HEADER ZINC FINGER DNA BINDING DOMAIN 09-JUL-90 4ZNF TITLE HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF A SINGLE ZINC FINGER TITLE 2 FROM A HUMAN ENHANCER BINDING PROTEIN IN SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS ZINC FINGER DNA BINDING DOMAIN EXPDTA SOLUTION NMR NUMMDL 41 AUTHOR A.M.GRONENBORN,G.M.CLORE,J.G.OMICHINSKI REVDAT 4 16-MAR-22 4ZNF 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 4ZNF 1 VERSN REVDAT 2 08-MAR-05 4ZNF 1 TITLE KEYWDS EXPDTA HETATM REVDAT 1 15-JAN-92 4ZNF 0 JRNL AUTH J.G.OMICHINSKI,G.M.CLORE,E.APPELLA,K.SAKAGUCHI, JRNL AUTH 2 A.M.GRONENBORN JRNL TITL HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF A SINGLE ZINC JRNL TITL 2 FINGER FROM A HUMAN ENHANCER BINDING PROTEIN IN SOLUTION. JRNL REF BIOCHEMISTRY V. 29 9324 1990 JRNL REFN ISSN 0006-2960 JRNL PMID 2248949 JRNL DOI 10.1021/BI00492A004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE 3D STRUCTURE OF THE ZINC FINGER IN SOLUTION REMARK 3 BY NMR IS BASED ON 487 APPROXIMATE INTERPROTON DISTANCE REMARK 3 RESTRAINTS AND 63 TORSION ANGLE RESTRAINTS DERIVED FROM REMARK 3 NOE AND COUPLING CONSTANT MEASUREMENTS. THE STRUCTURES REMARK 3 ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE REMARK 3 GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED REMARK 3 BY M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (1988) REMARK 3 FEBS LETT 229, 317. REMARK 3 REMARK 3 THIS ENTRY REPRESENTS 41 MODELS OF THE ZINC FINGER OF REMARK 3 HUMAN ENHANCER BINDING PROTEIN. THE RESTRAINED MINIMIZED REMARK 3 AVERAGE STRUCTURE (SA)$R DERIVED BY RESTRAINED LEAST REMARK 3 SQUARE REFINEMENT OF THE MEAN STRUCTURE OBTAINED BY REMARK 3 AVERAGING THE COORDINATES OF THE FINAL 41 SA STRUCTURES REMARK 3 BEST FITTED TO EACH OTHER CAN BE FOUND IN PDB ENTRY 3ZNF. REMARK 4 REMARK 4 4ZNF 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_1000179661. 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 : 41 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 1 HIS A 4 CG HIS A 4 ND1 -0.116 REMARK 500 1 HIS A 27 CG HIS A 27 CD2 0.057 REMARK 500 1 HIS A 27 CG HIS A 27 ND1 -0.095 REMARK 500 2 HIS A 4 CG HIS A 4 ND1 -0.117 REMARK 500 2 HIS A 21 CG HIS A 21 ND1 -0.091 REMARK 500 2 HIS A 27 CG HIS A 27 ND1 -0.097 REMARK 500 3 HIS A 4 CG HIS A 4 ND1 -0.116 REMARK 500 3 HIS A 27 CG HIS A 27 ND1 -0.098 REMARK 500 4 HIS A 4 CG HIS A 4 ND1 -0.113 REMARK 500 4 HIS A 21 CG HIS A 21 ND1 -0.093 REMARK 500 4 HIS A 27 CG HIS A 27 CD2 0.058 REMARK 500 4 HIS A 27 CG HIS A 27 ND1 -0.096 REMARK 500 5 HIS A 4 CG HIS A 4 ND1 -0.119 REMARK 500 5 HIS A 27 CG HIS A 27 CD2 0.054 REMARK 500 5 HIS A 27 CG HIS A 27 ND1 -0.097 REMARK 500 6 HIS A 4 CG HIS A 4 ND1 -0.115 REMARK 500 6 HIS A 21 CG HIS A 21 ND1 -0.090 REMARK 500 6 HIS A 27 CG HIS A 27 CD2 0.057 REMARK 500 6 HIS A 27 CG HIS A 27 ND1 -0.101 REMARK 500 7 HIS A 4 CG HIS A 4 ND1 -0.115 REMARK 500 7 HIS A 27 CG HIS A 27 CD2 0.059 REMARK 500 7 HIS A 27 CG HIS A 27 ND1 -0.101 REMARK 500 8 HIS A 4 CG HIS A 4 ND1 -0.118 REMARK 500 8 HIS A 21 CG HIS A 21 ND1 -0.090 REMARK 500 8 HIS A 27 CG HIS A 27 CD2 0.055 REMARK 500 8 HIS A 27 CG HIS A 27 ND1 -0.100 REMARK 500 9 HIS A 4 CG HIS A 4 ND1 -0.116 REMARK 500 9 HIS A 27 CG HIS A 27 CD2 0.060 REMARK 500 9 HIS A 27 CG HIS A 27 ND1 -0.099 REMARK 500 10 HIS A 4 CG HIS A 4 ND1 -0.115 REMARK 500 10 HIS A 21 CG HIS A 21 ND1 -0.090 REMARK 500 10 HIS A 27 CG HIS A 27 CD2 0.060 REMARK 500 10 HIS A 27 CG HIS A 27 ND1 -0.099 REMARK 500 11 HIS A 4 CG HIS A 4 ND1 -0.113 REMARK 500 11 HIS A 21 CG HIS A 21 ND1 -0.092 REMARK 500 11 HIS A 27 CG HIS A 27 CD2 0.056 REMARK 500 11 HIS A 27 CG HIS A 27 ND1 -0.098 REMARK 500 12 HIS A 4 CG HIS A 4 ND1 -0.115 REMARK 500 12 HIS A 27 CG HIS A 27 CD2 0.063 REMARK 500 12 HIS A 27 CG HIS A 27 ND1 -0.100 REMARK 500 13 HIS A 4 CG HIS A 4 ND1 -0.116 REMARK 500 13 HIS A 21 CG HIS A 21 ND1 -0.091 REMARK 500 13 HIS A 27 CG HIS A 27 CD2 0.055 REMARK 500 13 HIS A 27 CG HIS A 27 ND1 -0.098 REMARK 500 14 HIS A 4 CG HIS A 4 ND1 -0.115 REMARK 500 14 HIS A 27 CG HIS A 27 ND1 -0.099 REMARK 500 15 HIS A 4 CG HIS A 4 ND1 -0.117 REMARK 500 15 HIS A 21 CG HIS A 21 ND1 -0.091 REMARK 500 15 HIS A 27 CG HIS A 27 CD2 0.061 REMARK 500 15 HIS A 27 CG HIS A 27 ND1 -0.101 REMARK 500 REMARK 500 THIS ENTRY HAS 130 BOND 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 1 PRO A 2 37.04 -69.01 REMARK 500 1 TYR A 7 -75.55 -157.59 REMARK 500 1 CYS A 8 -157.45 -58.80 REMARK 500 1 PHE A 12 -163.39 -124.86 REMARK 500 1 ALA A 26 -90.26 -63.53 REMARK 500 1 HIS A 27 71.33 -175.51 REMARK 500 1 SER A 28 73.70 -152.15 REMARK 500 2 PRO A 2 7.32 -66.10 REMARK 500 2 CYS A 5 164.59 -47.88 REMARK 500 2 TYR A 7 -74.36 -160.94 REMARK 500 2 CYS A 8 -164.44 -61.10 REMARK 500 2 PHE A 10 69.06 -68.98 REMARK 500 2 ALA A 26 -89.25 -50.26 REMARK 500 2 HIS A 27 66.41 -175.43 REMARK 500 2 SER A 28 83.34 -169.28 REMARK 500 3 PRO A 2 30.52 -67.36 REMARK 500 3 CYS A 5 156.69 -48.07 REMARK 500 3 TYR A 7 -77.17 -161.07 REMARK 500 3 CYS A 8 -159.76 -57.79 REMARK 500 3 PHE A 10 92.76 -67.93 REMARK 500 3 PHE A 12 -154.59 -102.81 REMARK 500 3 LYS A 25 39.57 -76.93 REMARK 500 3 ALA A 26 -87.07 -64.05 REMARK 500 3 HIS A 27 81.55 -172.80 REMARK 500 3 SER A 28 95.66 -171.03 REMARK 500 4 PRO A 2 24.53 -65.00 REMARK 500 4 TYR A 7 -74.55 -156.25 REMARK 500 4 CYS A 8 -157.51 -61.36 REMARK 500 4 PHE A 10 92.11 -67.96 REMARK 500 4 LYS A 20 -19.13 -46.35 REMARK 500 4 LYS A 25 25.08 -73.21 REMARK 500 4 ALA A 26 -87.79 -52.20 REMARK 500 4 HIS A 27 76.16 -170.70 REMARK 500 4 SER A 28 87.85 -170.33 REMARK 500 5 TYR A 7 -74.38 -159.71 REMARK 500 5 CYS A 8 -170.25 -58.36 REMARK 500 5 PHE A 12 -164.45 -128.97 REMARK 500 5 SER A 24 -161.53 -64.24 REMARK 500 5 LYS A 25 57.38 -104.53 REMARK 500 5 ALA A 26 -84.34 -80.36 REMARK 500 5 HIS A 27 69.97 -175.16 REMARK 500 6 TYR A 7 -75.47 -160.60 REMARK 500 6 CYS A 8 -168.52 -57.09 REMARK 500 6 PHE A 10 88.50 -66.74 REMARK 500 6 ALA A 26 -87.54 -46.67 REMARK 500 6 HIS A 27 66.93 -173.54 REMARK 500 6 SER A 28 90.21 -171.36 REMARK 500 7 PRO A 2 27.39 -66.30 REMARK 500 7 CYS A 5 167.12 -49.92 REMARK 500 7 TYR A 7 -72.53 -159.06 REMARK 500 REMARK 500 THIS ENTRY HAS 353 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 ARG A 1 0.26 SIDE CHAIN REMARK 500 2 ARG A 1 0.30 SIDE CHAIN REMARK 500 3 ARG A 1 0.20 SIDE CHAIN REMARK 500 4 ARG A 1 0.30 SIDE CHAIN REMARK 500 5 ARG A 1 0.28 SIDE CHAIN REMARK 500 6 ARG A 1 0.21 SIDE CHAIN REMARK 500 7 ARG A 1 0.19 SIDE CHAIN REMARK 500 8 ARG A 1 0.31 SIDE CHAIN REMARK 500 9 ARG A 1 0.20 SIDE CHAIN REMARK 500 11 ARG A 1 0.10 SIDE CHAIN REMARK 500 12 ARG A 1 0.31 SIDE CHAIN REMARK 500 13 ARG A 1 0.32 SIDE CHAIN REMARK 500 14 ARG A 1 0.22 SIDE CHAIN REMARK 500 15 ARG A 1 0.24 SIDE CHAIN REMARK 500 16 ARG A 1 0.08 SIDE CHAIN REMARK 500 17 ARG A 1 0.32 SIDE CHAIN REMARK 500 18 ARG A 1 0.21 SIDE CHAIN REMARK 500 19 ARG A 1 0.31 SIDE CHAIN REMARK 500 20 ARG A 1 0.24 SIDE CHAIN REMARK 500 21 ARG A 1 0.29 SIDE CHAIN REMARK 500 22 ARG A 1 0.31 SIDE CHAIN REMARK 500 23 ARG A 1 0.09 SIDE CHAIN REMARK 500 24 ARG A 1 0.20 SIDE CHAIN REMARK 500 25 ARG A 1 0.15 SIDE CHAIN REMARK 500 26 ARG A 1 0.27 SIDE CHAIN REMARK 500 27 ARG A 1 0.19 SIDE CHAIN REMARK 500 28 ARG A 1 0.26 SIDE CHAIN REMARK 500 29 ARG A 1 0.27 SIDE CHAIN REMARK 500 30 ARG A 1 0.12 SIDE CHAIN REMARK 500 31 ARG A 1 0.13 SIDE CHAIN REMARK 500 32 ARG A 1 0.29 SIDE CHAIN REMARK 500 33 ARG A 1 0.27 SIDE CHAIN REMARK 500 34 ARG A 1 0.25 SIDE CHAIN REMARK 500 35 ARG A 1 0.11 SIDE CHAIN REMARK 500 36 ARG A 1 0.12 SIDE CHAIN REMARK 500 37 ARG A 1 0.15 SIDE CHAIN REMARK 500 38 ARG A 1 0.09 SIDE CHAIN REMARK 500 39 ARG A 1 0.18 SIDE CHAIN REMARK 500 40 ARG A 1 0.17 SIDE CHAIN REMARK 500 41 ARG A 1 0.23 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 31 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 8 SG 111.9 REMARK 620 3 HIS A 21 NE2 111.2 110.5 REMARK 620 4 HIS A 27 NE2 111.9 97.5 113.1 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 31 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZNF RELATED DB: PDB DBREF 4ZNF A 1 30 UNP P15822 ZEP1_HUMAN 2113 2142 SEQADV 4ZNF SER A 6 UNP P15822 THR 2118 CONFLICT SEQRES 1 A 30 ARG PRO TYR HIS CYS SER TYR CYS ASN PHE SER PHE LYS SEQRES 2 A 30 THR LYS GLY ASN LEU THR LYS HIS MET LYS SER LYS ALA SEQRES 3 A 30 HIS SER LYS LYS HET ZN A 31 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 THR A 14 SER A 24 1 11 LINK SG CYS A 5 ZN ZN A 31 1555 1555 2.30 LINK SG CYS A 8 ZN ZN A 31 1555 1555 2.31 LINK NE2 HIS A 21 ZN ZN A 31 1555 1555 2.01 LINK NE2 HIS A 27 ZN ZN A 31 1555 1555 2.02 SITE 1 AC1 4 CYS A 5 CYS A 8 HIS A 21 HIS A 27 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 MODEL 1