PDB Short entry for 1MEY HEADER TRANSFERASE/DNA 27-SEP-96 1MEY TITLE CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3'); COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CONSENSUS ZINC FINGER; COMPND 11 CHAIN: C, F, G; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS ZINC FINGER, PROTEIN-DNA INTERACTION, PROTEIN DESIGN, COMPLEX (ZINC KEYWDS 2 FINGER-DNA), TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.KIM,J.M.BERG REVDAT 3 14-FEB-24 1MEY 1 REMARK LINK REVDAT 2 24-FEB-09 1MEY 1 VERSN REVDAT 1 12-MAR-97 1MEY 0 JRNL AUTH C.A.KIM,J.M.BERG JRNL TITL A 2.2 A RESOLUTION CRYSTAL STRUCTURE OF A DESIGNED ZINC JRNL TITL 2 FINGER PROTEIN BOUND TO DNA JRNL REF NAT.STRUCT.BIOL. V. 3 940 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8901872 JRNL DOI 10.1038/NSB1196-940 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.KIM,J.M.BERG REMARK 1 TITL SERINE AT POSITION 2 IN THE DNA RECOGNITION HELIX OF A REMARK 1 TITL 2 CYS2-HIS2 ZINC FINGER PEPTIDE IS NOT, IN GENERAL, REMARK 1 TITL 3 RESPONSIBLE FOR BASE RECOGNITION REMARK 1 REF J.MOL.BIOL. V. 252 1 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.P.PAVLETICH,C.O.PABO REMARK 1 TITL CRYSTAL STRUCTURE OF A FIVE-FINGER GLI-DNA COMPLEX: NEW REMARK 1 TITL 2 PERSPECTIVES ON ZINC FINGERS REMARK 1 REF SCIENCE V. 261 1701 1993 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 3 REMARK 1 AUTH L.FAIRALL,J.W.SCHWABE,L.CHAPMAN,J.T.FINCH,D.RHODES REMARK 1 TITL THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS REMARK 1 TITL 2 AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION REMARK 1 REF NATURE V. 366 483 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH N.P.PAVLETICH,C.O.PABO REMARK 1 TITL ZINC FINGER-DNA RECOGNITION: CRYSTAL STRUCTURE OF A REMARK 1 TITL 2 ZIF268-DNA COMPLEX AT 2.1 A REMARK 1 REF SCIENCE V. 252 809 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19237 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) : 0.224 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 350 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.00 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 : 1576 REMARK 3 NUCLEIC ACID ATOMS : 1056 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 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) : 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.770 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.860 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 : TOPHCSDX.PRO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA.PARAM REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MEY 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_1000174983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.80 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23392 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.80, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.00K 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 31.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.13700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 82.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.13700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 82.76500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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 ENTRY CONTAINS TWO COMPLEXES AND ONE UNPAIRED PROTEIN REMARK 400 MOLECULE WHICH MAKE UP THE ASYMMETRIC UNIT. THE FIRST REMARK 400 COMPLEX WITH CHAIN IDENTIFIERS A, B AND C ARE BETTER REMARK 400 DEFINED SHOWING LESS DISORDER THAN THAT OF THE SECOND REMARK 400 COMPLEX IDENTIFIED BY CHAINS D, E AND F. ONLY THE THIRD REMARK 400 FINGER DOMAIN OF THE UNPAIRED PROTEIN MOLECULE IS MODELED REMARK 400 AS NO DENSITY WAS OBSERVED FOR THE OTHER TWO DOMAINS. REMARK 400 REMARK 400 NUCLEOSIDE +C B 12,E 12 IS A CYTOSINE WITH AN IODINE ATOM REMARK 400 COVALENTLY BOUND TO ATOM C5. THE IODINE IS PRESENTED AS REMARK 400 A HETATM AT THE END OF CHAIN *B*, *E" . 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 C 1 REMARK 465 ASN C 85 REMARK 465 LYS C 86 REMARK 465 LYS C 87 REMARK 465 ASN F 85 REMARK 465 LYS F 86 REMARK 465 LYS F 87 REMARK 465 MET G 1 REMARK 465 GLU G 2 REMARK 465 LYS G 3 REMARK 465 PRO G 4 REMARK 465 TYR G 5 REMARK 465 LYS G 6 REMARK 465 CYS G 7 REMARK 465 PRO G 8 REMARK 465 GLU G 9 REMARK 465 CYS G 10 REMARK 465 GLY G 11 REMARK 465 LYS G 12 REMARK 465 SER G 13 REMARK 465 PHE G 14 REMARK 465 SER G 15 REMARK 465 GLN G 16 REMARK 465 SER G 17 REMARK 465 SER G 18 REMARK 465 ASN G 19 REMARK 465 LEU G 20 REMARK 465 GLN G 21 REMARK 465 LYS G 22 REMARK 465 HIS G 23 REMARK 465 GLN G 24 REMARK 465 ARG G 25 REMARK 465 THR G 26 REMARK 465 HIS G 27 REMARK 465 THR G 28 REMARK 465 GLY G 29 REMARK 465 GLU G 30 REMARK 465 LYS G 31 REMARK 465 PRO G 32 REMARK 465 TYR G 33 REMARK 465 LYS G 34 REMARK 465 CYS G 35 REMARK 465 PRO G 36 REMARK 465 GLU G 37 REMARK 465 CYS G 38 REMARK 465 GLY G 39 REMARK 465 LYS G 40 REMARK 465 SER G 41 REMARK 465 PHE G 42 REMARK 465 SER G 43 REMARK 465 GLN G 44 REMARK 465 SER G 45 REMARK 465 SER G 46 REMARK 465 ASP G 47 REMARK 465 LEU G 48 REMARK 465 GLN G 49 REMARK 465 LYS G 50 REMARK 465 HIS G 51 REMARK 465 GLN G 52 REMARK 465 ARG G 53 REMARK 465 THR G 54 REMARK 465 HIS G 55 REMARK 465 GLN G 84 REMARK 465 ASN G 85 REMARK 465 LYS G 86 REMARK 465 LYS G 87 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 GLN F 84 CG CD OE1 NE2 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 DA A 1 N9 DA A 1 C4 -0.037 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 DG D 5 O4' - C1' - N9 ANGL. DEV. = 1.9 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 LYS C 3 49.55 -106.62 REMARK 500 ARG C 81 -4.62 -58.07 REMARK 500 CYS F 10 -66.41 -133.25 REMARK 500 GLU F 37 -73.12 -103.82 REMARK 500 GLU F 65 -83.80 -65.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 9 0.05 SIDE CHAIN REMARK 500 DT B 5 0.08 SIDE CHAIN REMARK 500 DC B 9 0.07 SIDE CHAIN REMARK 500 DC B 10 0.09 SIDE CHAIN REMARK 500 DG E 8 0.07 SIDE CHAIN REMARK 500 TYR F 5 0.08 SIDE CHAIN 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 ZN C 88 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 7 SG REMARK 620 2 CYS C 10 SG 116.8 REMARK 620 3 HIS C 23 NE2 106.4 100.1 REMARK 620 4 HIS C 27 NE2 102.7 124.3 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN G 91 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 27 ND1 REMARK 620 2 HOH C 110 O 89.4 REMARK 620 3 HIS G 75 ND1 108.2 128.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 89 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 35 SG REMARK 620 2 CYS C 38 SG 112.8 REMARK 620 3 HIS C 51 NE2 111.2 99.5 REMARK 620 4 HIS C 55 NE2 105.8 120.2 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 90 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 63 SG REMARK 620 2 CYS C 66 SG 117.9 REMARK 620 3 HIS C 79 NE2 104.3 103.0 REMARK 620 4 HIS C 83 NE2 112.6 113.9 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 88 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 7 SG REMARK 620 2 CYS F 10 SG 114.0 REMARK 620 3 HIS F 23 NE2 110.0 101.8 REMARK 620 4 HIS F 27 NE2 103.2 117.4 110.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 89 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 35 SG REMARK 620 2 CYS F 38 SG 110.2 REMARK 620 3 HIS F 51 NE2 115.1 105.5 REMARK 620 4 HIS F 55 NE2 104.1 117.4 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 90 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 63 SG REMARK 620 2 CYS F 66 SG 108.6 REMARK 620 3 HIS F 79 NE2 117.3 103.3 REMARK 620 4 HIS F 83 NE2 109.9 114.7 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN G 90 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS G 63 SG REMARK 620 2 CYS G 66 SG 118.5 REMARK 620 3 HIS G 79 NE2 107.6 98.8 REMARK 620 4 HIS G 83 NE2 102.2 118.9 110.5 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 ZN C 88 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 89 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 90 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 88 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 89 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 90 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN G 90 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN G 91 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL G 92 DBREF 1MEY A 1 13 PDB 1MEY 1MEY 1 13 DBREF 1MEY B 1 13 PDB 1MEY 1MEY 1 13 DBREF 1MEY D 1 13 PDB 1MEY 1MEY 1 13 DBREF 1MEY E 1 13 PDB 1MEY 1MEY 1 13 DBREF 1MEY C 1 87 PDB 1MEY 1MEY 1 87 DBREF 1MEY F 1 87 PDB 1MEY 1MEY 1 87 DBREF 1MEY G 1 87 PDB 1MEY 1MEY 1 87 SEQRES 1 A 13 DA DT DG DA DG DG DC DA DG DA DA DC DT SEQRES 1 B 13 DT DA DG DT DT DC DT DG DC DC DT C38 DA SEQRES 1 D 13 DA DT DG DA DG DG DC DA DG DA DA DC DT SEQRES 1 E 13 DT DA DG DT DT DC DT DG DC DC DT C38 DA SEQRES 1 C 87 MET GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY LYS SER SEQRES 2 C 87 PHE SER GLN SER SER ASN LEU GLN LYS HIS GLN ARG THR SEQRES 3 C 87 HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY SEQRES 4 C 87 LYS SER PHE SER GLN SER SER ASP LEU GLN LYS HIS GLN SEQRES 5 C 87 ARG THR HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU SEQRES 6 C 87 CYS GLY LYS SER PHE SER ARG SER ASP HIS LEU SER ARG SEQRES 7 C 87 HIS GLN ARG THR HIS GLN ASN LYS LYS SEQRES 1 F 87 MET GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY LYS SER SEQRES 2 F 87 PHE SER GLN SER SER ASN LEU GLN LYS HIS GLN ARG THR SEQRES 3 F 87 HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY SEQRES 4 F 87 LYS SER PHE SER GLN SER SER ASP LEU GLN LYS HIS GLN SEQRES 5 F 87 ARG THR HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU SEQRES 6 F 87 CYS GLY LYS SER PHE SER ARG SER ASP HIS LEU SER ARG SEQRES 7 F 87 HIS GLN ARG THR HIS GLN ASN LYS LYS SEQRES 1 G 87 MET GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY LYS SER SEQRES 2 G 87 PHE SER GLN SER SER ASN LEU GLN LYS HIS GLN ARG THR SEQRES 3 G 87 HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU CYS GLY SEQRES 4 G 87 LYS SER PHE SER GLN SER SER ASP LEU GLN LYS HIS GLN SEQRES 5 G 87 ARG THR HIS THR GLY GLU LYS PRO TYR LYS CYS PRO GLU SEQRES 6 G 87 CYS GLY LYS SER PHE SER ARG SER ASP HIS LEU SER ARG SEQRES 7 G 87 HIS GLN ARG THR HIS GLN ASN LYS LYS MODRES 1MEY C38 B 12 DC MODRES 1MEY C38 E 12 DC HET C38 B 12 20 HET C38 E 12 20 HET ZN C 88 1 HET ZN C 89 1 HET ZN C 90 1 HET ZN F 88 1 HET ZN F 89 1 HET ZN F 90 1 HET ZN G 90 1 HET ZN G 91 1 HET CL G 92 1 HETNAM C38 5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 C38 2(C9 H13 I N3 O7 P) FORMUL 8 ZN 8(ZN 2+) FORMUL 16 CL CL 1- FORMUL 17 HOH *132(H2 O) HELIX 1 1 SER C 17 THR C 28 1 12 HELIX 2 2 SER C 45 THR C 56 1 12 HELIX 3 3 SER C 73 HIS C 83 1 11 HELIX 4 4 SER F 17 THR F 28 1 12 HELIX 5 5 SER F 45 THR F 56 1 12 HELIX 6 6 SER F 73 HIS F 83 1 11 HELIX 7 7 SER G 73 GLN G 80 1 8 SHEET 1 A 2 TYR C 5 LYS C 6 0 SHEET 2 A 2 SER C 13 PHE C 14 -1 N PHE C 14 O TYR C 5 SHEET 1 B 2 TYR C 33 LYS C 34 0 SHEET 2 B 2 SER C 41 PHE C 42 -1 N PHE C 42 O TYR C 33 SHEET 1 C 2 TYR C 61 LYS C 62 0 SHEET 2 C 2 SER C 69 PHE C 70 -1 N PHE C 70 O TYR C 61 SHEET 1 D 2 TYR F 5 LYS F 6 0 SHEET 2 D 2 SER F 13 PHE F 14 -1 O PHE F 14 N TYR F 5 SHEET 1 E 2 TYR F 33 LYS F 34 0 SHEET 2 E 2 SER F 41 PHE F 42 -1 N PHE F 42 O TYR F 33 SHEET 1 F 2 TYR F 61 LYS F 62 0 SHEET 2 F 2 SER F 69 PHE F 70 -1 O PHE F 70 N TYR F 61 SHEET 1 G 2 TYR G 61 LYS G 62 0 SHEET 2 G 2 SER G 69 PHE G 70 -1 N PHE G 70 O TYR G 61 LINK O3' DT B 11 P C38 B 12 1555 1555 1.60 LINK O3' C38 B 12 P DA B 13 1555 1555 1.61 LINK O3' DT E 11 P C38 E 12 1555 1555 1.61 LINK O3' C38 E 12 P DA E 13 1555 1555 1.62 LINK SG CYS C 7 ZN ZN C 88 1555 1555 2.32 LINK SG CYS C 10 ZN ZN C 88 1555 1555 2.15 LINK NE2 HIS C 23 ZN ZN C 88 1555 1555 2.04 LINK NE2 HIS C 27 ZN ZN C 88 1555 1555 2.02 LINK ND1 HIS C 27 ZN ZN G 91 1555 1555 2.17 LINK SG CYS C 35 ZN ZN C 89 1555 1555 2.20 LINK SG CYS C 38 ZN ZN C 89 1555 1555 2.34 LINK NE2 HIS C 51 ZN ZN C 89 1555 1555 2.03 LINK NE2 HIS C 55 ZN ZN C 89 1555 1555 2.04 LINK SG CYS C 63 ZN ZN C 90 1555 1555 2.23 LINK SG CYS C 66 ZN ZN C 90 1555 1555 2.30 LINK NE2 HIS C 79 ZN ZN C 90 1555 1555 2.12 LINK NE2 HIS C 83 ZN ZN C 90 1555 1555 1.83 LINK O HOH C 110 ZN ZN G 91 1555 1555 1.81 LINK SG CYS F 7 ZN ZN F 88 1555 1555 2.46 LINK SG CYS F 10 ZN ZN F 88 1555 1555 2.27 LINK NE2 HIS F 23 ZN ZN F 88 1555 1555 2.00 LINK NE2 HIS F 27 ZN ZN F 88 1555 1555 2.04 LINK SG CYS F 35 ZN ZN F 89 1555 1555 2.33 LINK SG CYS F 38 ZN ZN F 89 1555 1555 2.30 LINK NE2 HIS F 51 ZN ZN F 89 1555 1555 2.04 LINK NE2 HIS F 55 ZN ZN F 89 1555 1555 1.88 LINK SG CYS F 63 ZN ZN F 90 1555 1555 2.37 LINK SG CYS F 66 ZN ZN F 90 1555 1555 2.32 LINK NE2 HIS F 79 ZN ZN F 90 1555 1555 2.04 LINK NE2 HIS F 83 ZN ZN F 90 1555 1555 1.85 LINK SG CYS G 63 ZN ZN G 90 1555 1555 2.26 LINK SG CYS G 66 ZN ZN G 90 1555 1555 2.30 LINK ND1 HIS G 75 ZN ZN G 91 1555 1555 2.02 LINK NE2 HIS G 79 ZN ZN G 90 1555 1555 2.04 LINK NE2 HIS G 83 ZN ZN G 90 1555 1555 1.96 SITE 1 AC1 4 CYS C 7 CYS C 10 HIS C 23 HIS C 27 SITE 1 AC2 4 CYS C 35 CYS C 38 HIS C 51 HIS C 55 SITE 1 AC3 4 CYS C 63 CYS C 66 HIS C 79 HIS C 83 SITE 1 AC4 4 CYS F 7 CYS F 10 HIS F 23 HIS F 27 SITE 1 AC5 4 CYS F 35 CYS F 38 HIS F 51 HIS F 55 SITE 1 AC6 4 CYS F 63 CYS F 66 HIS F 79 HIS F 83 SITE 1 AC7 4 CYS G 63 CYS G 66 HIS G 79 HIS G 83 SITE 1 AC8 4 HIS C 27 HOH C 110 HIS G 75 CL G 92 SITE 1 AC9 5 HIS C 27 LYS G 59 ARG G 72 HIS G 75 SITE 2 AC9 5 ZN G 91 CRYST1 62.070 165.530 46.274 90.00 90.00 90.00 P 21 21 21 12 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 0.016111 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021610 0.00000