Zinc in PDB 6e93: Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 in Complex with Methylated Dna

The structure of Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 in Complex with Methylated Dna, PDB code: 6e93 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)	21.54 / 1.75
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 (%)	18.6 / 21.1

The binding sites of Zinc atom in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 in Complex with Methylated Dna (pdb code 6e93). 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 in Complex with Methylated Dna, PDB code: 6e93:
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 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 in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:32.5 occ:1.00 NE2 A:HIS1088 2.1 33.4 1.0 NE2 A:HIS1084 2.1 28.2 1.0 SG A:CYS1071 2.2 32.3 1.0 SG A:CYS1068 2.3 29.0 1.0 CD2 A:HIS1088 2.9 30.5 1.0 CD2 A:HIS1084 3.1 26.3 1.0 CE1 A:HIS1084 3.2 33.1 1.0 CE1 A:HIS1088 3.2 36.8 1.0 CB A:CYS1068 3.2 31.0 1.0 CB A:CYS1071 3.3 35.0 1.0 N A:CYS1071 3.6 37.4 1.0 CA A:CYS1071 3.9 37.7 1.0 CG A:HIS1088 4.1 35.0 1.0 ND1 A:HIS1088 4.2 31.7 1.0 CG A:HIS1084 4.2 27.7 1.0 ND1 A:HIS1084 4.3 26.8 1.0 CB A:TYR1070 4.5 29.8 1.0 C A:CYS1071 4.6 37.5 1.0 C A:TYR1070 4.6 36.5 1.0 CA A:CYS1068 4.7 29.7 1.0 N A:ASN1072 4.7 31.4 1.0 CA A:TYR1070 4.9 33.4 1.0 N A:TYR1070 4.9 35.8 1.0 N A:LYS1073 4.9 33.4 1.0 CB A:LYS1073 4.9 33.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 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 in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:24.6 occ:1.00 NE2 A:HIS1060 2.0 25.2 1.0 NE2 A:HIS1056 2.1 20.8 1.0 SG A:CYS1040 2.3 22.6 1.0 SG A:CYS1043 2.3 21.7 1.0 CD2 A:HIS1060 2.9 25.9 1.0 CD2 A:HIS1056 3.0 24.9 1.0 CE1 A:HIS1060 3.1 30.9 1.0 CE1 A:HIS1056 3.1 23.9 1.0 CB A:CYS1040 3.2 22.7 1.0 CB A:CYS1043 3.3 20.9 1.0 N A:CYS1043 3.7 25.7 1.0 CA A:CYS1043 4.0 23.8 1.0 CG A:HIS1060 4.1 30.9 1.0 ND1 A:HIS1060 4.1 32.6 1.0 CG A:HIS1056 4.2 22.7 1.0 ND1 A:HIS1056 4.2 21.2 1.0 O A:HOH1371 4.3 38.5 1.0 CB A:THR1042 4.5 27.0 1.0 CA A:CYS1040 4.6 22.0 1.0 C A:CYS1043 4.7 23.5 1.0 C A:THR1042 4.7 24.5 1.0 N A:GLY1044 4.8 22.2 1.0 CB A:ARG1045 4.9 23.0 1.0 N A:THR1042 4.9 23.1 1.0 N A:ARG1045 5.0 23.6 1.0 CA A:THR1042 5.0 24.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 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 in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:24.4 occ:1.00 NE2 A:HIS1112 2.1 20.4 1.0 NE2 A:HIS1116 2.1 22.4 1.0 SG A:CYS1099 2.2 23.4 1.0 SG A:CYS1096 2.3 22.3 1.0 CD2 A:HIS1116 2.9 24.8 1.0 CD2 A:HIS1112 3.0 20.4 1.0 CE1 A:HIS1112 3.1 25.3 1.0 CE1 A:HIS1116 3.2 26.1 1.0 CB A:CYS1096 3.2 21.2 1.0 CB A:CYS1099 3.2 22.3 1.0 N A:CYS1099 3.8 25.6 1.0 CA A:CYS1099 4.0 26.6 1.0 CG A:HIS1116 4.1 28.4 1.0 CG A:HIS1112 4.1 23.3 1.0 ND1 A:HIS1112 4.2 21.1 1.0 ND1 A:HIS1116 4.2 26.8 1.0 C A:PHE1098 4.3 25.5 1.0 CG A:GLN1101 4.4 33.1 1.0 CB A:GLN1101 4.4 22.3 1.0 CB A:PHE1098 4.5 26.6 1.0 C A:CYS1099 4.6 24.9 1.0 CA A:CYS1096 4.6 22.6 1.0 N A:PHE1098 4.7 21.7 1.0 CA A:PHE1098 4.7 22.4 1.0 O A:CYS1099 4.8 23.6 1.0 N A:GLN1101 5.0 22.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of ZBTB38 C-Terminal Zinc Fingers 6-9 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 in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:40.9 occ:1.00 NE2 A:HIS1028 2.1 38.0 1.0 NE2 A:HIS1032 2.2 40.9 1.0 SG A:CYS1015 2.3 44.0 1.0 SG A:CYS1012 2.3 41.3 1.0 CD2 A:HIS1032 2.9 41.2 1.0 CD2 A:HIS1028 2.9 34.8 1.0 CE1 A:HIS1028 3.2 36.5 1.0 CB A:CYS1012 3.2 44.6 1.0 CE1 A:HIS1032 3.3 44.7 1.0 CB A:CYS1015 3.3 47.2 1.0 N A:CYS1015 3.8 42.6 1.0 CA A:CYS1015 4.1 45.3 1.0 CG A:HIS1028 4.1 32.2 1.0 CG A:HIS1032 4.2 39.9 1.0 ND1 A:HIS1028 4.2 34.3 1.0 ND1 A:HIS1032 4.3 41.5 1.0 C A:LEU1014 4.4 49.7 1.0 CB A:LEU1014 4.4 43.1 1.0 CA A:CYS1012 4.7 49.4 1.0 CA A:LEU1014 4.7 46.3 1.0 N A:LEU1014 4.8 51.5 1.0 C A:CYS1015 4.8 44.9 1.0 SD A:MET1029 5.0 51.3 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