PDB Short entry for 2KFZ HEADER TRANSFERASE/DNA 02-JUL-98 2KFZ TITLE KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND ZINC ONLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: KLENOW FRAGMENT OF DNA POLYMERASE I; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: LARGE FRAGMENT, KLENOW FRAGMENT; COMPND 9 SYNONYM: POL I, DNA-DIRECTED DNA POLYMERASE; COMPND 10 EC: 2.7.7.7; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CJ376; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCJ155 KEYWDS POLYMERASE (EXONUCLEASE)-DNA COMPLEX, TRANSFERASE, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.BRAUTIGAM,S.SUN,J.A.PICCIRILLI,T.A.STEITZ REVDAT 4 21-FEB-24 2KFZ 1 REMARK REVDAT 3 03-NOV-21 2KFZ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2KFZ 1 VERSN REVDAT 1 11-NOV-98 2KFZ 0 JRNL AUTH C.A.BRAUTIGAM,S.SUN,J.A.PICCIRILLI,T.A.STEITZ JRNL TITL STRUCTURES OF NORMAL SINGLE-STRANDED DNA AND JRNL TITL 2 DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES BOUND TO THE 3'-5' JRNL TITL 3 EXONUCLEOLYTIC ACTIVE SITE OF DNA POLYMERASE I FROM JRNL TITL 4 ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 38 696 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 9888810 JRNL DOI 10.1021/BI981537G REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.BRAUTIGAM,T.A.STEITZ REMARK 1 TITL STRUCTURAL PRINCIPLES FOR THE INHIBITION OF THE 3'-5' REMARK 1 TITL 2 EXONUCLEASE ACTIVITY OF ESCHERICHIA COLI DNA POLYMERASE I BY REMARK 1 TITL 3 PHOSPHOROTHIOATES REMARK 1 REF J.MOL.BIOL. V. 277 363 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 50156 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 SET) : 0.215 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5015 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 : 30 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1447 REMARK 3 BIN R VALUE (WORKING SET) : 0.3159 REMARK 3 BIN FREE R VALUE : 0.3285 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 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 : 4753 REMARK 3 NUCLEIC ACID ATOMS : 63 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : CHAD_PARAM.DNA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : CHAD_TOP.DNA REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 BULK-SOLVENT CORRECTION WAS USED TO EXTEND LOW-RES. LIMIT TO 20 REMARK 3 ANGSTROMS REMARK 3 REMARK 3 ONLY LAST THREE NUCLEOTIDES OF NUCLEIC ACID COULD BE REMARK 3 MODELED INTO ELECTRON DENSITY. ALTHOUGH MG2+ WAS SOAKED REMARK 3 INTO THESE CRYSTALS, IT COULD NOT BE LOCATED AT THE ACTIVE REMARK 3 SITE. REMARK 4 REMARK 4 2KFZ 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_1000178284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59988 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID-BODY REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: STRUCTURE WAS SOLVED USING IN-HOUSE HIGH-RESOLUTION REMARK 200 STRUCTURE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M NA CITRATE PH 5.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.20000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.80000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.60000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 DG B 1001 REMARK 465 DC B 1002 REMARK 465 DT B 1003 REMARK 465 PRO A 603 REMARK 465 GLY A 604 REMARK 465 GLY A 605 REMARK 465 ALA A 606 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 DT B1004 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DT B1004 C3' C2' C1' N1 C2 O2 N3 REMARK 470 DT B1004 C4 O4 C5 C7 C6 REMARK 470 LEU A 599 CG CD1 CD2 REMARK 470 LYS A 600 CG CD CE NZ REMARK 470 LYS A 601 CG CD CE NZ REMARK 470 THR A 602 OG1 CG2 REMARK 470 PRO A 607 CG CD REMARK 470 SER A 608 OG REMARK 470 THR A 609 OG1 CG2 REMARK 470 SER A 610 OG REMARK 470 GLU A 611 CG CD OE1 OE2 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 DA B1005 O3' - P - O5' ANGL. DEV. = -13.8 DEGREES REMARK 500 DA B1005 P - O5' - C5' ANGL. DEV. = 10.1 DEGREES REMARK 500 DA B1005 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B1005 C3' - C2' - C1' ANGL. DEV. = 12.1 DEGREES REMARK 500 DA B1005 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 DA B1005 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 DA B1005 N9 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 LYS A 597 N - CA - C ANGL. DEV. = 16.9 DEGREES 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 SER A 326 -167.02 -105.40 REMARK 500 ASN A 420 64.00 63.24 REMARK 500 ASN A 450 97.30 -171.14 REMARK 500 ALA A 574 -122.74 -108.80 REMARK 500 GLU A 576 -169.49 42.53 REMARK 500 LEU A 580 37.18 -97.07 REMARK 500 THR A 583 20.23 49.56 REMARK 500 LYS A 584 -76.19 -144.31 REMARK 500 ILE A 589 -67.32 -107.53 REMARK 500 GLN A 594 125.59 88.58 REMARK 500 LYS A 597 -53.97 0.89 REMARK 500 THR A 609 34.71 -83.09 REMARK 500 SER A 610 -30.99 -150.75 REMARK 500 ASP A 620 -45.33 -143.54 REMARK 500 VAL A 663 -44.12 -130.52 REMARK 500 GLN A 708 61.66 29.67 REMARK 500 LYS A 782 -12.74 65.11 REMARK 500 SER A 831 -9.52 81.26 REMARK 500 HIS A 881 -121.75 56.14 REMARK 500 THR A 908 -127.62 -130.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ATOM O3* OF RESIDUE 1006B HAS BEEN REPLACED BY THE REMARK 600 HETEROATOM S 1006 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B1007 OP1 REMARK 620 2 ASP A 355 OD2 126.2 REMARK 620 3 GLU A 357 OE2 111.1 95.7 REMARK 620 4 ASP A 501 OD2 102.5 103.0 119.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 293 O REMARK 620 2 GLU A 572 OE2 49.5 REMARK 620 3 HIS A 901 NE2 100.7 51.7 REMARK 620 4 GLU A 905 OE2 79.4 90.6 93.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 320 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 710 OE2 REMARK 620 2 ASP A 882 OD2 75.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 321 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 761 OD1 REMARK 620 2 TYR A 791 OH 97.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: EXO 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 ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 321 DBREF 2KFZ A 324 928 UNP P00582 DPO1_ECOLI 325 928 DBREF 2KFZ B 1001 1007 PDB 2KFZ 2KFZ 1001 1007 SEQADV 2KFZ MET A 324 UNP P00582 VAL 324 ENGINEERED MUTATION SEQRES 1 B 7 DG DC DT DT DA US1 DG SEQRES 1 A 605 MET ILE SER TYR ASP ASN TYR VAL THR ILE LEU ASP GLU SEQRES 2 A 605 GLU THR LEU LYS ALA TRP ILE ALA LYS LEU GLU LYS ALA SEQRES 3 A 605 PRO VAL PHE ALA PHE ASP THR GLU THR ASP SER LEU ASP SEQRES 4 A 605 ASN ILE SER ALA ASN LEU VAL GLY LEU SER PHE ALA ILE SEQRES 5 A 605 GLU PRO GLY VAL ALA ALA TYR ILE PRO VAL ALA HIS ASP SEQRES 6 A 605 TYR LEU ASP ALA PRO ASP GLN ILE SER ARG GLU ARG ALA SEQRES 7 A 605 LEU GLU LEU LEU LYS PRO LEU LEU GLU ASP GLU LYS ALA SEQRES 8 A 605 LEU LYS VAL GLY GLN ASN LEU LYS TYR ASP ARG GLY ILE SEQRES 9 A 605 LEU ALA ASN TYR GLY ILE GLU LEU ARG GLY ILE ALA PHE SEQRES 10 A 605 ASP THR MET LEU GLU SER TYR ILE LEU ASN SER VAL ALA SEQRES 11 A 605 GLY ARG HIS ASP MET ASP SER LEU ALA GLU ARG TRP LEU SEQRES 12 A 605 LYS HIS LYS THR ILE THR PHE GLU GLU ILE ALA GLY LYS SEQRES 13 A 605 GLY LYS ASN GLN LEU THR PHE ASN GLN ILE ALA LEU GLU SEQRES 14 A 605 GLU ALA GLY ARG TYR ALA ALA GLU ASP ALA ASP VAL THR SEQRES 15 A 605 LEU GLN LEU HIS LEU LYS MET TRP PRO ASP LEU GLN LYS SEQRES 16 A 605 HIS LYS GLY PRO LEU ASN VAL PHE GLU ASN ILE GLU MET SEQRES 17 A 605 PRO LEU VAL PRO VAL LEU SER ARG ILE GLU ARG ASN GLY SEQRES 18 A 605 VAL LYS ILE ASP PRO LYS VAL LEU HIS ASN HIS SER GLU SEQRES 19 A 605 GLU LEU THR LEU ARG LEU ALA GLU LEU GLU LYS LYS ALA SEQRES 20 A 605 HIS GLU ILE ALA GLY GLU GLU PHE ASN LEU SER SER THR SEQRES 21 A 605 LYS GLN LEU GLN THR ILE LEU PHE GLU LYS GLN GLY ILE SEQRES 22 A 605 LYS PRO LEU LYS LYS THR PRO GLY GLY ALA PRO SER THR SEQRES 23 A 605 SER GLU GLU VAL LEU GLU GLU LEU ALA LEU ASP TYR PRO SEQRES 24 A 605 LEU PRO LYS VAL ILE LEU GLU TYR ARG GLY LEU ALA LYS SEQRES 25 A 605 LEU LYS SER THR TYR THR ASP LYS LEU PRO LEU MET ILE SEQRES 26 A 605 ASN PRO LYS THR GLY ARG VAL HIS THR SER TYR HIS GLN SEQRES 27 A 605 ALA VAL THR ALA THR GLY ARG LEU SER SER THR ASP PRO SEQRES 28 A 605 ASN LEU GLN ASN ILE PRO VAL ARG ASN GLU GLU GLY ARG SEQRES 29 A 605 ARG ILE ARG GLN ALA PHE ILE ALA PRO GLU ASP TYR VAL SEQRES 30 A 605 ILE VAL SER ALA ASP TYR SER GLN ILE GLU LEU ARG ILE SEQRES 31 A 605 MET ALA HIS LEU SER ARG ASP LYS GLY LEU LEU THR ALA SEQRES 32 A 605 PHE ALA GLU GLY LYS ASP ILE HIS ARG ALA THR ALA ALA SEQRES 33 A 605 GLU VAL PHE GLY LEU PRO LEU GLU THR VAL THR SER GLU SEQRES 34 A 605 GLN ARG ARG SER ALA LYS ALA ILE ASN PHE GLY LEU ILE SEQRES 35 A 605 TYR GLY MET SER ALA PHE GLY LEU ALA ARG GLN LEU ASN SEQRES 36 A 605 ILE PRO ARG LYS GLU ALA GLN LYS TYR MET ASP LEU TYR SEQRES 37 A 605 PHE GLU ARG TYR PRO GLY VAL LEU GLU TYR MET GLU ARG SEQRES 38 A 605 THR ARG ALA GLN ALA LYS GLU GLN GLY TYR VAL GLU THR SEQRES 39 A 605 LEU ASP GLY ARG ARG LEU TYR LEU PRO ASP ILE LYS SER SEQRES 40 A 605 SER ASN GLY ALA ARG ARG ALA ALA ALA GLU ARG ALA ALA SEQRES 41 A 605 ILE ASN ALA PRO MET GLN GLY THR ALA ALA ASP ILE ILE SEQRES 42 A 605 LYS ARG ALA MET ILE ALA VAL ASP ALA TRP LEU GLN ALA SEQRES 43 A 605 GLU GLN PRO ARG VAL ARG MET ILE MET GLN VAL HIS ASP SEQRES 44 A 605 GLU LEU VAL PHE GLU VAL HIS LYS ASP ASP VAL ASP ALA SEQRES 45 A 605 VAL ALA LYS GLN ILE HIS GLN LEU MET GLU ASN CYS THR SEQRES 46 A 605 ARG LEU ASP VAL PRO LEU LEU VAL GLU VAL GLY SER GLY SEQRES 47 A 605 GLU ASN TRP ASP GLN ALA HIS MODRES 2KFZ US1 B 1006 DU HET US1 B1006 19 HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET ZN A 320 1 HET MG A 321 1 HETNAM US1 2'-DEOXY-3'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 1 US1 C9 H13 N2 O7 P S FORMUL 3 ZN 4(ZN 2+) FORMUL 7 MG MG 2+ FORMUL 8 HOH *313(H2 O) HELIX 1 1 GLU A 336 GLU A 347 1 12 HELIX 2 2 ARG A 398 LEU A 409 1 12 HELIX 3 3 LEU A 421 TYR A 431 1 11 HELIX 4 4 THR A 442 LEU A 449 1 8 HELIX 5 5 MET A 458 TRP A 465 1 8 HELIX 6 6 PHE A 473 ALA A 477 1 5 HELIX 7 7 PHE A 486 GLN A 488 5 3 HELIX 8 8 LEU A 491 GLN A 517 1 27 HELIX 9 9 LYS A 520 ASN A 528 1 9 HELIX 10 10 GLU A 530 ASN A 543 1 14 HELIX 11 11 PRO A 549 ILE A 573 1 25 HELIX 12 12 GLN A 587 LEU A 590 1 4 HELIX 13 13 VAL A 613 LEU A 619 1 7 HELIX 14 14 LEU A 623 THR A 639 1 17 HELIX 15 15 LEU A 644 MET A 647 5 4 HELIX 16 16 LEU A 676 ASN A 678 5 3 HELIX 17 17 GLU A 684 ALA A 692 1 9 HELIX 18 18 ILE A 709 LEU A 717 1 9 HELIX 19 19 LYS A 721 ALA A 728 1 8 HELIX 20 20 ILE A 733 VAL A 741 1 9 HELIX 21 21 LEU A 746 THR A 748 5 3 HELIX 22 22 SER A 751 ILE A 765 1 15 HELIX 23 23 GLY A 772 LEU A 777 1 6 HELIX 24 24 ALA A 784 ARG A 794 1 11 HELIX 25 25 PRO A 796 GLN A 812 1 17 HELIX 26 26 GLY A 833 GLU A 870 1 38 HELIX 27 27 VAL A 893 ASN A 906 1 14 SHEET 1 A 6 VAL A 331 THR A 332 0 SHEET 2 A 6 VAL A 379 PRO A 384 1 O ALA A 380 N VAL A 331 SHEET 3 A 6 LEU A 368 GLU A 376 -1 O LEU A 371 N ILE A 383 SHEET 4 A 6 PHE A 352 THR A 358 -1 N ALA A 353 O ALA A 374 SHEET 5 A 6 LYS A 416 GLY A 418 1 N VAL A 417 O PHE A 352 SHEET 6 A 6 ILE A 438 ASP A 441 1 N ALA A 439 O LYS A 416 SHEET 1 B 2 SER A 658 HIS A 660 0 SHEET 2 B 2 SER A 670 THR A 672 -1 O SER A 670 N HIS A 660 SHEET 1 C 4 VAL A 874 VAL A 880 0 SHEET 2 C 4 GLU A 883 HIS A 889 -1 N GLU A 883 O VAL A 880 SHEET 3 C 4 TYR A 699 TYR A 706 -1 N VAL A 700 O VAL A 888 SHEET 4 C 4 VAL A 916 GLY A 921 -1 N GLU A 917 O ASP A 705 SHEET 1 D 2 TYR A 814 GLU A 816 0 SHEET 2 D 2 ARG A 822 TYR A 824 -1 N LEU A 823 O VAL A 815 LINK O3' DA B1005 P US1 B1006 1555 1555 1.60 LINK S US1 B1006 P DG B1007 1555 1555 1.84 LINK OP1 DG B1007 ZN ZN A 1 1555 1555 2.09 LINK ZN ZN A 1 OD2 ASP A 355 1555 1555 2.02 LINK ZN ZN A 1 OE2 GLU A 357 1555 1555 2.09 LINK ZN ZN A 1 OD2 ASP A 501 1555 1555 2.20 LINK ZN ZN A 2 OD1 ASP A 355 1555 1555 2.35 LINK ZN ZN A 3 O HOH A 293 1555 1555 2.22 LINK ZN ZN A 3 OE2 GLU A 572 2655 1555 2.31 LINK ZN ZN A 3 NE2 HIS A 901 1555 1555 2.41 LINK ZN ZN A 3 OE2 GLU A 905 1555 1555 2.14 LINK ZN ZN A 320 OE2 GLU A 710 1555 1555 2.28 LINK ZN ZN A 320 OD2 ASP A 882 1555 1555 2.32 LINK MG MG A 321 OD1 ASN A 761 1555 1555 2.30 LINK MG MG A 321 OH TYR A 791 1555 1555 1.87 CISPEP 1 ASP A 673 PRO A 674 0 0.52 SITE 1 EXO 1 ASP A 355 SITE 1 AC1 4 ASP A 355 GLU A 357 ASP A 501 DG B1007 SITE 1 AC2 4 HOH A 4 ASP A 355 GLN A 419 US1 B1006 SITE 1 AC3 4 HOH A 293 GLU A 572 HIS A 901 GLU A 905 SITE 1 AC4 2 GLU A 710 ASP A 882 SITE 1 AC5 3 LEU A 723 ASN A 761 TYR A 791 CRYST1 102.900 102.900 86.400 90.00 90.00 90.00 P 43 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 0.009718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011574 0.00000