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Zinc in PDB 7dpk: The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine

Enzymatic activity of The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine

All present enzymatic activity of The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine:
3.5.4.15;

Protein crystallography data

The structure of The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine, PDB code: 7dpk 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) 23.65 / 2.15
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 119.027, 119.027, 38.919, 90, 90, 120
R / Rfree (%) 17.2 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine (pdb code 7dpk). 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 Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine, PDB code: 7dpk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7dpk

Go back to Zinc Binding Sites List in 7dpk
Zinc binding site 1 out of 2 in the The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine


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 Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:12.1
occ:1.00
 ND1 A:HIS80 2.1 10.5 1.0
SG A:CYS110 2.3 12.2 1.0
SG A:CYS113 2.3 8.2 1.0
O2 A:4UO201 2.4 17.4 1.0
C2 A:4UO201 2.5 19.0 1.0
CE1 A:HIS80 3.0 10.7 1.0
N1 A:4UO201 3.1 16.9 1.0
CB A:CYS113 3.1 7.6 1.0
CG A:HIS80 3.1 10.9 1.0
N3 A:4UO201 3.2 18.9 1.0
CB A:CYS110 3.4 9.1 1.0
CB A:HIS80 3.5 10.6 1.0
N A:CYS110 3.8 10.6 1.0
N A:CYS113 3.9 12.0 1.0
C6 A:4UO201 4.0 14.5 1.0
CA A:CYS113 4.1 8.4 1.0
CE A:MET112 4.1 8.4 1.0
NE2 A:HIS80 4.1 9.5 1.0
CA A:CYS110 4.1 13.8 1.0
C4 A:4UO201 4.2 16.8 1.0
CD2 A:HIS80 4.2 10.1 1.0
OE1 A:GLU82 4.3 13.6 1.0
C5 A:4UO201 4.5 13.7 1.0
C A:CYS110 4.7 13.2 1.0
CD A:GLU82 4.7 15.8 1.0
O A:CYS110 4.8 10.0 1.0
O6 A:4UO201 4.8 14.9 1.0
O A:HOH301 4.9 13.5 1.0
CB A:MET112 4.9 10.0 1.0
C A:PRO109 4.9 13.2 1.0
OE2 A:GLU82 5.0 20.3 1.0
C A:MET112 5.0 11.3 1.0

Zinc binding site 2 out of 2 in 7dpk

Go back to Zinc Binding Sites List in 7dpk
Zinc binding site 2 out of 2 in the The Structure of the Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine


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 Exchange Reaction of the Arabidopsis Thaliana Guanosine Deaminase in Complex with 7-Deazaguaosine By Guanosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:13.6
occ:1.00
 ND1 D:HIS80 2.0 13.6 1.0
O D:HOH341 2.2 14.1 1.0
SG D:CYS110 2.3 11.4 1.0
SG D:CYS113 2.3 11.1 1.0
CE1 D:HIS80 3.0 14.7 1.0
CG D:HIS80 3.1 12.8 1.0
CB D:CYS113 3.1 7.7 1.0
CB D:CYS110 3.2 12.8 1.0
CB D:HIS80 3.5 9.0 1.0
O D:HOH386 3.6 21.9 1.0
N D:CYS110 3.7 11.4 1.0
O D:HOH377 3.9 35.8 1.0
N D:CYS113 3.9 12.0 1.0
CA D:CYS110 4.0 12.8 1.0
NE2 D:HIS80 4.1 13.5 1.0
CE D:MET112 4.1 9.2 1.0
CA D:CYS113 4.1 8.2 1.0
OE2 D:GLU82 4.1 21.9 1.0
CD2 D:HIS80 4.2 10.5 1.0
OE1 D:GLU82 4.5 10.8 1.0
O D:HOH359 4.5 30.1 1.0
CD D:GLU82 4.5 15.1 1.0
C D:CYS110 4.7 11.5 1.0
O D:HOH370 4.7 19.0 1.0
O D:HOH380 4.8 21.0 1.0
O D:CYS110 4.9 12.3 1.0
C D:PRO109 4.9 13.9 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 29 19:12:24 2024

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