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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7dgc:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the The Structure of the Arabidopsis Thaliana Guanosine Deaminase in Reaction with 2'-O-Methylguanosine, PDB code: 7dgc:

Sodium binding site 1 out of 1 in 7dgc

Go back to Sodium Binding Sites List in 7dgc
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na203

b:52.8
occ:1.00
 O A:SER66 2.4 30.9 1.0
O A:HOH346 2.5 38.2 1.0
O A:HOH356 2.7 43.5 1.0
O A:HOH359 3.3 44.4 1.0
C A:SER66 3.6 32.1 1.0
O A:HOH304 3.8 44.9 1.0
OE2 A:GLU40 4.1 31.2 1.0
O A:HOH355 4.4 49.9 1.0
CB A:SER66 4.4 28.6 1.0
CA A:SER66 4.4 32.3 1.0
N A:SER66 4.6 32.8 1.0
N A:CYS67 4.6 29.4 1.0
OE2 A:GLU88 4.6 34.4 1.0
CA A:CYS67 4.7 30.4 1.0
CD A:GLU40 4.8 33.4 1.0
OE1 A:GLU40 4.9 33.9 1.0
SG A:CYS67 4.9 32.9 1.0
O A:HOH315 5.0 42.7 1.0

Reference:

W.Xie, Q.Jia, H.Zeng. Asymmetric Catalysis of Arabidopsis Thaliana Guanosine Deaminase Revealed By Crystal Structures To Be Published.
Page generated: Tue Oct 8 16:34:53 2024

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