Zinc in PDB 7dbf: The Structure of the Arabidopsis Thaliana Guanosine Deaminase

All present enzymatic activity of The Structure of the Arabidopsis Thaliana Guanosine Deaminase:
3.5.4.15;

The structure of The Structure of the Arabidopsis Thaliana Guanosine Deaminase, PDB code: 7dbf was solved by W.Xie, Q.Jia, H.Zeng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 1.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	119.117, 119.117, 39.453, 90, 90, 120
R / Rfree (%)	16.6 / 19

The binding sites of Zinc atom in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase (pdb code 7dbf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase, PDB code: 7dbf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Arabidopsis Thaliana Guanosine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:27.8 occ:1.00 O A:HOH314 2.1 28.2 1.0 ND1 A:HIS80 2.1 27.4 1.0 SG A:CYS110 2.3 27.6 1.0 SG A:CYS113 2.3 27.2 1.0 CE1 A:HIS80 3.0 31.5 1.0 CG A:HIS80 3.1 29.7 1.0 CB A:CYS113 3.2 26.7 1.0 CB A:CYS110 3.4 24.7 1.0 CB A:HIS80 3.5 25.6 1.0 N A:CYS110 3.8 27.0 1.0 N A:CYS113 3.9 27.8 1.0 OE1 A:GLU82 4.0 35.5 1.0 CE A:MET112 4.0 23.1 1.0 NE2 A:HIS80 4.1 28.9 1.0 CA A:CYS113 4.1 25.7 1.0 CA A:CYS110 4.2 26.0 1.0 CD2 A:HIS80 4.2 26.7 1.0 OE2 A:GLU82 4.4 29.0 1.0 CD A:GLU82 4.5 31.3 1.0 O A:HOH309 4.6 39.3 1.0 O A:HOH358 4.6 32.3 1.0 C A:CYS110 4.7 27.0 1.0 O A:CYS110 4.8 25.5 1.0 CB A:MET112 4.8 26.7 1.0 O A:HOH360 4.8 37.5 1.0 C A:PRO109 4.9 31.1 1.0 C A:MET112 5.0 26.2 1.0

Zinc binding site 2 out of 2 in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Arabidopsis Thaliana Guanosine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:27.3 occ:1.00 O D:HOH324 2.0 25.4 1.0 ND1 D:HIS80 2.1 28.5 1.0 SG D:CYS113 2.3 26.6 1.0 SG D:CYS110 2.3 26.1 1.0 CE1 D:HIS80 3.0 27.6 1.0 CB D:CYS113 3.0 26.3 1.0 CG D:HIS80 3.1 27.3 1.0 CB D:CYS110 3.4 27.1 1.0 CB D:HIS80 3.5 25.3 1.0 N D:CYS110 3.8 23.4 1.0 N D:CYS113 3.8 25.9 1.0 OE1 D:GLU82 4.0 33.4 1.0 CA D:CYS113 4.0 27.4 1.0 CA D:CYS110 4.1 21.8 1.0 NE2 D:HIS80 4.1 26.8 1.0 CE D:MET112 4.2 25.1 1.0 CD2 D:HIS80 4.2 23.9 1.0 OE2 D:GLU82 4.3 28.0 1.0 CD D:GLU82 4.4 30.7 1.0 C D:CYS110 4.6 26.6 1.0 O D:CYS110 4.7 25.1 1.0 O D:HOH362 4.7 38.5 1.0 O D:HOH358 4.7 32.5 1.0 C D:PRO109 4.9 28.4 1.0 C D:MET112 4.9 25.1 1.0 CB D:MET112 5.0 26.1 1.0

Q.Jia, H.Zeng, H.Li, N.Xiao, J.Tang, S.Gao, J.Zhang, W.Xie. The C-Terminal Loop of Arabidopsis Thaliana Guanosine Deaminase Is Essential to Catalysis. Chem.Commun.(Camb.) 2021.
ISSN: ESSN 1364-548X
PubMed: 34477187
DOI: 10.1039/D1CC03042F