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Zinc in PDB 1jtk: Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine

Enzymatic activity of Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine

All present enzymatic activity of Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine:
3.5.4.5;

Protein crystallography data

The structure of Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine, PDB code: 1jtk was solved by E.Johansson, N.Mejlhede, J.Neuhard, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 2.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.086, 66.142, 55.476, 90.00, 115.92, 90.00
R / Rfree (%) 20.7 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine (pdb code 1jtk). 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 Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine, PDB code: 1jtk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1jtk

Go back to Zinc Binding Sites List in 1jtk
Zinc binding site 1 out of 2 in the Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine


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 Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn137

b:9.2
occ:1.00
O4 A:THU138 2.2 6.7 1.0
SG A:CYS86 2.3 4.7 1.0
SG A:CYS89 2.3 6.0 1.0
SG A:CYS53 2.4 5.4 1.0
CB A:CYS53 3.0 6.1 1.0
C4 A:THU138 3.2 6.8 1.0
CB A:CYS89 3.3 6.7 1.0
CB A:CYS86 3.4 5.5 1.0
N3 A:THU138 3.5 7.8 1.0
N A:CYS86 3.8 6.0 1.0
C5 A:THU138 3.8 6.8 1.0
C6 A:THU138 3.8 6.9 1.0
OE2 A:GLU55 3.9 5.9 1.0
C2 A:THU138 4.0 7.5 1.0
N A:CYS89 4.1 6.3 1.0
CA A:CYS86 4.1 6.2 1.0
NH2 A:ARG56 4.2 8.0 1.0
CA A:CYS89 4.3 6.8 1.0
OE1 A:GLU55 4.3 7.7 1.0
CD A:GLU55 4.3 7.2 1.0
N1 A:THU138 4.4 7.9 1.0
NE A:ARG56 4.4 7.0 1.0
O A:CYS86 4.5 6.4 1.0
CA A:CYS53 4.5 6.4 1.0
C A:CYS86 4.6 6.3 1.0
CZ A:ARG56 4.7 7.2 1.0
O2 A:THU138 4.8 6.7 1.0
C A:PRO85 4.9 6.3 1.0

Zinc binding site 2 out of 2 in 1jtk

Go back to Zinc Binding Sites List in 1jtk
Zinc binding site 2 out of 2 in the Crystal Structure of Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine


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 Cytidine Deaminase From Bacillus Subtilis in Complex with the Inhibitor Tetrahydrodeoxyuridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn137

b:10.4
occ:1.00
O4 B:THU1138 2.2 7.1 1.0
SG B:CYS86 2.3 5.6 1.0
SG B:CYS53 2.3 5.7 1.0
SG B:CYS89 2.4 7.3 1.0
CB B:CYS53 3.0 6.2 1.0
C4 B:THU1138 3.3 7.0 1.0
CB B:CYS89 3.3 7.1 1.0
CB B:CYS86 3.4 5.8 1.0
N3 B:THU1138 3.5 8.0 1.0
N B:CYS86 3.8 5.8 1.0
C5 B:THU1138 3.9 7.2 1.0
C6 B:THU1138 3.9 7.0 1.0
OE2 B:GLU55 3.9 7.1 1.0
N B:CYS89 4.1 6.6 1.0
C2 B:THU1138 4.1 7.7 1.0
CA B:CYS86 4.1 5.9 1.0
NH2 B:ARG56 4.2 7.6 1.0
CA B:CYS89 4.3 6.8 1.0
OE1 B:GLU55 4.3 7.8 1.0
CD B:GLU55 4.3 7.5 1.0
N1 B:THU1138 4.4 8.1 1.0
NE B:ARG56 4.4 6.9 1.0
O B:CYS86 4.5 6.1 1.0
CA B:CYS53 4.5 6.3 1.0
C B:CYS86 4.6 6.1 1.0
CZ B:ARG56 4.7 7.2 1.0
O2 B:THU1138 4.8 7.1 1.0
C B:PRO85 4.9 6.3 1.0

Reference:

E.Johansson, N.Mejlhede, J.Neuhard, S.Larsen. Crystal Structure of the Tetrameric Cytidine Deaminase From Bacillus Subtilis at 2.0 A Resolution. Biochemistry V. 41 2563 2002.
ISSN: ISSN 0006-2960
PubMed: 11851403
DOI: 10.1021/BI011849A
Page generated: Wed Dec 16 02:54:07 2020

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