HEADER OXIDOREDUCTASE/DNA 14-NOV-13 4NM6 TITLE CRYSTAL STRUCTURE OF TET2-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCYTOSINE DIOXYGENASE TET2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'; COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TET2, KIAA1546, NBLA00191; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS DNA HYDROXYLATION, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.HU,Z.LI,J.CHENG,Q.RAO,W.GONG,M.LIU,P.WANG,Y.XU REVDAT 4 28-FEB-24 4NM6 1 REMARK SEQADV LINK REVDAT 3 26-JUL-17 4NM6 1 SOURCE REVDAT 2 15-JAN-14 4NM6 1 JRNL REVDAT 1 18-DEC-13 4NM6 0 JRNL AUTH L.HU,Z.LI,J.CHENG,Q.RAO,W.GONG,M.LIU,Y.G.SHI,J.ZHU,P.WANG, JRNL AUTH 2 Y.XU JRNL TITL CRYSTAL STRUCTURE OF TET2-DNA COMPLEX: INSIGHT INTO JRNL TITL 2 TET-MEDIATED 5MC OXIDATION. JRNL REF CELL(CAMBRIDGE,MASS.) V. 155 1545 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 24315485 JRNL DOI 10.1016/J.CELL.2013.11.020 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 34834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.8137 - 4.6372 0.91 2857 137 0.1930 0.2220 REMARK 3 2 4.6372 - 3.6814 0.95 2801 164 0.1818 0.2041 REMARK 3 3 3.6814 - 3.2162 0.96 2822 159 0.2028 0.2606 REMARK 3 4 3.2162 - 2.9223 0.95 2799 154 0.2147 0.2572 REMARK 3 5 2.9223 - 2.7128 0.96 2809 158 0.2261 0.2748 REMARK 3 6 2.7128 - 2.5529 0.96 2799 162 0.2279 0.2677 REMARK 3 7 2.5529 - 2.4251 0.95 2766 123 0.2083 0.2784 REMARK 3 8 2.4251 - 2.3195 0.95 2799 123 0.2164 0.2668 REMARK 3 9 2.3195 - 2.2302 0.93 2712 129 0.2203 0.2527 REMARK 3 10 2.2302 - 2.1533 0.93 2710 133 0.2152 0.2826 REMARK 3 11 2.1533 - 2.0860 0.92 2624 156 0.2119 0.2914 REMARK 3 12 2.0860 - 2.0260 0.90 2605 133 0.2149 0.2766 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3761 REMARK 3 ANGLE : 1.294 5159 REMARK 3 CHIRALITY : 0.087 559 REMARK 3 PLANARITY : 0.005 598 REMARK 3 DIHEDRAL : 20.344 1450 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -8.9709 0.5435 -34.3880 REMARK 3 T TENSOR REMARK 3 T11: 0.4230 T22: 0.4315 REMARK 3 T33: 0.4500 T12: -0.0042 REMARK 3 T13: -0.1287 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 1.9659 L22: 1.6766 REMARK 3 L33: 1.9267 L12: 0.0231 REMARK 3 L13: 0.3465 L23: 0.3348 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.1304 S13: -0.1602 REMARK 3 S21: 0.0434 S22: -0.0890 S23: 0.0845 REMARK 3 S31: -0.1744 S32: -0.1692 S33: -0.0118 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792, 1.2818 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34839 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48800 REMARK 200 R SYM FOR SHELL (I) : 0.48800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG2000 MME, 0.1 M MES, PH 6.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 131.48100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 131.48100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.14800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.09300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.14800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.09300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 131.48100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.14800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.09300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 131.48100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.14800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.09300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL 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 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 GLY A 1126 REMARK 465 GLY A 1127 REMARK 465 SER A 1128 REMARK 465 ASP A 1129 REMARK 465 PHE A 1130 REMARK 465 PRO A 1131 REMARK 465 VAL A 1136 REMARK 465 GLU A 1137 REMARK 465 GLN A 1138 REMARK 465 ILE A 1139 REMARK 465 ILE A 1140 REMARK 465 GLU A 1141 REMARK 465 LYS A 1142 REMARK 465 ASP A 1143 REMARK 465 CYS A 1812 REMARK 465 ARG A 1813 REMARK 465 GLN A 1814 REMARK 465 ARG A 1815 REMARK 465 LYS A 1816 REMARK 465 LEU A 1817 REMARK 465 GLU A 1818 REMARK 465 ALA A 1819 REMARK 465 LYS A 1820 REMARK 465 LYS A 1821 REMARK 465 ALA A 1822 REMARK 465 ALA A 1823 REMARK 465 ALA A 1824 REMARK 465 GLU A 1825 REMARK 465 LYS A 1826 REMARK 465 LEU A 1827 REMARK 465 SER A 1828 REMARK 465 GLY A 1829 REMARK 465 GLY A 1830 REMARK 465 GLY A 1831 REMARK 465 GLY A 1832 REMARK 465 SER A 1833 REMARK 465 GLY A 1834 REMARK 465 GLY A 1835 REMARK 465 GLY A 1836 REMARK 465 GLY A 1837 REMARK 465 SER A 1838 REMARK 465 GLY A 1839 REMARK 465 GLY A 1840 REMARK 465 GLY A 1841 REMARK 465 ALA A 1925 REMARK 465 ARG A 1926 REMARK 465 GLU A 1927 REMARK 465 LYS A 1928 REMARK 465 GLU A 1929 REMARK 465 GLU A 1930 REMARK 465 GLU A 1931 REMARK 465 CYS A 1932 REMARK 465 GLU A 1933 REMARK 465 LYS A 1934 REMARK 465 TYR A 1935 REMARK 465 GLY A 1936 REMARK 465 DT B 12 REMARK 465 DA C 1 REMARK 465 DC C 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O2 DC B 2 N2 DG C 11 2.14 REMARK 500 O HOH A 2198 O HOH A 2202 2.16 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 LEU A1229 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 7 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.2 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 SER A1190 0.72 -63.12 REMARK 500 GLU A1234 72.28 -100.32 REMARK 500 ILE A1305 87.55 49.98 REMARK 500 ASP A1315 100.57 -36.52 REMARK 500 GLU A1411 99.83 48.91 REMARK 500 SER A1448 49.39 115.12 REMARK 500 LYS A1462 93.58 59.41 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 A2002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1135 SG 108.0 REMARK 620 3 HIS A1219 ND1 91.9 100.7 REMARK 620 4 CYS A1221 SG 109.8 123.4 118.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1193 SG REMARK 620 2 CYS A1271 SG 119.1 REMARK 620 3 CYS A1273 SG 99.0 117.1 REMARK 620 4 HIS A1380 NE2 117.5 92.2 113.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1289 SG REMARK 620 2 CYS A1298 SG 107.5 REMARK 620 3 CYS A1358 SG 112.3 117.9 REMARK 620 4 HIS A1912 ND1 106.1 107.6 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A2004 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1382 NE2 REMARK 620 2 ASP A1384 OD1 80.9 REMARK 620 3 HIS A1881 NE2 98.2 105.5 REMARK 620 4 OGA A2005 O1 89.7 95.6 158.3 REMARK 620 5 OGA A2005 O2' 95.1 165.1 89.2 69.9 REMARK 620 6 HOH A2149 O 168.6 102.4 91.5 79.1 79.0 REMARK 620 N 1 2 3 4 5 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 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 2005 REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN CONSTRUCT COMPRISES UNP RESIDUES 1129-1480 AND 1844-1936 REMARK 999 CONNECTED BY A (GGGGS)3 LINKER. DBREF 4NM6 A 1129 1828 UNP Q6N021 TET2_HUMAN 1129 1480 DBREF 4NM6 A 1844 1936 UNP Q6N021 TET2_HUMAN 1844 1936 DBREF 4NM6 B 1 12 PDB 4NM6 4NM6 1 12 DBREF 4NM6 C 1 12 PDB 4NM6 4NM6 1 12 SEQADV 4NM6 GLY A 1126 UNP Q6N021 EXPRESSION TAG SEQADV 4NM6 GLY A 1127 UNP Q6N021 EXPRESSION TAG SEQADV 4NM6 SER A 1128 UNP Q6N021 EXPRESSION TAG SEQADV 4NM6 GLY A 1829 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1830 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1831 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1832 UNP Q6N021 LINKER SEQADV 4NM6 SER A 1833 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1834 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1835 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1836 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1837 UNP Q6N021 LINKER SEQADV 4NM6 SER A 1838 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1839 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1840 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1841 UNP Q6N021 LINKER SEQADV 4NM6 GLY A 1842 UNP Q6N021 LINKER SEQADV 4NM6 SER A 1843 UNP Q6N021 LINKER SEQRES 1 A 463 GLY GLY SER ASP PHE PRO SER CYS ARG CYS VAL GLU GLN SEQRES 2 A 463 ILE ILE GLU LYS ASP GLU GLY PRO PHE TYR THR HIS LEU SEQRES 3 A 463 GLY ALA GLY PRO ASN VAL ALA ALA ILE ARG GLU ILE MET SEQRES 4 A 463 GLU GLU ARG PHE GLY GLN LYS GLY LYS ALA ILE ARG ILE SEQRES 5 A 463 GLU ARG VAL ILE TYR THR GLY LYS GLU GLY LYS SER SER SEQRES 6 A 463 GLN GLY CYS PRO ILE ALA LYS TRP VAL VAL ARG ARG SER SEQRES 7 A 463 SER SER GLU GLU LYS LEU LEU CYS LEU VAL ARG GLU ARG SEQRES 8 A 463 ALA GLY HIS THR CYS GLU ALA ALA VAL ILE VAL ILE LEU SEQRES 9 A 463 ILE LEU VAL TRP GLU GLY ILE PRO LEU SER LEU ALA ASP SEQRES 10 A 463 LYS LEU TYR SER GLU LEU THR GLU THR LEU ARG LYS TYR SEQRES 11 A 463 GLY THR LEU THR ASN ARG ARG CYS ALA LEU ASN GLU GLU SEQRES 12 A 463 ARG THR CYS ALA CYS GLN GLY LEU ASP PRO GLU THR CYS SEQRES 13 A 463 GLY ALA SER PHE SER PHE GLY CYS SER TRP SER MET TYR SEQRES 14 A 463 TYR ASN GLY CYS LYS PHE ALA ARG SER LYS ILE PRO ARG SEQRES 15 A 463 LYS PHE LYS LEU LEU GLY ASP ASP PRO LYS GLU GLU GLU SEQRES 16 A 463 LYS LEU GLU SER HIS LEU GLN ASN LEU SER THR LEU MET SEQRES 17 A 463 ALA PRO THR TYR LYS LYS LEU ALA PRO ASP ALA TYR ASN SEQRES 18 A 463 ASN GLN ILE GLU TYR GLU HIS ARG ALA PRO GLU CYS ARG SEQRES 19 A 463 LEU GLY LEU LYS GLU GLY ARG PRO PHE SER GLY VAL THR SEQRES 20 A 463 ALA CYS LEU ASP PHE CYS ALA HIS ALA HIS ARG ASP LEU SEQRES 21 A 463 HIS ASN MET GLN ASN GLY SER THR LEU VAL CYS THR LEU SEQRES 22 A 463 THR ARG GLU ASP ASN ARG GLU PHE GLY GLY LYS PRO GLU SEQRES 23 A 463 ASP GLU GLN LEU HIS VAL LEU PRO LEU TYR LYS VAL SER SEQRES 24 A 463 ASP VAL ASP GLU PHE GLY SER VAL GLU ALA GLN GLU GLU SEQRES 25 A 463 LYS LYS ARG SER GLY ALA ILE GLN VAL LEU SER SER PHE SEQRES 26 A 463 ARG ARG LYS VAL ARG MET LEU ALA GLU PRO VAL LYS THR SEQRES 27 A 463 CYS ARG GLN ARG LYS LEU GLU ALA LYS LYS ALA ALA ALA SEQRES 28 A 463 GLU LYS LEU SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 29 A 463 SER GLY GLY GLY GLY SER ASP GLU VAL TRP SER ASP SER SEQRES 30 A 463 GLU GLN SER PHE LEU ASP PRO ASP ILE GLY GLY VAL ALA SEQRES 31 A 463 VAL ALA PRO THR HIS GLY SER ILE LEU ILE GLU CYS ALA SEQRES 32 A 463 LYS ARG GLU LEU HIS ALA THR THR PRO LEU LYS ASN PRO SEQRES 33 A 463 ASN ARG ASN HIS PRO THR ARG ILE SER LEU VAL PHE TYR SEQRES 34 A 463 GLN HIS LYS SER MET ASN GLU PRO LYS HIS GLY LEU ALA SEQRES 35 A 463 LEU TRP GLU ALA LYS MET ALA GLU LYS ALA ARG GLU LYS SEQRES 36 A 463 GLU GLU GLU CYS GLU LYS TYR GLY SEQRES 1 B 12 DA DC DC DA DC 5CM DG DG DT DG DG DT SEQRES 1 C 12 DA DC DC DA DC 5CM DG DG DT DG DG DT MODRES 4NM6 5CM B 6 DC MODRES 4NM6 5CM C 6 DC HET 5CM B 6 20 HET 5CM C 6 20 HET ZN A2001 1 HET ZN A2002 1 HET ZN A2003 1 HET FE2 A2004 1 HET OGA A2005 10 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM OGA N-OXALYLGLYCINE FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 FE2 FE 2+ FORMUL 8 OGA C4 H5 N O5 FORMUL 9 HOH *131(H2 O) HELIX 1 1 ASN A 1156 GLY A 1169 1 14 HELIX 2 2 LYS A 1171 LYS A 1173 5 3 HELIX 3 3 PRO A 1237 GLY A 1256 1 20 HELIX 4 4 ARG A 1261 LEU A 1265 5 5 HELIX 5 5 ASP A 1315 ALA A 1341 1 27 HELIX 6 6 ALA A 1341 GLU A 1350 1 10 HELIX 7 7 ALA A 1355 ARG A 1359 5 5 HELIX 8 8 GLU A 1401 ARG A 1404 5 4 HELIX 9 9 SER A 1431 GLY A 1442 1 12 HELIX 10 10 SER A 1850 ASP A 1856 1 7 HELIX 11 11 GLU A 1909 HIS A 1912 5 4 HELIX 12 12 GLY A 1913 GLU A 1923 1 11 SHEET 1 A 7 ALA A1153 GLY A1154 0 SHEET 2 A 7 VAL A1225 VAL A1232 -1 O VAL A1225 N GLY A1154 SHEET 3 A 7 ILE A1871 GLU A1874 -1 O ILE A1873 N ILE A1230 SHEET 4 A 7 THR A1393 THR A1399 -1 N THR A1393 O GLU A1874 SHEET 5 A 7 ARG A1896 TYR A1902 -1 O PHE A1901 N LEU A1394 SHEET 6 A 7 GLY A1370 LEU A1375 -1 N THR A1372 O VAL A1900 SHEET 7 A 7 ALA A1283 GLY A1288 -1 N PHE A1287 O VAL A1371 SHEET 1 B 5 ALA A1153 GLY A1154 0 SHEET 2 B 5 VAL A1225 VAL A1232 -1 O VAL A1225 N GLY A1154 SHEET 3 B 5 LEU A1209 GLU A1215 -1 N LEU A1212 O ILE A1228 SHEET 4 B 5 ILE A1175 TYR A1182 1 N VAL A1180 O VAL A1213 SHEET 5 B 5 TYR A1421 VAL A1423 -1 O LYS A1422 N ILE A1181 SHEET 1 C 5 ILE A1444 VAL A1446 0 SHEET 2 C 5 TRP A1198 VAL A1200 -1 N VAL A1199 O GLN A1445 SHEET 3 C 5 VAL A1862 VAL A1864 1 O ALA A1863 N VAL A1200 SHEET 4 C 5 HIS A1416 LEU A1418 -1 N LEU A1418 O VAL A1862 SHEET 5 C 5 ALA A1882 THR A1883 -1 O ALA A1882 N VAL A1417 SHEET 1 D 2 TRP A1291 SER A1292 0 SHEET 2 D 2 GLY A1297 CYS A1298 -1 O GLY A1297 N SER A1292 SHEET 1 E 2 ARG A1451 LEU A1457 0 SHEET 2 E 2 SER A1843 ASP A1849 -1 O VAL A1846 N VAL A1454 LINK O3' DC B 5 P 5CM B 6 1555 1555 1.61 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.61 LINK O3' DC C 5 P 5CM C 6 1555 1555 1.61 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK SG CYS A1133 ZN ZN A2002 1555 1555 2.42 LINK SG CYS A1135 ZN ZN A2002 1555 1555 2.20 LINK SG CYS A1193 ZN ZN A2001 1555 1555 2.43 LINK ND1 HIS A1219 ZN ZN A2002 1555 1555 2.23 LINK SG CYS A1221 ZN ZN A2002 1555 1555 2.24 LINK SG CYS A1271 ZN ZN A2001 1555 1555 2.53 LINK SG CYS A1273 ZN ZN A2001 1555 1555 2.48 LINK SG CYS A1289 ZN ZN A2003 1555 1555 2.54 LINK SG CYS A1298 ZN ZN A2003 1555 1555 2.47 LINK SG CYS A1358 ZN ZN A2003 1555 1555 2.53 LINK NE2 HIS A1380 ZN ZN A2001 1555 1555 2.28 LINK NE2 HIS A1382 FE FE2 A2004 1555 1555 2.35 LINK OD1 ASP A1384 FE FE2 A2004 1555 1555 2.47 LINK NE2 HIS A1881 FE FE2 A2004 1555 1555 2.23 LINK ND1 HIS A1912 ZN ZN A2003 1555 1555 2.28 LINK FE FE2 A2004 O1 OGA A2005 1555 1555 2.40 LINK FE FE2 A2004 O2' OGA A2005 1555 1555 2.42 LINK FE FE2 A2004 O HOH A2149 1555 1555 2.41 CISPEP 1 LEU A 1151 GLY A 1152 0 15.84 CISPEP 2 GLN A 1191 GLY A 1192 0 -19.58 CISPEP 3 GLU A 1411 ASP A 1412 0 19.26 CISPEP 4 LEU A 1447 SER A 1448 0 7.06 SITE 1 AC1 4 CYS A1193 CYS A1271 CYS A1273 HIS A1380 SITE 1 AC2 4 CYS A1133 CYS A1135 HIS A1219 CYS A1221 SITE 1 AC3 4 CYS A1289 CYS A1298 CYS A1358 HIS A1912 SITE 1 AC4 5 HIS A1382 ASP A1384 HIS A1881 OGA A2005 SITE 2 AC4 5 HOH A2149 SITE 1 AC5 13 ARG A1261 CYS A1374 HIS A1382 ASP A1384 SITE 2 AC5 13 HIS A1416 HIS A1881 THR A1883 ARG A1896 SITE 3 AC5 13 SER A1898 FE2 A2004 HOH A2142 HOH A2149 SITE 4 AC5 13 5CM B 6 CRYST1 48.296 88.186 262.962 90.00 90.00 90.00 C 2 2 21 16 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 0.020706 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003803 0.00000