Zinc in PDB 8is4: Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu

The structure of Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu, PDB code: 8is4 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)	34.67 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.388, 107.986, 120.571, 90, 90, 90
R / Rfree (%)	15.5 / 18.9

The structure of Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu (pdb code 8is4). 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 in Complexed with 5-Fu, PDB code: 8is4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu


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 in Complexed with 5-Fu within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:19.4 occ:1.00 O A:HOH688 2.0 19.1 1.0 NE2 A:HIS68 2.2 18.2 1.0 NE2 A:HIS70 2.2 20.4 1.0 NE2 A:HIS234 2.2 18.5 1.0 OD1 A:ASP322 2.5 17.5 1.0 CD2 A:HIS70 3.1 15.5 1.0 CD2 A:HIS234 3.1 21.5 1.0 CE1 A:HIS68 3.1 17.1 1.0 CD2 A:HIS68 3.1 17.4 1.0 CE1 A:HIS70 3.2 18.2 1.0 CE1 A:HIS234 3.3 23.1 1.0 CG A:ASP322 3.4 19.2 1.0 OD2 A:ASP322 3.6 21.2 1.0 NE2 A:HIS271 3.9 18.8 1.0 N3 A:URF501 3.9 33.5 0.6 O4 A:URF501 4.2 28.6 0.6 C4 A:URF501 4.2 34.5 0.6 CG A:HIS70 4.2 15.7 1.0 ND1 A:HIS70 4.2 18.4 1.0 ND1 A:HIS68 4.2 17.2 1.0 CG A:HIS68 4.3 14.5 1.0 CG A:HIS234 4.3 22.5 1.0 ND1 A:HIS234 4.3 22.7 1.0 O A:HOH667 4.4 23.0 1.0 C2 A:URF501 4.5 32.9 0.6 CE1 A:HIS271 4.7 21.0 1.0 CB A:ASP322 4.7 16.5 1.0 O2 A:URF501 4.8 34.0 0.6 CD2 A:HIS271 4.8 20.4 1.0 N A:GLY323 4.8 17.3 1.0

Zinc binding site 2 out of 2 in the Structure of An Isocytosine Specific Deaminase Vcz in Complexed with 5-Fu


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 in Complexed with 5-Fu within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:22.3 occ:1.00 O B:HOH619 2.1 23.3 1.0 NE2 B:HIS70 2.2 21.9 1.0 NE2 B:HIS68 2.2 19.5 1.0 NE2 B:HIS234 2.2 21.9 1.0 OD1 B:ASP322 2.4 19.1 1.0 CD2 B:HIS70 3.0 19.3 1.0 CE1 B:HIS68 3.1 19.7 1.0 CD2 B:HIS234 3.1 21.8 1.0 CE1 B:HIS70 3.2 22.9 1.0 CD2 B:HIS68 3.2 17.1 1.0 CE1 B:HIS234 3.2 27.0 1.0 CG B:ASP322 3.3 20.6 1.0 OD2 B:ASP322 3.6 21.3 1.0 N3 B:URF502 3.9 35.1 0.6 NE2 B:HIS271 3.9 19.8 1.0 C4 B:URF502 4.1 35.8 0.6 CG B:HIS70 4.2 21.1 1.0 ND1 B:HIS68 4.2 20.2 1.0 ND1 B:HIS70 4.2 21.0 1.0 CG B:HIS234 4.3 23.1 1.0 CG B:HIS68 4.3 18.9 1.0 ND1 B:HIS234 4.3 26.2 1.0 O4 B:URF502 4.3 30.3 0.6 C2 B:URF502 4.4 37.9 0.6 O B:HOH726 4.5 28.7 1.0 CB B:ASP322 4.6 19.9 1.0 O2 B:URF502 4.7 36.5 0.6 C5 B:URF502 4.7 38.1 0.6 CD2 B:HIS271 4.8 21.9 1.0 N B:GLY323 4.8 20.2 1.0 CE1 B:HIS271 4.8 19.9 1.0 N1 B:URF502 4.9 36.3 0.6 CA B:ASP322 5.0 18.5 1.0 ND1 B:HIS128 5.0 21.2 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