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:
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
|