HEADER TRANSCRIPTION/DNA 18-MAY-10 2KY8 TITLE SOLUTION STRUCTURE AND DYNAMIC ANALYSIS OF CHICKEN MBD2 METHYL BINDING TITLE 2 DOMAIN BOUND TO A TARGET METHYLATED DNA SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-71; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*AP*AP*TP*(5CM)P*GP*GP*CP*(TED)P*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*(TED)P*CP*C)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: MBD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS DNA BINDING DOMAIN, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.C.WILLIAMS JR.,J.N.SCARSDALE JR. REVDAT 3 05-FEB-20 2KY8 1 REMARK DBREF SEQADV LINK REVDAT 2 07-SEP-11 2KY8 1 JRNL VERSN REVDAT 1 18-MAY-11 2KY8 0 JRNL AUTH J.N.SCARSDALE,H.D.WEBB,G.D.GINDER,D.C.WILLIAMS JRNL TITL SOLUTION STRUCTURE AND DYNAMIC ANALYSIS OF CHICKEN MBD2 JRNL TITL 2 METHYL BINDING DOMAIN BOUND TO A TARGET-METHYLATED DNA JRNL TITL 3 SEQUENCE. JRNL REF NUCLEIC ACIDS RES. V. 39 6741 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21531701 JRNL DOI 10.1093/NAR/GKR262 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EXPERIMENTAL TARGET FUNCTION INCLUDED REMARK 3 NOE DISTANCES, BACKBONE TORSION ANGLE RESTRAINTS BASED ON REMARK 3 CHEMICAL SHIFTS, RESIDUAL DIPOLAR COUPLINGS AND PARAMAGNETIC REMARK 3 RELAXATION ENHANCEMENT DATA. REMARK 4 REMARK 4 2KY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000101722. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 CMBD2, 1 MM DNA, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-13C; U-15N; U-2H] REMARK 210 CMBD2, 0.8 MM DNA, 12 MG/ML OF1 REMARK 210 BACTERIOPHAGE, 90% H2O/10% D2O; REMARK 210 0.5 MM [U-13C; U-15N; U-2H] REMARK 210 CMBD2, 0.5 MM DNA, 0.5 MM REMARK 210 MANGANESE (II) ION, 90% H2O/10% REMARK 210 D2O; 0.5 MM [U-13C; U-15N; U-2H] REMARK 210 CMBD2, 0.5 MM DNA, 0.5 MM CA2+, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HN(CO)CA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 C(CO)NH; 3D CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 2D 13C, REMARK 210 15N FILTERED NOESY; 2D 1H-15N REMARK 210 HSQC-T1; 3D-HNCO-JNH; 2D 1H-15N REMARK 210 HSQC,JNCO; 2D 1H-15N HSQC.JNCO; REMARK 210 3D HNCO,JCOCA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, NMRPIPE, TOPSPIN, VNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: TRIMERIC 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 MET A 72 O 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 O LEU A 28 H ALA A 30 1.59 REMARK 500 O ASP A 65 H GLY A 69 1.60 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 DG B 100 O4' DG B 100 C1' 0.073 REMARK 500 1 DA B 103 O4' DA B 103 C1' 0.067 REMARK 500 1 DT B 104 O4' DT B 104 C1' 0.071 REMARK 500 1 DC B 110 O4' DC B 110 C1' 0.080 REMARK 500 1 DG C 111 O4' DG C 111 C1' 0.077 REMARK 500 1 DA C 117 O4' DA C 117 C1' 0.069 REMARK 500 1 DT C 118 O4' DT C 118 C1' 0.078 REMARK 500 1 DC C 120 O4' DC C 120 C1' 0.075 REMARK 500 2 DG B 100 O4' DG B 100 C1' 0.077 REMARK 500 2 DA B 103 O4' DA B 103 C1' 0.067 REMARK 500 2 DT B 104 O4' DT B 104 C1' 0.071 REMARK 500 2 DC B 110 O4' DC B 110 C1' 0.083 REMARK 500 2 DG C 111 O4' DG C 111 C1' 0.076 REMARK 500 2 DG C 113 O4' DG C 113 C1' 0.069 REMARK 500 2 DC C 114 O4' DC C 114 C1' 0.067 REMARK 500 2 DT C 118 O4' DT C 118 C1' 0.074 REMARK 500 2 DC C 120 O4' DC C 120 C1' 0.070 REMARK 500 3 DG B 100 O4' DG B 100 C1' 0.074 REMARK 500 3 DA B 103 O4' DA B 103 C1' 0.073 REMARK 500 3 DT B 104 O4' DT B 104 C1' 0.073 REMARK 500 3 DC B 110 O4' DC B 110 C1' 0.083 REMARK 500 3 DG C 111 O4' DG C 111 C1' 0.079 REMARK 500 3 DG C 113 O4' DG C 113 C1' 0.068 REMARK 500 3 DA C 117 O4' DA C 117 C1' 0.066 REMARK 500 3 DT C 118 O4' DT C 118 C1' 0.077 REMARK 500 3 DC C 120 O4' DC C 120 C1' 0.075 REMARK 500 4 DG B 100 O4' DG B 100 C1' 0.077 REMARK 500 4 DA B 103 O4' DA B 103 C1' 0.066 REMARK 500 4 DT B 104 O4' DT B 104 C1' 0.075 REMARK 500 4 DC B 110 O4' DC B 110 C1' 0.083 REMARK 500 4 DG C 111 O4' DG C 111 C1' 0.077 REMARK 500 4 DA C 117 O4' DA C 117 C1' 0.071 REMARK 500 4 DT C 118 O4' DT C 118 C1' 0.081 REMARK 500 4 DC C 120 O4' DC C 120 C1' 0.077 REMARK 500 5 DA B 103 O4' DA B 103 C1' 0.067 REMARK 500 5 DT B 104 O4' DT B 104 C1' 0.069 REMARK 500 5 DC B 110 O4' DC B 110 C1' 0.081 REMARK 500 5 DG C 111 O4' DG C 111 C1' 0.079 REMARK 500 5 DG C 113 O4' DG C 113 C1' 0.069 REMARK 500 5 DT C 118 O4' DT C 118 C1' 0.072 REMARK 500 5 DC C 120 O4' DC C 120 C1' 0.070 REMARK 500 6 DG B 100 O4' DG B 100 C1' 0.081 REMARK 500 6 DT B 104 O4' DT B 104 C1' 0.072 REMARK 500 6 DC B 110 O4' DC B 110 C1' 0.079 REMARK 500 6 DG C 111 O4' DG C 111 C1' 0.075 REMARK 500 6 DA C 117 O4' DA C 117 C1' 0.066 REMARK 500 6 DT C 118 O4' DT C 118 C1' 0.076 REMARK 500 6 DC C 120 O4' DC C 120 C1' 0.070 REMARK 500 7 DA B 103 O4' DA B 103 C1' 0.067 REMARK 500 7 DT B 104 O4' DT B 104 C1' 0.069 REMARK 500 REMARK 500 THIS ENTRY HAS 140 BOND DEVIATIONS. 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 DG B 100 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DG B 101 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DA B 102 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DA B 103 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT B 104 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT B 104 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 106 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG B 107 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC B 108 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC B 110 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG C 111 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DA C 112 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG C 113 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC C 114 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG C 116 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DA C 117 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT C 118 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT C 118 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC C 120 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DC C 121 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DG B 100 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DG B 101 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DA B 102 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DA B 103 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DT B 104 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DT B 104 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 106 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DG B 107 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DC B 108 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DC B 110 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DG C 111 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DA C 112 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DG C 113 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DC C 114 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DG C 116 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DA C 117 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DT C 118 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DT C 118 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC C 120 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DC C 121 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 3 DG B 100 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DG B 101 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 3 DA B 102 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 3 DA B 103 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 3 DT B 104 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DT B 104 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DG B 106 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DG B 107 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DC B 108 C4' - C3' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 3 DC B 110 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 414 ANGLE 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 GLN A 5 -166.07 -177.93 REMARK 500 1 PRO A 14 135.63 -38.32 REMARK 500 1 ARG A 24 106.86 -55.71 REMARK 500 1 SER A 29 25.91 -62.85 REMARK 500 1 SER A 47 154.07 92.77 REMARK 500 2 LYS A 4 -85.62 -62.72 REMARK 500 2 GLN A 5 96.00 41.13 REMARK 500 2 ARG A 24 107.39 -59.56 REMARK 500 2 SER A 29 25.12 -61.75 REMARK 500 2 SER A 47 149.91 95.94 REMARK 500 2 ASP A 65 -109.94 -99.86 REMARK 500 2 PHE A 66 -30.67 -176.82 REMARK 500 3 PRO A 14 157.08 -43.37 REMARK 500 3 ARG A 24 151.15 -42.43 REMARK 500 3 ARG A 46 66.88 -159.23 REMARK 500 3 SER A 47 119.87 166.27 REMARK 500 4 GLN A 5 67.96 39.12 REMARK 500 4 PRO A 14 152.55 -39.19 REMARK 500 4 SER A 29 23.71 -71.16 REMARK 500 4 ARG A 46 86.63 -169.67 REMARK 500 4 SER A 47 138.10 154.26 REMARK 500 4 ASP A 65 -92.99 -70.34 REMARK 500 4 PHE A 66 -69.08 163.65 REMARK 500 5 LYS A 4 23.62 42.86 REMARK 500 5 GLN A 5 152.72 54.73 REMARK 500 5 PRO A 14 160.67 -41.03 REMARK 500 5 SER A 29 24.45 -61.72 REMARK 500 5 SER A 47 144.19 99.44 REMARK 500 5 THR A 68 -38.36 -139.99 REMARK 500 6 GLN A 5 -40.65 -145.20 REMARK 500 6 SER A 29 26.04 -60.36 REMARK 500 6 SER A 47 115.13 164.63 REMARK 500 6 PHE A 66 -53.53 -130.94 REMARK 500 7 LYS A 4 93.46 46.37 REMARK 500 7 SER A 29 25.55 -61.01 REMARK 500 7 SER A 47 151.77 94.35 REMARK 500 7 MET A 71 95.07 -52.74 REMARK 500 8 GLN A 5 19.50 42.56 REMARK 500 8 PRO A 14 153.29 -40.18 REMARK 500 8 ARG A 24 106.37 -48.51 REMARK 500 8 SER A 29 24.20 -64.11 REMARK 500 8 SER A 47 155.67 96.51 REMARK 500 8 ASP A 65 -117.45 -78.58 REMARK 500 8 PHE A 66 -17.46 -178.45 REMARK 500 9 PRO A 14 136.99 -39.47 REMARK 500 9 ARG A 24 108.08 -51.11 REMARK 500 9 SER A 29 24.92 -62.71 REMARK 500 9 SER A 47 152.29 98.53 REMARK 500 10 ARG A 24 105.46 -53.81 REMARK 500 10 SER A 29 23.59 -68.45 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. 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 MN C 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED C 119 OY4 REMARK 620 2 TED C 119 OY1 66.2 REMARK 620 3 TED C 119 OY2 152.6 89.0 REMARK 620 4 TED C 119 OY3 133.3 142.7 61.9 REMARK 620 5 TED C 119 NYA 75.0 71.4 109.1 137.5 REMARK 620 6 TED C 119 NYB 131.5 122.6 71.1 72.0 66.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED B 109 OY2 REMARK 620 2 TED B 109 OY1 73.2 REMARK 620 3 TED B 109 OY3 72.6 145.5 REMARK 620 4 TED B 109 OY4 159.0 106.1 107.4 REMARK 620 5 TED B 109 NYA 126.8 71.7 128.2 70.5 REMARK 620 6 TED B 109 NYB 81.1 101.0 69.6 119.0 68.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED C 119 OY2 REMARK 620 2 TED C 119 OY1 89.0 REMARK 620 3 TED C 119 OY3 99.6 165.5 REMARK 620 4 TED C 119 OY4 149.3 61.0 108.6 REMARK 620 5 TED C 119 NYB 70.8 124.5 69.7 130.3 REMARK 620 6 TED C 119 NYA 106.7 71.2 116.6 71.5 66.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED C 119 OY1 REMARK 620 2 TED C 119 OY2 86.5 REMARK 620 3 TED C 119 OY4 103.7 164.3 REMARK 620 4 TED C 119 OY3 156.6 111.1 63.0 REMARK 620 5 TED C 119 NYB 102.7 70.2 118.0 70.9 REMARK 620 6 TED C 119 NYA 70.4 124.8 70.4 86.6 67.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED B 109 OY2 REMARK 620 2 TED B 109 OY1 73.7 REMARK 620 3 TED B 109 NYB 73.8 101.4 REMARK 620 4 TED B 109 OY4 160.2 102.5 125.7 REMARK 620 5 TED B 109 OY3 110.5 169.7 71.7 76.7 REMARK 620 6 TED B 109 NYA 124.1 72.1 71.3 71.0 98.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TED B 109 OY2 REMARK 620 2 TED B 109 OY1 74.1 REMARK 620 3 TED B 109 NYB 81.2 133.8 REMARK 620 4 TED B 109 OY4 128.6 56.9 121.3 REMARK 620 5 TED B 109 OY3 120.6 157.5 68.2 110.8 REMARK 620 6 TED B 109 NYA 76.7 70.5 66.1 73.6 127.1 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 MN C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C2I RELATED DB: PDB REMARK 900 MECP2 BOUND TO METHYLATED DNA REMARK 900 RELATED ID: 1IG4 RELATED DB: PDB REMARK 900 MBD1 BOUND TO METHYLATED DNA REMARK 900 RELATED ID: 16936 RELATED DB: BMRB DBREF 2KY8 A 3 72 UNP Q5EFL0 Q5EFL0_CHICK 2 71 DBREF 2KY8 B 100 110 PDB 2KY8 2KY8 100 110 DBREF 2KY8 C 111 121 PDB 2KY8 2KY8 111 121 SEQADV 2KY8 GLY A 1 UNP Q5EFL0 EXPRESSION TAG SEQADV 2KY8 SER A 2 UNP Q5EFL0 EXPRESSION TAG SEQRES 1 A 72 GLY SER ASP LYS GLN GLY ARG THR ASP CYS PRO ALA LEU SEQRES 2 A 72 PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SER SEQRES 3 A 72 GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SER SEQRES 4 A 72 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 A 72 ARG TYR LEU GLY ASN ALA VAL ASP LEU SER CYS PHE ASP SEQRES 6 A 72 PHE ARG THR GLY LYS MET MET SEQRES 1 B 11 DG DG DA DA DT 5CM DG DG DC TED DC SEQRES 1 C 11 DG DA DG DC 5CM DG DA DT TED DC DC MODRES 2KY8 5CM B 105 DC MODRES 2KY8 TED B 109 DT MODRES 2KY8 5CM C 115 DC MODRES 2KY8 TED C 119 DT HET 5CM B 105 33 HET TED B 109 167 HET 5CM C 115 33 HET TED C 119 167 HET MN B 302 3 HET MN C 301 3 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM TED 5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO- HETNAM 2 TED 4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2'-DEOXYURIDINE HETNAM 3 TED 5'-(DIHYDROGEN PHOSPHATE) HETNAM MN MANGANESE (II) ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 2 TED 2(C24 H35 N6 O16 P) FORMUL 4 MN 2(MN 2+) HELIX 1 1 SER A 47 GLY A 56 1 10 SHEET 1 A 4 ARG A 7 ASP A 9 0 SHEET 2 A 4 LYS A 18 ILE A 23 -1 O LYS A 19 N THR A 8 SHEET 3 A 4 SER A 33 PHE A 38 -1 O PHE A 38 N LYS A 18 SHEET 4 A 4 LYS A 44 ARG A 46 -1 O PHE A 45 N TYR A 37 SHEET 1 B 2 PHE A 64 ASP A 65 0 SHEET 2 B 2 LYS A 70 MET A 71 -1 O LYS A 70 N ASP A 65 LINK O3' DT B 104 P 5CM B 105 1555 1555 1.61 LINK O3' 5CM B 105 P DG B 106 1555 1555 1.61 LINK O3' DC B 108 P TED B 109 1555 1555 1.61 LINK O3' DC C 114 P 5CM C 115 1555 1555 1.61 LINK O3' 5CM C 115 P DG C 116 1555 1555 1.61 LINK O3' DT C 118 P TED C 119 1555 1555 1.61 LINK OY4ATED C 119 MN A MN C 301 1555 1555 2.24 LINK OY2ATED B 109 MN A MN B 302 1555 1555 2.24 LINK OY2CTED C 119 MN C MN C 301 1555 1555 2.24 LINK OY1BTED C 119 MN B MN C 301 1555 1555 2.24 LINK OY1ATED C 119 MN A MN C 301 1555 1555 2.24 LINK OY1ATED B 109 MN A MN B 302 1555 1555 2.24 LINK OY2BTED B 109 MN B MN B 302 1555 1555 2.24 LINK OY2CTED B 109 MN C MN B 302 1555 1555 2.24 LINK OY1CTED C 119 MN C MN C 301 1555 1555 2.24 LINK OY2ATED C 119 MN A MN C 301 1555 1555 2.24 LINK OY2BTED C 119 MN B MN C 301 1555 1555 2.24 LINK OY1CTED B 109 MN C MN B 302 1555 1555 2.24 LINK OY1BTED B 109 MN B MN B 302 1555 1555 2.24 LINK OY4BTED C 119 MN B MN C 301 1555 1555 2.29 LINK OY3CTED C 119 MN C MN C 301 1555 1555 2.27 LINK OY3ATED B 109 MN A MN B 302 1555 1555 2.35 LINK NYBCTED B 109 MN C MN B 302 1555 1555 2.36 LINK NYBBTED B 109 MN B MN B 302 1555 1555 2.25 LINK OY4ATED B 109 MN A MN B 302 1555 1555 2.29 LINK OY3BTED C 119 MN B MN C 301 1555 1555 2.30 LINK OY4CTED C 119 MN C MN C 301 1555 1555 2.31 LINK OY4CTED B 109 MN C MN B 302 1555 1555 2.24 LINK OY4BTED B 109 MN B MN B 302 1555 1555 2.29 LINK NYBCTED C 119 MN C MN C 301 1555 1555 2.42 LINK OY3CTED B 109 MN C MN B 302 1555 1555 2.39 LINK OY3BTED B 109 MN B MN B 302 1555 1555 2.36 LINK OY3ATED C 119 MN A MN C 301 1555 1555 2.32 LINK NYAATED C 119 MN A MN C 301 1555 1555 2.41 LINK NYAATED B 109 MN A MN B 302 1555 1555 2.38 LINK NYBATED B 109 MN A MN B 302 1555 1555 2.34 LINK NYABTED B 109 MN B MN B 302 1555 1555 2.36 LINK NYACTED B 109 MN C MN B 302 1555 1555 2.37 LINK NYBBTED C 119 MN B MN C 301 1555 1555 2.40 LINK NYABTED C 119 MN B MN C 301 1555 1555 2.41 LINK NYACTED C 119 MN C MN C 301 1555 1555 2.43 LINK NYBATED C 119 MN A MN C 301 1555 1555 2.40 SITE 1 AC1 1 TED C 119 SITE 1 AC2 1 TED B 109 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