Zinc in PDB 8is5: Structure of An Isocytosine Specific Deaminase Vcz with Close State

The structure of Structure of An Isocytosine Specific Deaminase Vcz with Close State, PDB code: 8is5 was solved by W.T.Guo, X.J.Li, B.X.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.592, 107.63, 120.91, 90, 90, 90
R / Rfree (%)	16 / 19.6

The binding sites of Zinc atom in the Structure of An Isocytosine Specific Deaminase Vcz with Close State (pdb code 8is5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of An Isocytosine Specific Deaminase Vcz with Close State, PDB code: 8is5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of An Isocytosine Specific Deaminase Vcz with Close State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An Isocytosine Specific Deaminase Vcz with Close State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.9 occ:1.00 O A:HOH635 2.0 27.3 1.0 NE2 A:HIS70 2.2 26.0 1.0 NE2 A:HIS234 2.2 27.1 1.0 NE2 A:HIS68 2.2 24.4 1.0 OD1 A:ASP322 2.4 24.3 1.0 CD2 A:HIS70 3.0 24.6 1.0 CD2 A:HIS234 3.1 29.2 1.0 CE1 A:HIS68 3.2 25.1 1.0 CD2 A:HIS68 3.2 24.6 1.0 CE1 A:HIS70 3.2 28.0 1.0 CE1 A:HIS234 3.3 30.4 1.0 CG A:ASP322 3.4 25.8 1.0 OD2 A:ASP322 3.6 30.0 1.0 NE2 A:HIS271 3.9 30.1 1.0 CG A:HIS70 4.2 27.6 1.0 O A:HOH780 4.2 34.0 1.0 ND1 A:HIS70 4.3 26.1 1.0 ND1 A:HIS68 4.3 25.4 1.0 O A:HOH645 4.3 28.1 1.0 CG A:HIS234 4.3 33.2 1.0 CG A:HIS68 4.3 24.1 1.0 ND1 A:HIS234 4.4 32.1 1.0 CE1 A:HIS271 4.6 30.1 1.0 CB A:ASP322 4.7 21.8 1.0 CD2 A:HIS271 4.8 30.7 1.0 N A:GLY323 4.8 24.9 1.0

Zinc binding site 2 out of 2 in the Structure of An Isocytosine Specific Deaminase Vcz with Close State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An Isocytosine Specific Deaminase Vcz with Close State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:32.2 occ:1.00 O B:HOH621 2.0 30.4 1.0 NE2 B:HIS68 2.2 29.7 1.0 NE2 B:HIS70 2.2 29.7 1.0 NE2 B:HIS234 2.3 30.3 1.0 OD1 B:ASP322 2.4 31.9 1.0 CD2 B:HIS70 3.0 29.7 1.0 CE1 B:HIS68 3.1 29.9 1.0 CD2 B:HIS234 3.2 32.1 1.0 CD2 B:HIS68 3.2 29.0 1.0 CE1 B:HIS234 3.2 33.5 1.0 CE1 B:HIS70 3.3 33.9 1.0 CG B:ASP322 3.3 31.9 1.0 OD2 B:ASP322 3.6 29.9 1.0 NE2 B:HIS271 4.1 30.3 1.0 O B:HOH735 4.1 38.2 1.0 CG B:HIS70 4.2 32.6 1.0 O B:HOH611 4.2 38.4 1.0 ND1 B:HIS68 4.2 29.0 1.0 ND1 B:HIS70 4.3 30.4 1.0 CG B:HIS68 4.3 27.0 1.0 ND1 B:HIS234 4.3 36.4 1.0 CG B:HIS234 4.4 33.4 1.0 CB B:ASP322 4.7 29.0 1.0 N B:GLY323 4.8 28.3 1.0 CD2 B:HIS271 4.9 29.7 1.0 CE1 B:HIS271 4.9 30.8 1.0 CA B:ASP322 5.0 26.9 1.0

W.Guo, X.Li, J.Fan, H.Li, Y.Wen, C.Meng, H.Chen, Z.Zhao, Y.Zhang, Y.Du, B.Wu. Structural Characterization of An Isocytosine-Specific Deaminase Vcz Reveals Its Application Potential in the Anti-Cancer Therapy Iscience 2023.
ISSN: ESSN 2589-0042
DOI: 10.1016/J.ISCI.2023.107672