Zinc in PDB 6oh9: Yeast Guanine Deaminase

Enzymatic activity of Yeast Guanine Deaminase

All present enzymatic activity of Yeast Guanine Deaminase:
3.5.4.3;

Protein crystallography data

The structure of Yeast Guanine Deaminase, PDB code: 6oh9 was solved by R.S.Shek, J.B.French, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 1.75
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 107.229, 107.229, 114.831, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Guanine Deaminase (pdb code 6oh9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Yeast Guanine Deaminase, PDB code: 6oh9:

Zinc binding site 1 out of 1 in 6oh9

Go back to Zinc Binding Sites List in 6oh9
Zinc binding site 1 out of 1 in the Yeast Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Guanine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.9
occ:1.00
NE2 A:HIS102 2.1 17.6 1.0
NE2 A:HIS100 2.1 17.6 1.0
NE2 A:HIS258 2.1 28.9 1.0
OD1 A:ASP348 2.2 15.7 1.0
O A:HOH889 2.3 25.1 1.0
HE1 A:HIS258 2.7 50.8 1.0
CE1 A:HIS258 2.7 42.3 1.0
CD2 A:HIS102 2.9 17.9 1.0
CE1 A:HIS100 3.0 25.9 1.0
HD2 A:HIS102 3.0 21.4 1.0
CD2 A:HIS100 3.1 19.7 1.0
CG A:ASP348 3.1 15.6 1.0
HE1 A:HIS100 3.1 31.1 1.0
CE1 A:HIS102 3.2 18.7 1.0
HE2 A:HIS297 3.2 18.8 1.0
CD2 A:HIS258 3.3 34.7 1.0
HD2 A:HIS100 3.3 23.6 1.0
HE1 A:HIS102 3.5 22.4 1.0
OD2 A:ASP348 3.5 18.4 1.0
HD2 A:HIS258 3.7 41.6 1.0
O A:HOH690 3.9 15.8 1.0
NE2 A:HIS297 4.0 15.6 1.0
ND1 A:HIS258 4.0 35.5 1.0
O A:HOH940 4.1 20.5 1.0
CG A:HIS102 4.1 13.0 1.0
ND1 A:HIS100 4.1 23.4 1.0
ND1 A:HIS102 4.2 14.1 1.0
CG A:HIS100 4.2 14.6 1.0
O A:HOH623 4.2 30.5 1.0
HA A:ASP348 4.2 17.4 1.0
CG A:HIS258 4.3 24.0 1.0
O A:HOH908 4.3 29.3 1.0
CB A:ASP348 4.4 13.3 1.0
HB2 A:ASP348 4.6 15.9 1.0
HD1 A:HIS258 4.7 42.6 1.0
HB1 A:ALA296 4.7 18.2 1.0
CE1 A:HIS297 4.8 17.8 1.0
HE1 A:HIS297 4.8 21.4 1.0
CA A:ASP348 4.8 14.5 1.0
CD2 A:HIS297 4.9 15.0 1.0
HD2 A:HIS297 4.9 18.0 1.0
HD1 A:HIS100 4.9 28.1 1.0
HB3 A:ALA296 4.9 18.2 1.0
HG A:CYS319 4.9 17.9 1.0

Reference:

R.Shek, T.Hilaire, J.Sim, J.B.French. Structural Determinants For Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Biochemistry V. 58 3280 2019.
ISSN: ISSN 0006-2960
PubMed: 31283204
DOI: 10.1021/ACS.BIOCHEM.9B00341
Page generated: Wed Dec 16 12:26:30 2020

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