PDB Short entry for 1ZNM HEADER ZINC FINGER 20-NOV-97 1ZNM TITLE A ZINC FINGER WITH AN ARTIFICIAL BETA-TURN, ORIGINAL SEQUENCE TAKEN TITLE 2 FROM THE THIRD ZINC FINGER DOMAIN OF THE HUMAN TRANSCRIPTIONAL TITLE 3 REPRESSOR PROTEIN YY1 (YING AND YANG 1, A DELTA TRANSCRIPTION TITLE 4 FACTOR), NMR, 34 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: YY1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DNA BINDING DOMAIN 3 FROM YY1; COMPND 5 SYNONYM: ZN-BTD(7,8)-3YY1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: DOES NOT BIND DNA SPECIFICALLY AS A SINGLE ZINC FINGER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE SYNTHESISED USING FMOC CHEMISTRY, WITH BETA- SOURCE 4 TURN MIMETIC BTD IN POSITIONS 7 AND 8 KEYWDS ZINC FINGER, ZN-BTD(7, 8)-3YY1, BETA-TURN MIMETIC, TRANSCRIPTION KEYWDS 2 REGULATION EXPDTA SOLUTION NMR NUMMDL 34 AUTHOR J.H.VILES,S.U.PATEL,J.B.O.MITCHELL,C.M.MOODY,D.E.JUSTICE, AUTHOR 2 J.UPPENBRINK,P.M.DOYLE,C.J.HARRIS,P.J.SADLER,J.M.THORNTON REVDAT 3 29-NOV-17 1ZNM 1 REMARK HELIX REVDAT 2 24-FEB-09 1ZNM 1 VERSN REVDAT 1 01-APR-98 1ZNM 0 JRNL AUTH J.H.VILES,S.U.PATEL,J.B.MITCHELL,C.M.MOODY,D.E.JUSTICE, JRNL AUTH 2 J.UPPENBRINK,P.M.DOYLE,C.J.HARRIS,P.J.SADLER,J.M.THORNTON JRNL TITL DESIGN, SYNTHESIS AND STRUCTURE OF A ZINC FINGER WITH AN JRNL TITL 2 ARTIFICIAL BETA-TURN. JRNL REF J.MOL.BIOL. V. 279 973 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9642075 JRNL DOI 10.1006/JMBI.1998.1764 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED USING AN REMARK 3 AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED REMARK 3 WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI REMARK 3 AND PSI ANGLES. THE ZINC ION WAS INCORPORATED WITH THE REMARK 3 APPROPRIATE GEOMETRIC CONSTRAINTS TO PRODUCE TETRAHEDRAL ZINC CO- REMARK 3 ORDINATION. REMARK 4 REMARK 4 1ZNM 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_1000177497. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ROESY; NOESY; COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX; VXR600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 34 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE VIOLATIONS ABOVE 0.2 REMARK 210 ANGSTROM AND 5 DEGREE DIHEDRAL REMARK 210 ANGLE 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-34 REMARK 465 RES C SSSEQI REMARK 465 PRO A 1 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: 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 THR A 5 39.42 -164.12 REMARK 500 1 NVA A 7 -150.10 44.36 REMARK 500 1 HIS A 22 -72.23 -104.85 REMARK 500 2 THR A 5 36.96 -154.88 REMARK 500 2 NVA A 7 -157.48 50.30 REMARK 500 2 HIS A 22 -68.93 -101.90 REMARK 500 3 THR A 5 36.07 -162.00 REMARK 500 3 NVA A 7 -161.20 48.82 REMARK 500 3 SER A 14 -64.12 -94.44 REMARK 500 3 HIS A 22 -69.37 -104.19 REMARK 500 4 THR A 5 38.77 -140.67 REMARK 500 4 NVA A 7 -157.07 45.23 REMARK 500 4 HIS A 22 -69.31 -105.25 REMARK 500 5 THR A 5 39.23 -163.26 REMARK 500 5 NVA A 7 -150.38 46.31 REMARK 500 5 HIS A 22 -70.45 -100.66 REMARK 500 6 THR A 5 36.02 -162.88 REMARK 500 6 NVA A 7 -159.06 52.44 REMARK 500 6 HIS A 22 -70.23 -102.74 REMARK 500 7 THR A 5 36.11 -158.99 REMARK 500 7 NVA A 7 -157.35 51.96 REMARK 500 7 HIS A 22 -69.54 -102.53 REMARK 500 8 GLN A 3 105.32 -178.76 REMARK 500 8 THR A 5 42.04 -165.90 REMARK 500 8 NVA A 7 -152.25 51.50 REMARK 500 8 CYS A 9 -73.67 -79.26 REMARK 500 8 HIS A 22 -64.21 -92.21 REMARK 500 9 THR A 5 36.26 -158.25 REMARK 500 9 NVA A 7 -157.62 48.01 REMARK 500 9 HIS A 22 -71.74 -107.73 REMARK 500 9 LYS A 24 -19.90 -47.62 REMARK 500 10 GLN A 3 108.60 -179.06 REMARK 500 10 THR A 5 34.05 -172.91 REMARK 500 10 NVA A 7 -162.64 45.22 REMARK 500 10 SER A 14 -76.93 -75.74 REMARK 500 10 HIS A 22 -68.35 -106.64 REMARK 500 11 GLN A 3 148.63 -178.07 REMARK 500 11 THR A 5 38.13 -147.73 REMARK 500 11 NVA A 7 -157.75 43.08 REMARK 500 11 HIS A 22 -69.66 -104.15 REMARK 500 12 THR A 5 37.39 -149.80 REMARK 500 12 NVA A 7 -158.35 46.10 REMARK 500 12 SER A 14 -67.87 -94.39 REMARK 500 12 HIS A 22 -71.47 -89.85 REMARK 500 13 THR A 5 36.24 -156.82 REMARK 500 13 NVA A 7 -156.87 52.09 REMARK 500 13 SER A 14 -56.13 -120.55 REMARK 500 13 HIS A 22 -71.64 -92.11 REMARK 500 14 THR A 5 38.30 -145.22 REMARK 500 14 NVA A 7 -156.90 48.72 REMARK 500 REMARK 500 THIS ENTRY HAS 126 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 12 0.22 SIDE CHAIN REMARK 500 2 ARG A 12 0.26 SIDE CHAIN REMARK 500 3 ARG A 12 0.09 SIDE CHAIN REMARK 500 4 ARG A 12 0.10 SIDE CHAIN REMARK 500 5 ARG A 12 0.31 SIDE CHAIN REMARK 500 6 ARG A 12 0.08 SIDE CHAIN REMARK 500 7 ARG A 12 0.27 SIDE CHAIN REMARK 500 8 ARG A 12 0.32 SIDE CHAIN REMARK 500 9 ARG A 12 0.22 SIDE CHAIN REMARK 500 10 ARG A 12 0.14 SIDE CHAIN REMARK 500 11 ARG A 12 0.30 SIDE CHAIN REMARK 500 12 ARG A 12 0.28 SIDE CHAIN REMARK 500 13 ARG A 12 0.24 SIDE CHAIN REMARK 500 14 ARG A 12 0.09 SIDE CHAIN REMARK 500 15 ARG A 12 0.31 SIDE CHAIN REMARK 500 16 ARG A 12 0.13 SIDE CHAIN REMARK 500 17 ARG A 12 0.32 SIDE CHAIN REMARK 500 18 ARG A 12 0.31 SIDE CHAIN REMARK 500 19 ARG A 12 0.26 SIDE CHAIN REMARK 500 20 ARG A 12 0.19 SIDE CHAIN REMARK 500 21 ARG A 12 0.20 SIDE CHAIN REMARK 500 22 ARG A 12 0.31 SIDE CHAIN REMARK 500 23 ARG A 12 0.23 SIDE CHAIN REMARK 500 24 ARG A 12 0.29 SIDE CHAIN REMARK 500 25 ARG A 12 0.24 SIDE CHAIN REMARK 500 26 ARG A 12 0.19 SIDE CHAIN REMARK 500 27 ARG A 12 0.15 SIDE CHAIN REMARK 500 28 ARG A 12 0.32 SIDE CHAIN REMARK 500 29 ARG A 12 0.30 SIDE CHAIN REMARK 500 30 ARG A 12 0.09 SIDE CHAIN REMARK 500 31 ARG A 12 0.17 SIDE CHAIN REMARK 500 32 ARG A 12 0.25 SIDE CHAIN REMARK 500 33 ARG A 12 0.24 SIDE CHAIN REMARK 500 34 ARG A 12 0.28 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 29 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 CYS A 9 SG 112.0 REMARK 620 3 HIS A 22 NE2 116.1 106.2 REMARK 620 4 HIS A 26 NE2 109.0 109.5 103.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: BTD REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: BETA TURN DIPEPTIDE (TYPE II' BETA TURN REMARK 800 MIMETIC). REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 29 DBREF 1ZNM A 1 28 UNP P25490 TYY1_HUMAN 352 379 SEQADV 1ZNM NVA A 7 UNP P25490 GLU 358 MODIFIED RESIDUE SEQADV 1ZNM CYS A 8 UNP P25490 GLY 359 MODIFIED RESIDUE SEQADV 1ZNM LYS A 20 UNP P25490 ARG 371 CONFLICT SEQADV 1ZNM LYS A 24 UNP P25490 ARG 375 CONFLICT SEQRES 1 A 28 PRO PHE GLN CYS THR PHE NVA CYS CYS GLY LYS ARG PHE SEQRES 2 A 28 SER LEU ASP PHE ASN LEU LYS THR HIS VAL LYS ILE HIS SEQRES 3 A 28 THR GLY MODRES 1ZNM NVA A 7 VAL NORVALINE HET NVA A 7 14 HET ZN A 29 1 HETNAM NVA NORVALINE HETNAM ZN ZINC ION FORMUL 1 NVA C5 H11 N O2 FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 16 THR A 27 1SEE REMARK 650 12 SHEET 1 A 2 PHE A 2 PHE A 6 0 SHEET 2 A 2 LYS A 11 PHE A 13 -1 O PHE A 13 N PHE A 2 LINK N NVA A 7 C PHE A 6 1555 1555 1.30 LINK CD NVA A 7 N CYS A 8 1555 1555 1.51 LINK CD NVA A 7 SG CYS A 8 1555 1555 1.81 LINK C NVA A 7 N CYS A 8 1555 1555 1.31 LINK C CYS A 8 N CYS A 9 1555 1555 1.31 LINK ZN ZN A 29 SG CYS A 4 1555 1555 2.30 LINK ZN ZN A 29 SG CYS A 9 1555 1555 2.31 LINK ZN ZN A 29 NE2 HIS A 22 1555 1555 1.99 LINK ZN ZN A 29 NE2 HIS A 26 1555 1555 1.99 SITE 1 ZNB 4 CYS A 4 CYS A 9 HIS A 22 HIS A 26 SITE 1 BTD 1 NVA A 7 SITE 1 AC1 4 CYS A 4 CYS A 9 HIS A 22 HIS A 26 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