Zinc in PDB 7dgc: The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine

All present enzymatic activity of The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine:
3.5.4.15;

The structure of The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine, PDB code: 7dgc 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)	31.51 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	119.052, 119.052, 39.809, 90, 90, 120
R / Rfree (%)	18.3 / 21.9

The structure of The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine (pdb code 7dgc). 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 in Reaction with 2'-O-Methylguanosine, PDB code: 7dgc:
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 in Reaction with 2'-O-Methylguanosine


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 in Reaction with 2'-O-Methylguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:28.1 occ:1.00 ND1 A:HIS80 2.1 27.8 1.0 SG A:CYS113 2.3 27.6 1.0 O21 A:H5C201 2.3 33.6 1.0 SG A:CYS110 2.3 29.1 1.0 C19 A:H5C201 2.5 42.6 1.0 N18 A:H5C201 2.9 39.2 1.0 CE1 A:HIS80 2.9 31.1 1.0 CB A:CYS113 3.1 27.7 1.0 CG A:HIS80 3.1 29.1 1.0 N20 A:H5C201 3.3 37.0 1.0 CB A:CYS110 3.3 28.9 1.0 CB A:HIS80 3.6 27.7 1.0 N A:CYS110 3.7 30.6 1.0 N A:CYS113 3.9 25.4 1.0 C17 A:H5C201 3.9 39.8 1.0 CE A:MET112 4.0 26.3 1.0 CA A:CYS113 4.0 26.9 1.0 CA A:CYS110 4.1 32.1 1.0 NE2 A:HIS80 4.1 25.2 1.0 C02 A:H5C201 4.2 32.1 1.0 CD2 A:HIS80 4.2 31.1 1.0 C03 A:H5C201 4.4 34.5 1.0 OE1 A:GLU82 4.5 28.9 1.0 C A:CYS110 4.6 29.2 1.0 O A:CYS110 4.7 28.7 1.0 CD A:GLU82 4.9 31.0 1.0 C A:PRO109 4.9 31.7 1.0 C A:MET112 4.9 30.4 1.0 N06 A:H5C201 4.9 41.2 1.0 CB A:MET112 5.0 27.8 1.0

Zinc binding site 2 out of 2 in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine


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 in Reaction with 2'-O-Methylguanosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:27.4 occ:1.00 ND1 D:HIS80 2.1 25.8 1.0 O21 D:H5C201 2.2 33.1 1.0 SG D:CYS110 2.3 26.2 1.0 SG D:CYS113 2.3 29.4 1.0 C19 D:H5C201 2.4 32.1 1.0 N18 D:H5C201 2.8 35.5 1.0 CE1 D:HIS80 2.9 27.5 1.0 CB D:CYS113 3.1 29.7 1.0 CG D:HIS80 3.2 30.0 1.0 N20 D:H5C201 3.2 35.2 1.0 CB D:CYS110 3.2 28.2 1.0 CB D:HIS80 3.6 26.5 1.0 N D:CYS110 3.7 32.4 1.0 C17 D:H5C201 3.8 38.2 1.0 N D:CYS113 3.9 26.2 1.0 CA D:CYS110 4.0 29.0 1.0 CA D:CYS113 4.1 28.5 1.0 NE2 D:HIS80 4.1 28.3 1.0 C02 D:H5C201 4.1 31.2 1.0 CE D:MET112 4.2 24.5 1.0 CD2 D:HIS80 4.2 27.9 1.0 C03 D:H5C201 4.4 32.8 1.0 OE1 D:GLU82 4.4 30.0 1.0 C D:CYS110 4.6 32.0 1.0 O D:CYS110 4.7 27.5 1.0 CD D:GLU82 4.8 34.9 1.0 C D:PRO109 4.8 29.6 1.0 O D:HOH305 4.8 40.1 1.0 N06 D:H5C201 4.8 38.0 1.0 OE2 D:GLU82 4.9 41.8 1.0 C D:MET112 5.0 29.1 1.0

W.Xie, Q.Jia, H.Zeng. Asymmetric Catalysis of Arabidopsis Thaliana Guanosine Deaminase Revealed By Crystal Structures To Be Published.