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Zinc in PDB 1wkq: Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily

Enzymatic activity of Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily

All present enzymatic activity of Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily:
3.5.4.3;

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily, PDB code: 1wkq was solved by S.H.Liaw, Y.J.Chang, C.T.Lai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.17
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.566, 91.267, 80.481, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily (pdb code 1wkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily, PDB code: 1wkq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1wkq

Go back to Zinc Binding Sites List in 1wkq
Zinc binding site 1 out of 2 in the Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:6.7
occ:1.00
 O A:HOH1302 2.0 8.5 1.0
ND1 A:HIS53 2.1 5.5 1.0
SG A:CYS86 2.3 6.7 1.0
SG A:CYS83 2.3 6.4 1.0
CE1 A:HIS53 3.0 6.0 1.0
CG A:HIS53 3.1 5.1 1.0
CB A:CYS86 3.2 6.1 1.0
CB A:CYS83 3.4 7.0 1.0
CB A:HIS53 3.5 5.5 1.0
N A:CYS83 3.9 6.4 1.0
OE2 A:GLU55 3.9 10.6 1.0
N A:CYS86 3.9 5.9 1.0
C4 A:IMD1301 4.1 12.3 1.0
NE2 A:HIS53 4.1 6.2 1.0
CE A:MET85 4.2 6.8 1.0
CA A:CYS86 4.2 6.5 1.0
OE1 A:GLU55 4.2 9.7 1.0
CD2 A:HIS53 4.2 6.3 1.0
CA A:CYS83 4.2 6.8 1.0
C5 A:IMD1301 4.2 12.5 1.0
CD A:GLU55 4.3 7.5 1.0
O A:HOH1304 4.6 24.9 1.0
O A:HOH1303 4.7 8.2 1.0
C A:CYS83 4.7 7.3 1.0
NE1 B:TRP92 4.7 6.6 1.0
CB A:MET85 4.8 5.5 1.0
O A:CYS83 4.8 6.6 1.0
N3 A:IMD1301 4.9 14.3 1.0
C A:PRO82 5.0 6.9 1.0
C A:MET85 5.0 6.6 1.0
CA A:HIS53 5.0 5.6 1.0

Zinc binding site 2 out of 2 in 1wkq

Go back to Zinc Binding Sites List in 1wkq
Zinc binding site 2 out of 2 in the Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bacillus Subtilis Guanine Deaminase. the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:6.9
occ:1.00
 ND1 B:HIS53 2.1 7.0 1.0
O B:HOH1303 2.1 9.0 1.0
SG B:CYS86 2.3 6.7 1.0
SG B:CYS83 2.3 6.9 1.0
CE1 B:HIS53 3.0 6.9 1.0
CG B:HIS53 3.1 6.4 1.0
CB B:CYS86 3.2 6.4 1.0
CB B:CYS83 3.5 7.7 1.0
CB B:HIS53 3.5 6.7 1.0
N B:CYS83 3.9 6.8 1.0
N B:CYS86 3.9 5.7 1.0
OE2 B:GLU55 3.9 11.7 1.0
C4 B:IMD1302 4.0 13.1 1.0
NE2 B:HIS53 4.1 6.8 1.0
CE B:MET85 4.2 7.6 1.0
C5 B:IMD1302 4.2 12.2 1.0
CA B:CYS86 4.2 5.8 1.0
OE1 B:GLU55 4.2 9.9 1.0
CD2 B:HIS53 4.2 7.5 1.0
CA B:CYS83 4.2 7.0 1.0
CD B:GLU55 4.3 10.8 1.0
O B:HOH1305 4.6 22.5 1.0
O B:HOH1304 4.7 9.0 1.0
NE1 A:TRP92 4.7 8.3 1.0
CB B:MET85 4.7 6.3 1.0
C B:CYS83 4.7 7.2 1.0
O B:CYS83 4.8 6.7 1.0
N3 B:IMD1302 4.9 15.5 1.0
C B:MET85 5.0 5.7 1.0
CA B:HIS53 5.0 6.9 1.0

Reference:

S.H.Liaw, Y.J.Chang, C.T.Lai, H.C.Chang, G.G.Chang. Crystal Structure of Bacillus Subtilis Guanine Deaminase: the First Domain-Swapped Structure in the Cytidine Deaminase Superfamily J.Biol.Chem. V. 279 35479 2004.
ISSN: ISSN 0021-9258
PubMed: 15180998
DOI: 10.1074/JBC.M405304200
Page generated: Wed Oct 16 20:06:48 2024

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