PDB Short entry for 1ZNF HEADER ZINC FINGER DNA BINDING DOMAIN 25-SEP-89 1ZNF TITLE THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER DNA- TITLE 2 BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 31ST ZINC FINGER FROM XFIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355 KEYWDS ZINC FINGER DNA BINDING DOMAIN EXPDTA SOLUTION NMR NUMMDL 37 AUTHOR M.S.LEE,G.P.GIPPERT,K.V.SOMAN,D.A.CASE,P.E.WRIGHT REVDAT 4 29-NOV-17 1ZNF 1 REMARK HELIX REVDAT 3 24-FEB-09 1ZNF 1 VERSN REVDAT 2 15-OCT-91 1ZNF 3 COMPND HETATM REVDAT 1 15-JUL-91 1ZNF 0 JRNL AUTH M.S.LEE,G.P.GIPPERT,K.V.SOMAN,D.A.CASE,P.E.WRIGHT JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER JRNL TITL 2 DNA-BINDING DOMAIN. JRNL REF SCIENCE V. 245 635 1989 JRNL REFN ISSN 0036-8075 JRNL PMID 2503871 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.S.LEE,G.P.GIPPERT,K.V.SOMAN,D.A.CASE,P.E.WRIGHT REMARK 1 TITL PROTON NUCLEAR MAGNETIC RESONANCE ASSIGNMENTS AND SOLUTION REMARK 1 TITL 2 STRUCTURE OF A SYNTHETIC ZINC FINGER FROM XFIN REMARK 1 EDIT R.H.SARMA, M.H.SARMA REMARK 1 REF STRUCTURE AND METHODS. V. 2. 83 1990 REMARK 1 REF 2 DNA PROTEIN COMPLEXES AND REMARK 1 REF 3 PROTEINS REMARK 1 PUBL ADENINE PRESS, ALBANY, NEW YORK REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH M.S.LEE,J.CAVANAGH,P.E.WRIGHT REMARK 1 TITL COMPLETE ASSIGNMENT OF THE 1H NUCLEAR MAGNETIC RESONANCE REMARK 1 TITL 2 SPECTRUM OF A SYNTHETIC ZINC FINGER FROM XFIN. SEQUENTIAL REMARK 1 TITL 3 RESONANCE ASSIGNMENTS AND SECONDARY STRUCTURE REMARK 1 REF FEBS LETT. V. 254 159 1989 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : HAVEL,WUTHRICH (DISGEO), REMARK 3 PEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZNF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177494. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 37 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 4 CYS A 6 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 23 CYS A 6 CA - CB - SG ANGL. DEV. = 8.8 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 1 GLU A 7 25.73 38.59 REMARK 500 1 HIS A 23 -48.57 -133.16 REMARK 500 2 CYS A 6 18.54 -159.41 REMARK 500 2 GLU A 7 34.16 33.46 REMARK 500 3 CYS A 6 19.08 -156.82 REMARK 500 3 GLU A 7 41.54 31.04 REMARK 500 4 CYS A 6 -99.51 -155.01 REMARK 500 4 GLU A 7 -125.25 -164.52 REMARK 500 4 ARG A 8 119.67 60.76 REMARK 500 4 VAL A 11 -32.57 70.60 REMARK 500 5 LYS A 24 52.51 32.51 REMARK 500 6 CYS A 6 105.04 -165.64 REMARK 500 6 GLU A 7 58.01 -67.92 REMARK 500 6 HIS A 23 82.56 -154.24 REMARK 500 7 CYS A 6 15.12 -154.92 REMARK 500 7 GLU A 7 17.25 43.72 REMARK 500 8 GLU A 7 59.27 -70.00 REMARK 500 8 HIS A 23 74.54 -158.03 REMARK 500 10 GLU A 7 49.96 -72.06 REMARK 500 11 GLU A 7 59.07 -55.46 REMARK 500 11 ARG A 21 -37.79 -36.02 REMARK 500 12 LYS A 24 71.72 -68.32 REMARK 500 13 CYS A 6 93.25 -165.02 REMARK 500 13 GLU A 7 61.16 -65.84 REMARK 500 13 HIS A 23 -49.10 72.41 REMARK 500 14 CYS A 6 -175.28 -171.47 REMARK 500 14 VAL A 11 -7.71 57.30 REMARK 500 15 GLN A 20 1.71 -64.17 REMARK 500 15 HIS A 23 -61.70 72.24 REMARK 500 16 VAL A 11 -0.90 53.34 REMARK 500 16 GLN A 20 -9.76 -55.84 REMARK 500 17 CYS A 6 -19.65 -163.67 REMARK 500 17 GLU A 7 55.40 38.73 REMARK 500 17 VAL A 11 -23.67 61.87 REMARK 500 17 LYS A 24 112.69 91.03 REMARK 500 18 CYS A 6 21.38 -159.45 REMARK 500 18 GLU A 7 23.51 35.34 REMARK 500 19 CYS A 6 10.56 -151.52 REMARK 500 19 GLU A 7 19.05 45.98 REMARK 500 19 GLN A 20 0.69 -63.08 REMARK 500 19 HIS A 23 -58.64 73.20 REMARK 500 20 CYS A 6 30.54 -152.44 REMARK 500 20 GLU A 7 19.57 21.76 REMARK 500 20 LYS A 24 65.68 -64.61 REMARK 500 21 CYS A 6 18.79 -154.67 REMARK 500 21 GLU A 7 34.21 36.76 REMARK 500 21 VAL A 11 -36.44 72.58 REMARK 500 21 HIS A 23 -55.30 -123.25 REMARK 500 21 LYS A 24 34.74 39.55 REMARK 500 22 CYS A 6 20.86 -152.99 REMARK 500 REMARK 500 THIS ENTRY HAS 102 RAMACHANDRAN OUTLIERS. 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 1 PHE A 10 0.09 SIDE CHAIN REMARK 500 2 PHE A 10 0.13 SIDE CHAIN REMARK 500 3 PHE A 10 0.08 SIDE CHAIN REMARK 500 7 PHE A 10 0.08 SIDE CHAIN REMARK 500 9 PHE A 10 0.08 SIDE CHAIN REMARK 500 10 TYR A 1 0.07 SIDE CHAIN REMARK 500 11 HIS A 19 0.10 SIDE CHAIN REMARK 500 15 PHE A 10 0.09 SIDE CHAIN REMARK 500 17 TYR A 1 0.09 SIDE CHAIN REMARK 500 21 PHE A 10 0.10 SIDE CHAIN REMARK 500 27 PHE A 10 0.10 SIDE CHAIN REMARK 500 32 PHE A 10 0.09 SIDE CHAIN REMARK 500 33 PHE A 10 0.08 SIDE CHAIN REMARK 500 34 HIS A 19 0.09 SIDE CHAIN REMARK 500 37 TYR A 1 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 A 27 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 HIS A 19 NE2 102.1 REMARK 620 3 CYS A 3 SG 113.8 110.9 REMARK 620 4 HIS A 23 NE2 119.7 105.1 104.9 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 A 27 DBREF 1ZNF A 1 25 UNP P08045 XFIN_XENLA 1044 1068 SEQRES 1 A 27 ACE TYR LYS CYS GLY LEU CYS GLU ARG SER PHE VAL GLU SEQRES 2 A 27 LYS SER ALA LEU SER ARG HIS GLN ARG VAL HIS LYS ASN SEQRES 3 A 27 NH2 HET ACE A 0 6 HET NH2 A 26 3 HET ZN A 27 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 ZN ZN 2+ HELIX 1 1H GLU A 12 LYS A 24 1 13 SHEET 1 S1 2 TYR A 1 GLY A 4 0 SHEET 2 S1 2 GLU A 7 PHE A 10 -1 N PHE A 10 O TYR A 1 LINK C ACE A 0 N TYR A 1 1555 1555 1.33 LINK C ASN A 25 N NH2 A 26 1555 1555 1.33 LINK ZN ZN A 27 SG CYS A 6 1555 1555 2.31 LINK ZN ZN A 27 NE2 HIS A 19 1555 1555 1.95 LINK ZN ZN A 27 SG CYS A 3 1555 1555 2.29 LINK ZN ZN A 27 NE2 HIS A 23 1555 1555 1.99 SITE 1 AC1 4 CYS A 3 CYS A 6 HIS A 19 HIS A 23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000