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Zinc in PDB 4lc5: Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase

Protein crystallography data

The structure of Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase, PDB code: 4lc5 was solved by A.Bitra, A.Biswas, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.09 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.150, 74.180, 109.780, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase (pdb code 4lc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase, PDB code: 4lc5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4lc5

Go back to Zinc Binding Sites List in 4lc5
Zinc binding site 1 out of 2 in the Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:23.8
occ:1.00
ND1 A:HIS77 2.1 15.5 1.0
O A:HOH310 2.1 24.7 1.0
SG A:CYS115 2.3 18.5 1.0
SG A:CYS112 2.3 20.9 1.0
CE1 A:HIS77 2.9 14.3 1.0
CB A:CYS115 3.1 13.6 1.0
CG A:HIS77 3.1 13.3 1.0
CB A:CYS112 3.4 17.0 1.0
CB A:HIS77 3.5 12.8 1.0
N A:CYS115 3.8 14.9 1.0
N A:CYS112 3.9 15.6 1.0
CA A:CYS115 4.0 13.7 1.0
OE2 A:GLU79 4.0 23.7 1.0
NE2 A:HIS77 4.1 15.7 1.0
CA A:CYS112 4.1 16.3 1.0
CE A:MET114 4.2 15.6 1.0
OE1 A:GLU79 4.2 14.3 1.0
CD2 A:HIS77 4.2 15.5 1.0
C12 A:9MG202 4.4 23.1 1.0
N11 A:9MG202 4.4 24.1 1.0
CD A:GLU79 4.4 19.5 1.0
C5 A:9MG202 4.4 21.6 1.0
C9 A:9MG202 4.4 25.8 1.0
C6 A:9MG202 4.4 21.2 1.0
N8 A:9MG202 4.4 21.5 1.0
C A:CYS112 4.6 15.7 1.0
CB A:MET114 4.6 15.5 1.0
O A:CYS112 4.7 13.1 1.0
C A:MET114 4.8 16.0 1.0
N2 A:9MG202 5.0 25.3 1.0

Zinc binding site 2 out of 2 in 4lc5

Go back to Zinc Binding Sites List in 4lc5
Zinc binding site 2 out of 2 in the Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Substrate Specificity of Cda Superfamily Guanine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:19.6
occ:1.00
ND1 B:HIS77 2.1 11.9 1.0
O B:HOH355 2.2 18.8 1.0
SG B:CYS115 2.3 16.8 1.0
SG B:CYS112 2.3 16.3 1.0
CE1 B:HIS77 3.0 12.2 1.0
CG B:HIS77 3.1 13.2 1.0
CB B:CYS115 3.2 15.0 1.0
CB B:CYS112 3.4 14.6 1.0
CB B:HIS77 3.5 12.4 1.0
N B:CYS115 3.8 14.8 1.0
N B:CYS112 3.8 15.2 1.0
OE2 B:GLU79 3.9 21.7 1.0
O2 B:EDO203 4.0 31.6 1.0
CE B:MET114 4.0 13.9 1.0
CA B:CYS115 4.1 15.4 1.0
OE1 B:GLU79 4.1 14.8 1.0
CA B:CYS112 4.1 14.3 1.0
NE2 B:HIS77 4.2 11.9 1.0
CD2 B:HIS77 4.2 12.9 1.0
CD B:GLU79 4.3 17.7 1.0
C B:CYS112 4.6 14.1 1.0
CB B:MET114 4.7 14.2 1.0
O B:CYS112 4.7 13.3 1.0
C B:MET114 4.8 15.3 1.0
O1 B:EDO203 4.9 37.5 1.0
C B:PRO111 4.9 16.6 1.0
C2 B:EDO203 5.0 35.1 1.0
CA B:HIS77 5.0 11.6 1.0

Reference:

A.Bitra, A.Biswas, R.Anand. Structural Basis of the Substrate Specificity of Cytidine Deaminase Superfamily Guanine Deaminase Biochemistry V. 52 8106 2013.
ISSN: ISSN 0006-2960
PubMed: 24083949
DOI: 10.1021/BI400818E
Page generated: Wed Dec 16 05:31:42 2020

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