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Zinc in PDB 1ox7: Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound

Enzymatic activity of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound

All present enzymatic activity of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound:
3.5.4.1;

Protein crystallography data

The structure of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound, PDB code: 1ox7 was solved by G.C.Ireton, M.E.Black, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.491, 70.467, 71.941, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 17.9

Other elements in 1ox7:

The structure of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound (pdb code 1ox7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound, PDB code: 1ox7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ox7

Go back to Zinc Binding Sites List in 1ox7
Zinc binding site 1 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound


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 Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:5.8
occ:1.00
 O A:HOH550 1.8 5.4 1.0
O A:HOH552 1.8 7.7 1.0
O A:HOH551 2.0 12.5 1.0
O A:HOH549 2.0 13.0 1.0
ZN A:ZN402 3.2 5.2 1.0
OE1 A:GLU64 3.6 6.8 1.0
OE2 A:GLU64 3.6 8.7 1.0
O A:HOH553 3.7 8.9 1.0
ND1 A:HIS62 3.7 4.8 1.0
CD A:GLU64 4.1 7.0 1.0
N A:CYS91 4.1 4.1 1.0
CE1 A:HIS62 4.3 6.3 1.0
CD1 A:ILE33 4.3 6.6 1.0
CG A:HIS62 4.4 5.0 1.0
CB A:CYS91 4.5 5.9 1.0
O A:SER89 4.5 5.2 1.0
CB A:HIS62 4.6 4.3 1.0
SG A:CYS94 4.6 4.8 1.0
CA A:PRO90 4.6 4.7 1.0
CG2 A:ILE33 4.7 6.0 1.0
SG A:CYS91 4.8 5.3 1.0
CE2 A:PHE114 4.8 6.3 1.0
C A:PRO90 4.9 3.7 1.0
CA A:CYS91 4.9 4.6 1.0
OD2 A:ASP155 5.0 9.8 1.0

Zinc binding site 2 out of 4 in 1ox7

Go back to Zinc Binding Sites List in 1ox7
Zinc binding site 2 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound


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 Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:5.2
occ:1.00
 O A:HOH550 2.0 5.4 1.0
ND1 A:HIS62 2.1 4.8 1.0
SG A:CYS94 2.3 4.8 1.0
SG A:CYS91 2.3 5.3 1.0
CE1 A:HIS62 3.0 6.3 1.0
CG A:HIS62 3.1 5.0 1.0
ZN A:ZN401 3.2 5.8 1.0
CB A:CYS94 3.3 4.3 1.0
CB A:CYS91 3.3 5.9 1.0
CB A:HIS62 3.5 4.3 1.0
O A:HOH552 3.6 7.7 1.0
N A:CYS91 3.8 4.1 1.0
N A:CYS94 3.8 3.9 1.0
O A:HOH549 4.1 13.0 1.0
CA A:CYS91 4.1 4.6 1.0
NE2 A:HIS62 4.1 7.2 1.0
CA A:CYS94 4.2 3.6 1.0
CE A:MSE93 4.2 7.6 1.0
CD2 A:HIS62 4.2 5.6 1.0
OE1 A:GLU64 4.3 6.8 1.0
OE2 A:GLU64 4.4 8.7 1.0
CD A:GLU64 4.5 7.0 1.0
C A:CYS91 4.7 4.0 1.0
CB A:MSE93 4.8 6.1 1.0
O A:CYS91 4.8 4.3 1.0
O A:HOH551 4.9 12.5 1.0
C A:MSE93 4.9 3.9 1.0
C A:PRO90 5.0 3.7 1.0

Zinc binding site 3 out of 4 in 1ox7

Go back to Zinc Binding Sites List in 1ox7
Zinc binding site 3 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:4.5
occ:1.00
 O B:HOH507 2.0 4.7 1.0
ND1 B:HIS262 2.1 3.5 1.0
SG B:CYS294 2.3 4.4 1.0
SG B:CYS291 2.3 4.1 1.0
CE1 B:HIS262 3.0 4.0 1.0
CG B:HIS262 3.1 3.4 1.0
CB B:CYS294 3.2 4.0 1.0
ZN B:ZN403 3.2 4.8 1.0
CB B:CYS291 3.4 4.1 1.0
CB B:HIS262 3.5 3.9 1.0
O B:HOH508 3.5 5.9 1.0
N B:CYS291 3.8 4.1 1.0
N B:CYS294 3.8 3.9 1.0
O B:HOH504 4.1 13.7 1.0
CA B:CYS294 4.1 4.3 1.0
CA B:CYS291 4.1 3.3 1.0
NE2 B:HIS262 4.2 5.7 1.0
CE B:MSE293 4.2 4.7 1.0
CD2 B:HIS262 4.2 5.1 1.0
OE1 B:GLU264 4.3 5.6 1.0
OE2 B:GLU264 4.5 8.5 1.0
CD B:GLU264 4.6 5.6 1.0
C B:CYS291 4.7 3.0 1.0
CB B:MSE293 4.7 4.5 1.0
O B:CYS291 4.8 3.8 1.0
O B:HOH506 4.9 12.1 1.0
C B:MSE293 4.9 3.8 1.0
C B:PRO290 5.0 4.1 1.0

Zinc binding site 4 out of 4 in 1ox7

Go back to Zinc Binding Sites List in 1ox7
Zinc binding site 4 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Yeast Cytosine Deaminase Apo-Enzyme: Inorganic Zinc Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:4.8
occ:1.00
 O B:HOH508 1.7 5.9 1.0
O B:HOH507 1.7 4.7 1.0
O B:HOH504 2.0 13.7 1.0
O B:HOH506 2.0 12.1 1.0
ZN B:ZN400 3.2 4.5 1.0
OE1 B:GLU264 3.6 5.6 1.0
OE2 B:GLU264 3.6 8.5 1.0
O B:HOH505 3.8 6.4 1.0
ND1 B:HIS262 3.8 3.5 1.0
CD B:GLU264 4.1 5.6 1.0
N B:CYS291 4.1 4.1 1.0
CD1 B:ILE233 4.2 6.5 1.0
CE1 B:HIS262 4.3 4.0 1.0
CG B:HIS262 4.4 3.4 1.0
CB B:CYS291 4.5 4.1 1.0
O B:SER289 4.5 5.3 1.0
SG B:CYS294 4.6 4.4 1.0
CB B:HIS262 4.7 3.9 1.0
CA B:PRO290 4.7 4.0 1.0
CG2 B:ILE233 4.7 5.2 1.0
SG B:CYS291 4.8 4.1 1.0
CE1 B:PHE314 4.8 5.0 1.0
C B:PRO290 4.9 4.1 1.0
CA B:CYS291 4.9 3.3 1.0

Reference:

G.C.Ireton, M.E.Black, B.L.Stoddard. The 1.14 A Crystal Structure of Yeast Cytosine Deaminase. Evolution of Nucleotide Salvage Enzymes and Implications For Genetic Chemotherapy. Structure V. 11 961 2003.
ISSN: ISSN 0969-2126
PubMed: 12906827
DOI: 10.1016/S0969-2126(03)00153-9
Page generated: Wed Oct 16 17:35:03 2024

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