE , PH 5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.04700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.15700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.70550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.15700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.04700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.70550 REMARK 290 SMTRY3 4 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 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 241 REMARK 465 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 HIS A 252 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 253 CG OD1 ND2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 SER A 288 OG REMARK 470 PHE A 289 CG CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 290 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 SER A 295 OG REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 ILE A 302 CG1 CG2 CD1 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ILE A 313 CG1 CG2 CD1 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ILE A 316 CG1 CG2 CD1 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 SER A 408 OG REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 ARG A 538 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 545 CG1 CG2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 -0.083 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 THR A 294 -38.59 -137.63 REMARK 500 ALA A 299 -70.67 -91.70 REMARK 500 ASN A 407 96.20 -177.83 REMARK 500 CYS A 415 -132.52 -110.63 REMARK 500 ARG A 438 -31.59 -151.47 REMARK 500 SER A 463 93.12 -164.12 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 600 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 117 O REMARK 620 2 HOH T 157 O 99.0 REMARK 620 3 HOH T 241 O 92.5 79.0 REMARK 620 4 SER A 463 O 90.0 107.1 173.0 REMARK 620 5 HOH A2848 O 76.6 167.1 89.0 85.2 REMARK 620 6 HOH A2905 O 153.0 108.0 93.6 81.2 77.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 5 OP1 REMARK 620 2 HOH P 80 O 90.5 REMARK 620 3 HOH P 152 O 86.5 90.0 REMARK 620 4 SER A 339 O 164.1 74.7 87.7 REMARK 620 5 ILE A 341 O 98.4 170.1 94.8 96.9 REMARK 620 6 ALA A 344 O 93.3 86.4 176.4 91.5 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 951 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 6 O3' REMARK 620 2 ASP A 427 OD1 163.0 REMARK 620 3 ASP A 429 OD1 92.4 96.1 REMARK 620 4 ASP A 490 OD2 72.7 91.9 94.8 REMARK 620 5 DUP A 952 O2A 96.1 98.6 90.1 167.9 REMARK 620 6 HOH A2807 O 88.3 85.5 171.7 93.3 81.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 80 O REMARK 620 2 HOH P 152 O 89.4 REMARK 620 3 HOH P 217 O 89.6 51.6 REMARK 620 4 SER A 339 O 69.9 75.4 123.7 REMARK 620 5 HOH A2895 O 165.1 82.7 95.3 95.8 REMARK 620 6 HOH A3013 O 88.3 170.0 138.1 94.6 97.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 104.3 REMARK 620 3 HOH A2978 O 82.2 152.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 950 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD2 86.9 REMARK 620 3 DUP A 952 O2A 98.9 86.5 REMARK 620 4 DUP A 952 O2B 160.4 98.0 100.3 REMARK 620 5 DUP A 952 O3G 83.8 169.5 99.8 89.2 REMARK 620 6 DUP A 952 N3A 137.9 119.2 55.0 54.7 71.2 REMARK 620 7 HOH A2812 O 75.8 80.8 166.5 86.3 92.1 136.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 952 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PFN RELATED DB: PDB REMARK 900 NA IN THE ACTIVE SITE OF DNA POLYMERASE LAMBDA REMARK 900 RELATED ID: 2PFP RELATED DB: PDB REMARK 900 DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND DCTP REMARK 900 RELATED ID: 2PFQ RELATED DB: PDB REMARK 900 MN PROMOTES CATALYSIS IN A DNA POLYMERASE LAMBDA-DNA CRYSTAL DBREF 2PFO A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 2PFO T 1 11 PDB 2PFO 2PFO 1 11 DBREF 2PFO P 1 6 PDB 2PFO 2PFO 1 6 DBREF 2PFO D 1 4 PDB 2PFO 2PFO 1 4 SEQADV 2PFO MET A 241 UNP Q9UGP5 INITIATING METHIONINE SEQADV 2PFO ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 D 4 DG DC DC DG SEQRES 1 A 335 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 A 335 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 A 335 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 A 335 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 A 335 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 A 335 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 A 335 SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER SEQRES 8 A 335 VAL PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA SEQRES 9 A 335 GLY THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE SEQRES 10 A 335 ARG SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR SEQRES 11 A 335 THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE SEQRES 12 A 335 LEU GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU SEQRES 13 A 335 GLN THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY SEQRES 14 A 335 LEU LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS SEQRES 15 A 335 ALA THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO SEQRES 16 A 335 ASP GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU SEQRES 17 A 335 ASP SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU SEQRES 18 A 335 VAL SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU SEQRES 19 A 335 GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG SEQRES 20 A 335 ARG LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA SEQRES 21 A 335 CYS ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN SEQRES 22 A 335 ARG SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER SEQRES 23 A 335 LEU SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN SEQRES 24 A 335 THR HIS GLY ALA LYS VAL GLY PRO GLY ARG VAL LEU PRO SEQRES 25 A 335 THR PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU SEQRES 26 A 335 PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP HET MG A 950 1 HET MN A 951 1 HET NA A 600 1 HET NA A 601 1 HET NA A 602 1 HET NA A 603 1 HET DUP A 952 28 HET EDO A2801 4 HETNAM MG MAGNESIUM ION HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG MG 2+ FORMUL 6 MN MN 2+ FORMUL 7 NA 4(NA 1+) FORMUL 11 DUP C9 H16 N3 O13 P3 FORMUL 12 EDO C2 H6 O2 FORMUL 13 HOH *329(H2 O) HELIX 1 1 ILE A 256 GLY A 271 1 16 HELIX 2 2 ASP A 272 LYS A 287 1 16 HELIX 3 3 SER A 295 SER A 301 1 7 HELIX 4 4 GLY A 306 SER A 319 1 14 HELIX 5 5 LEU A 322 HIS A 327 5 6 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ALA A 405 1 17 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 ILE A 443 GLU A 454 1 12 HELIX 14 14 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 GLU A 569 ASP A 574 5 6 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 ASP A 427 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 B 5 LEU A 457 SER A 463 -1 N THR A 458 O VAL A 476 SHEET 1 C 3 MET A 525 LEU A 527 0 SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 C 3 ARG A 549 VAL A 550 -1 O ARG A 549 N THR A 534 LINK O HOH T 117 NA NA A 600 1555 1555 2.63 LINK O HOH T 157 NA NA A 600 1555 1555 2.32 LINK O HOH T 241 NA NA A 600 1555 1555 2.59 LINK OP1 DA P 5 NA NA A 601 1555 1555 2.25 LINK O3' DC P 6 MN MN A 951 1555 1555 2.37 LINK O HOH P 80 NA NA A 601 1555 1555 2.68 LINK O HOH P 80 NA NA A 602 1555 1555 2.52 LINK O HOH P 152 NA NA A 601 1555 1555 2.53 LINK O HOH P 152 NA NA A 602 1555 1555 2.72 LINK O HOH P 217 NA NA A 602 1555 1555 2.72 LINK O CYS A 300 NA NA A 603 1555 1555 2.07 LINK O ILE A 302 NA NA A 603 1555 1555 1.68 LINK O SER A 339 NA NA A 601 1555 1555 2.35 LINK O SER A 339 NA NA A 602 1555 1555 2.81 LINK O ILE A 341 NA NA A 601 1555 1555 2.54 LINK O ALA A 344 NA NA A 601 1555 1555 2.26 LINK OD2 ASP A 427 MG MG A 950 1555 1555 2.10 LINK OD1 ASP A 427 MN MN A 951 1555 1555 2.01 LINK OD2 ASP A 429 MG MG A 950 1555 1555 2.12 LINK OD1 ASP A 429 MN MN A 951 1555 1555 2.08 LINK O SER A 463 NA NA A 600 1555 1555 2.28 LINK OD2 ASP A 490 MN MN A 951 1555 1555 2.01 LINK NA NA A 600 O HOH A2848 1555 1555 2.96 LINK NA NA A 600 O HOH A2905 1555 1555 2.68 LINK NA NA A 602 O HOH A2895 1555 1555 2.44 LINK NA NA A 602 O HOH A3013 1555 1555 2.59 LINK NA NA A 603 O HOH A2978 1555 1555 2.04 LINK MG MG A 950 O2A DUP A 952 1555 1555 1.99 LINK MG MG A 950 O2B DUP A 952 1555 1555 1.88 LINK MG MG A 950 O3G DUP A 952 1555 1555 2.10 LINK MG MG A 950 N3A DUP A 952 1555 1555 3.14 LINK MG MG A 950 O HOH A2812 1555 1555 2.26 LINK MN MN A 951 O2A DUP A 952 1555 1555 2.24 LINK MN MN A 951 O HOH A2807 1555 1555 2.29 CISPEP 1 GLY A 508 SER A 509 0 1.22 SITE 1 AC1 5 ASP A 427 ASP A 429 MN A 951 DUP A 952 SITE 2 AC1 5 HOH A2812 SITE 1 AC2 7 ASP A 427 ASP A 429 ASP A 490 MG A 950 SITE 2 AC2 7 DUP A 952 HOH A2807 DC P 6 SITE 1 AC3 7 SER A 463 HOH A2848 HOH A2905 DT T 10 SITE 2 AC3 7 HOH T 117 HOH T 157 HOH T 241 SITE 1 AC4 7 SER A 339 ILE A 341 ALA A 344 NA A 602 SITE 2 AC4 7 DA P 5 HOH P 80 HOH P 152 SITE 1 AC5 7 SER A 339 NA A 601 HOH A2895 HOH A3013 SITE 2 AC5 7 HOH P 80 HOH P 152 HOH P 217 SITE 1 AC6 7 CYS A 300 SER A 301 ILE A 302 PRO A 303 SITE 2 AC6 7 ILE A 305 HOH A2978 DC D 3 SITE 1 AC7 24 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC7 24 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC7 24 PHE A 506 THR A 507 GLY A 508 ASN A 513 SITE 4 AC7 24 MG A 950 MN A 951 HOH A2807 HOH A2812 SITE 5 AC7 24 HOH A2813 HOH A2856 HOH A2864 HOH A2947 SITE 6 AC7 24 HOH A2948 HOH A2994 DC P 6 DA T 5 SITE 1 AC8 4 THR A 348 GLU A 385 HOH A2920 DG P 3 CRYST1 56.094 61.411 140.314 90.00 90.00 90.00 P 21 21 21 4 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 0.017827 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007127 0.00000