Zinc in PDB 6e94: Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna

The structure of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna, PDB code: 6e94 was solved by N.O.Hudson, F.G.Whitby, B.A.Buck-Koehntop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.40 / 1.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.804, 77.270, 103.756, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.8

The binding sites of Zinc atom in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna (pdb code 6e94). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna, PDB code: 6e94:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:18.0 occ:1.00 NE2 A:HIS1060 1.9 19.8 1.0 NE2 A:HIS1056 2.1 16.8 1.0 SG A:CYS1040 2.3 16.3 1.0 SG A:CYS1043 2.3 17.1 1.0 CD2 A:HIS1060 2.9 17.8 1.0 CE1 A:HIS1060 3.0 21.4 1.0 CE1 A:HIS1056 3.0 20.6 1.0 CD2 A:HIS1056 3.1 19.0 1.0 CB A:CYS1040 3.1 18.8 1.0 CB A:CYS1043 3.3 15.5 1.0 N A:CYS1043 3.7 14.9 1.0 CG A:HIS1060 4.0 21.9 1.0 CA A:CYS1043 4.1 15.1 1.0 ND1 A:HIS1060 4.1 23.4 1.0 ND1 A:HIS1056 4.2 17.3 1.0 CG A:HIS1056 4.2 15.0 1.0 O A:HOH1399 4.2 26.8 1.0 CB A:THR1042 4.5 17.6 1.0 CA A:CYS1040 4.6 16.9 1.0 C A:CYS1043 4.7 15.8 1.0 C A:THR1042 4.8 15.6 1.0 N A:GLY1044 4.8 16.9 1.0 CB A:ARG1045 4.8 14.5 1.0 N A:ARG1045 4.9 15.9 1.0 N A:THR1042 5.0 15.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:17.9 occ:1.00 NE2 A:HIS1112 2.1 16.1 1.0 NE2 A:HIS1116 2.1 19.6 1.0 SG A:CYS1099 2.3 17.0 1.0 SG A:CYS1096 2.3 16.5 1.0 CD2 A:HIS1116 2.9 21.1 1.0 CD2 A:HIS1112 3.0 17.0 1.0 CE1 A:HIS1112 3.1 20.8 1.0 CE1 A:HIS1116 3.2 20.6 1.0 CB A:CYS1096 3.2 19.1 1.0 CB A:CYS1099 3.3 17.0 1.0 N A:CYS1099 3.8 16.7 1.0 CA A:CYS1099 4.1 18.3 1.0 CG A:HIS1116 4.1 19.2 1.0 CG A:HIS1112 4.1 19.2 1.0 ND1 A:HIS1112 4.1 18.4 1.0 ND1 A:HIS1116 4.2 20.9 1.0 C A:PHE1098 4.3 21.9 1.0 CB A:PHE1098 4.4 19.1 1.0 CB A:GLN1101 4.5 13.7 1.0 C A:CYS1099 4.6 17.0 1.0 CA A:CYS1096 4.6 13.2 1.0 N A:PHE1098 4.7 14.9 1.0 CA A:PHE1098 4.7 16.3 1.0 O A:CYS1099 4.8 19.8 1.0 CG A:GLN1101 4.8 15.4 1.0 N A:GLN1101 5.0 14.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:27.5 occ:1.00 NE2 A:HIS1084 2.1 22.9 1.0 NE2 A:HIS1088 2.1 27.1 1.0 SG A:CYS1071 2.2 28.3 1.0 SG A:CYS1068 2.3 24.7 1.0 CD2 A:HIS1088 2.9 29.7 1.0 CD2 A:HIS1084 3.0 19.0 1.0 CE1 A:HIS1084 3.2 23.1 1.0 CB A:CYS1068 3.2 24.3 1.0 CE1 A:HIS1088 3.2 31.3 1.0 CB A:CYS1071 3.3 29.4 1.0 N A:CYS1071 3.6 29.2 1.0 CA A:CYS1071 4.0 24.7 1.0 CG A:HIS1088 4.1 29.4 1.0 CG A:HIS1084 4.2 20.1 1.0 ND1 A:HIS1088 4.2 28.8 1.0 ND1 A:HIS1084 4.2 20.9 1.0 C A:CYS1071 4.6 29.3 1.0 CB A:TYR1070 4.6 25.9 1.0 C A:TYR1070 4.6 30.8 1.0 CA A:CYS1068 4.6 21.3 1.0 N A:ASN1072 4.7 26.1 1.0 CB A:LYS1073 4.9 31.0 1.0 N A:LYS1073 4.9 30.2 1.0 N A:TYR1070 4.9 29.1 1.0 CA A:TYR1070 4.9 28.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 K1055R in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:32.5 occ:1.00 NE2 A:HIS1028 2.0 28.6 1.0 NE2 A:HIS1032 2.1 31.0 1.0 SG A:CYS1015 2.3 33.7 1.0 SG A:CYS1012 2.3 36.2 1.0 CD2 A:HIS1028 2.9 27.7 1.0 CD2 A:HIS1032 3.0 34.5 1.0 CE1 A:HIS1028 3.1 29.6 1.0 CE1 A:HIS1032 3.2 30.6 1.0 CB A:CYS1015 3.3 34.5 1.0 CB A:CYS1012 3.3 31.4 1.0 N A:CYS1015 3.7 35.1 1.0 CA A:CYS1015 4.0 33.9 1.0 CG A:HIS1028 4.1 26.2 1.0 ND1 A:HIS1028 4.2 26.5 1.0 CG A:HIS1032 4.2 29.2 1.0 ND1 A:HIS1032 4.3 33.5 1.0 C A:LEU1014 4.4 42.8 1.0 CB A:LEU1014 4.5 35.2 1.0 CA A:CYS1012 4.7 34.9 1.0 C A:CYS1015 4.7 41.3 1.0 N A:LEU1014 4.8 41.8 1.0 CA A:LEU1014 4.8 39.4 1.0 SD A:MET1029 5.0 40.1 1.0 CB A:LYS1017 5.0 41.3 1.0 N A:ALA1016 5.0 47.2 1.0

N.O.Hudson, F.G.Whitby, B.A.Buck-Koehntop. Structural Insights Into Methylated Dna Recognition By the C-Terminal Zinc Fingers of the Dna Reader Protein ZBTB38. J. Biol. Chem. V. 293 19835 2018.
ISSN: ESSN 1083-351X
PubMed: 30355731
DOI: 10.1074/JBC.RA118.005147