HEADER METAL BINDING PROTEIN 31-JUL-10 2L1O TITLE ZINC TO CADMIUM REPLACEMENT IN THE A. THALIANA SUPERMAN CYS2HIS2 ZINC TITLE 2 FINGER INDUCES STRUCTURAL REARRANGEMENTS OF TYPICAL DNA BASE TITLE 3 DETERMINANT POSITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR SUPERMAN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYS2HIS2 ZINC FINGER; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 4 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 5 ORGANISM_TAXID: 3702 KEYWDS ZINC FINGER DOMAIN, CADMIUM, SUPERMAN PROTEIN, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.MALGIERI,L.ZACCARO,M.LEONE,E.BUCCI,S.ESPOSITO,I.BAGLIVO,A.DEL AUTHOR 2 GATTO,R.SCANDURRA,P.V.PEDONE,R.FATTORUSSO,C.ISERNIA REVDAT 3 06-NOV-24 2L1O 1 REMARK SEQADV LINK REVDAT 2 21-DEC-11 2L1O 1 JRNL VERSN REVDAT 1 08-JUN-11 2L1O 0 JRNL AUTH G.MALGIERI,L.ZACCARO,M.LEONE,E.BUCCI,S.ESPOSITO,I.BAGLIVO, JRNL AUTH 2 A.DEL GATTO,L.RUSSO,R.SCANDURRA,P.V.PEDONE,R.FATTORUSSO, JRNL AUTH 3 C.ISERNIA JRNL TITL ZINC TO CADMIUM REPLACEMENT IN THE A. THALIANA SUPERMAN JRNL TITL 2 CYS(2) HIS(2) ZINC FINGER INDUCES STRUCTURAL REARRANGEMENTS JRNL TITL 3 OF TYPICAL DNA BASE DETERMINANT POSITIONS. JRNL REF BIOPOLYMERS V. 95 801 2011 JRNL REFN ISSN 0006-3525 JRNL PMID 21618209 JRNL DOI 10.1002/BIP.21680 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XEASY, CYANA REMARK 3 AUTHORS : BARTELS ET AL. (XEASY), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101844. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM PROTEIN, 90% H2O/10% D2O; 1 REMARK 210 MM PROTEIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MOLMOL, VNMRJ, GROMOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 CD2 HIS A 24 CD CD A 39 2.17 REMARK 500 O ACE A 0 OG1 THR A 7 2.19 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 1 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 LEU A 37 CA - C - N ANGL. DEV. = -90.4 DEGREES REMARK 500 3 LEU A 37 CA - C - N ANGL. DEV. = -25.2 DEGREES REMARK 500 4 LEU A 37 CA - C - N ANGL. DEV. = -83.2 DEGREES REMARK 500 5 LEU A 37 CA - C - N ANGL. DEV. = -19.2 DEGREES REMARK 500 6 LEU A 37 CA - C - N ANGL. DEV. = -52.2 DEGREES REMARK 500 7 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 LEU A 37 CA - C - N ANGL. DEV. = -91.2 DEGREES REMARK 500 8 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 LEU A 37 CA - C - N ANGL. DEV. = -38.4 DEGREES REMARK 500 9 LEU A 37 CA - C - N ANGL. DEV. = -33.2 DEGREES REMARK 500 10 LEU A 37 CA - C - N ANGL. DEV. = -89.3 DEGREES REMARK 500 12 LEU A 37 CA - C - N ANGL. DEV. = -24.9 DEGREES REMARK 500 13 LEU A 37 CA - C - N ANGL. DEV. = -60.8 DEGREES REMARK 500 14 LEU A 37 CA - C - N ANGL. DEV. = -17.2 DEGREES REMARK 500 15 LEU A 37 CA - C - N ANGL. DEV. = -69.5 DEGREES REMARK 500 16 LEU A 37 CA - C - N ANGL. DEV. = -92.8 DEGREES REMARK 500 19 LEU A 37 CA - C - N ANGL. DEV. = -28.1 DEGREES REMARK 500 20 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 LEU A 37 CA - C - N ANGL. DEV. = -44.9 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 1 SER A 5 146.19 178.16 REMARK 500 1 SER A 9 -54.93 73.77 REMARK 500 1 LYS A 12 25.90 30.01 REMARK 500 1 ARG A 16 40.33 -103.45 REMARK 500 1 ALA A 18 -65.48 -124.16 REMARK 500 1 ARG A 29 95.17 -178.67 REMARK 500 1 ARG A 30 169.79 60.49 REMARK 500 1 ARG A 34 -142.52 -68.14 REMARK 500 1 LEU A 35 121.38 70.06 REMARK 500 2 SER A 5 150.20 58.35 REMARK 500 2 SER A 9 -54.85 68.83 REMARK 500 2 LYS A 12 22.35 33.94 REMARK 500 2 ARG A 16 44.46 -84.99 REMARK 500 2 ARG A 29 93.50 -173.21 REMARK 500 2 ARG A 32 -154.41 47.12 REMARK 500 2 ALA A 33 134.69 57.57 REMARK 500 2 LEU A 35 143.33 64.86 REMARK 500 3 SER A 9 -52.05 72.92 REMARK 500 3 LYS A 12 23.84 34.38 REMARK 500 3 ALA A 18 -66.41 -123.49 REMARK 500 3 ARG A 29 98.16 67.42 REMARK 500 3 ARG A 30 85.55 56.80 REMARK 500 3 ARG A 32 -77.92 57.02 REMARK 500 3 LEU A 35 106.67 66.01 REMARK 500 4 PRO A 3 -160.38 -72.55 REMARK 500 4 ARG A 4 -151.12 66.31 REMARK 500 4 SER A 9 -55.02 70.28 REMARK 500 4 LYS A 12 25.43 32.99 REMARK 500 4 ARG A 16 39.43 -83.61 REMARK 500 4 ALA A 18 -78.55 -79.61 REMARK 500 4 ARG A 29 52.14 -172.53 REMARK 500 4 ARG A 30 80.76 52.17 REMARK 500 4 LEU A 35 119.13 63.66 REMARK 500 4 ARG A 36 94.72 -161.27 REMARK 500 5 ARG A 4 -179.71 -58.29 REMARK 500 5 SER A 9 -52.97 74.03 REMARK 500 5 LYS A 12 23.86 29.38 REMARK 500 5 ARG A 16 48.88 -85.18 REMARK 500 5 ARG A 29 71.35 46.76 REMARK 500 5 ARG A 30 74.78 46.46 REMARK 500 5 ASP A 31 -70.01 -81.13 REMARK 500 5 ARG A 32 80.94 54.34 REMARK 500 5 ALA A 33 81.06 46.28 REMARK 500 6 SER A 5 151.28 57.99 REMARK 500 6 SER A 9 -56.03 77.29 REMARK 500 6 LYS A 12 23.34 33.01 REMARK 500 6 ARG A 16 40.14 -81.02 REMARK 500 6 ALA A 18 -73.47 -114.66 REMARK 500 6 HIS A 28 -76.21 -59.72 REMARK 500 6 ARG A 29 129.09 -173.55 REMARK 500 REMARK 500 THIS ENTRY HAS 176 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 2 TYR A 6 0.07 SIDE CHAIN REMARK 500 3 PHE A 10 0.08 SIDE CHAIN REMARK 500 4 PHE A 10 0.08 SIDE CHAIN REMARK 500 5 TYR A 6 0.08 SIDE CHAIN REMARK 500 6 TYR A 6 0.07 SIDE CHAIN REMARK 500 8 TYR A 6 0.11 SIDE CHAIN REMARK 500 8 PHE A 10 0.08 SIDE CHAIN REMARK 500 12 PHE A 10 0.09 SIDE CHAIN REMARK 500 13 TYR A 6 0.08 SIDE CHAIN REMARK 500 14 PHE A 10 0.07 SIDE CHAIN REMARK 500 15 PHE A 10 0.08 SIDE CHAIN REMARK 500 17 TYR A 6 0.06 SIDE CHAIN REMARK 500 18 TYR A 6 0.10 SIDE CHAIN REMARK 500 19 PHE A 10 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 SER A 9 -10.03 REMARK 500 5 SER A 9 -10.01 REMARK 500 8 SER A 9 -10.43 REMARK 500 9 SER A 9 -10.20 REMARK 500 10 SER A 9 -10.45 REMARK 500 13 PHE A 15 -10.19 REMARK 500 16 SER A 9 -10.14 REMARK 500 17 SER A 9 -10.43 REMARK 500 19 SER A 9 -10.23 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 CD A 39 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 CYS A 11 SG 117.9 REMARK 620 3 HIS A 24 NE2 123.0 109.1 REMARK 620 4 HIS A 28 NE2 86.0 112.9 104.3 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 CD A 39 DBREF 2L1O A 1 37 UNP Q38895 SUP_ARATH 42 78 SEQADV 2L1O ACE A 0 UNP Q38895 ACETYLATION SEQADV 2L1O NH2 A 38 UNP Q38895 AMIDATION SEQRES 1 A 39 ACE TRP PRO PRO ARG SER TYR THR CYS SER PHE CYS LYS SEQRES 2 A 39 ARG GLU PHE ARG SER ALA GLN ALA LEU GLY GLY HIS MET SEQRES 3 A 39 ASN VAL HIS ARG ARG ASP ARG ALA ARG LEU ARG LEU NH2 HET ACE A 0 6 HET NH2 A 38 3 HET CD A 39 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM CD CADMIUM ION FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 CD CD 2+ HELIX 1 1 ALA A 18 VAL A 27 1 10 SHEET 1 A 2 TYR A 6 THR A 7 0 SHEET 2 A 2 GLU A 14 PHE A 15 -1 O PHE A 15 N TYR A 6 LINK C ACE A 0 N TRP A 1 1555 1555 1.33 LINK C LEU A 37 N NH2 A 38 1555 1555 1.32 LINK SG CYS A 8 CD CD A 39 1555 1555 2.78 LINK SG CYS A 11 CD CD A 39 1555 1555 2.54 LINK NE2 HIS A 24 CD CD A 39 1555 1555 2.11 LINK NE2 HIS A 28 CD CD A 39 1555 1555 2.56 SITE 1 AC1 4 CYS A 8 CYS A 11 HIS A 24 HIS A 28 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 HETATM 1 C ACE A 0 9.986 -4.177 -4.867 1.00 0.00 C HETATM 2 O ACE A 0 8.965 -3.863 -4.256 1.00 0.00 O HETATM 3 CH3 ACE A 0 11.229 -3.368 -4.728 1.00 0.00 C HETATM 4 H1 ACE A 0 11.161 -2.746 -3.836 1.00 0.00 H HETATM 5 H2 ACE A 0 12.088 -4.035 -4.641 1.00 0.00 H HETATM 6 H3 ACE A 0 11.351 -2.734 -5.605 1.00 0.00 H