Zinc in PDB 1ux1: Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
Enzymatic activity of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
All present enzymatic activity of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution:
3.5.4.5;
Protein crystallography data
The structure of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution, PDB code: 1ux1
was solved by
E.Johansson,
J.Neuhard,
M.Willemoes,
S.Larsen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.66 /
2.36
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.484,
62.484,
221.604,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.3 /
24.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
(pdb code 1ux1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution, PDB code: 1ux1:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1ux1
Go back to
Zinc Binding Sites List in 1ux1
Zinc binding site 1 out
of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1132
b:21.6
occ:1.00
|
ND1
|
A:HIS53
|
2.1
|
20.7
|
1.0
|
SG
|
A:CYS86
|
2.3
|
18.1
|
1.0
|
O4
|
A:THU138
|
2.3
|
18.4
|
1.0
|
SG
|
A:CYS89
|
2.3
|
16.7
|
1.0
|
CE1
|
A:HIS53
|
3.1
|
20.2
|
1.0
|
CG
|
A:HIS53
|
3.1
|
21.3
|
1.0
|
CB
|
A:CYS89
|
3.1
|
18.3
|
1.0
|
C4
|
A:THU138
|
3.2
|
20.2
|
1.0
|
N3
|
A:THU138
|
3.4
|
20.4
|
1.0
|
CB
|
A:CYS86
|
3.4
|
17.6
|
1.0
|
CB
|
A:HIS53
|
3.4
|
21.5
|
1.0
|
C5
|
A:THU138
|
3.7
|
21.2
|
1.0
|
OE2
|
A:GLU55
|
3.8
|
18.3
|
1.0
|
N
|
A:CYS86
|
3.8
|
19.7
|
1.0
|
N
|
A:CYS89
|
4.0
|
21.6
|
1.0
|
C6
|
A:THU138
|
4.1
|
21.1
|
1.0
|
C2
|
A:THU138
|
4.1
|
21.9
|
1.0
|
CA
|
A:CYS89
|
4.1
|
21.5
|
1.0
|
CA
|
A:CYS86
|
4.1
|
19.1
|
1.0
|
NE2
|
A:HIS53
|
4.2
|
22.9
|
1.0
|
OE1
|
A:GLU55
|
4.2
|
19.6
|
1.0
|
CD2
|
A:HIS53
|
4.2
|
22.0
|
1.0
|
CD
|
A:GLU55
|
4.3
|
22.4
|
1.0
|
N1
|
A:THU138
|
4.5
|
21.8
|
1.0
|
O
|
A:CYS86
|
4.6
|
15.8
|
1.0
|
NE2
|
A:GLN56
|
4.6
|
30.9
|
1.0
|
C
|
A:CYS86
|
4.6
|
18.2
|
1.0
|
O2
|
A:THU138
|
4.8
|
18.0
|
1.0
|
CA
|
A:HIS53
|
5.0
|
23.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1ux1
Go back to
Zinc Binding Sites List in 1ux1
Zinc binding site 2 out
of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1131
b:23.7
occ:1.00
|
ND1
|
B:HIS53
|
2.2
|
21.6
|
1.0
|
O4
|
B:THU138
|
2.3
|
26.1
|
1.0
|
SG
|
B:CYS89
|
2.4
|
21.1
|
1.0
|
SG
|
B:CYS86
|
2.4
|
19.9
|
1.0
|
CE1
|
B:HIS53
|
3.1
|
23.8
|
1.0
|
CG
|
B:HIS53
|
3.1
|
21.8
|
1.0
|
C4
|
B:THU138
|
3.3
|
28.6
|
1.0
|
CB
|
B:CYS89
|
3.3
|
20.4
|
1.0
|
CB
|
B:CYS86
|
3.4
|
19.8
|
1.0
|
CB
|
B:HIS53
|
3.4
|
21.4
|
1.0
|
N3
|
B:THU138
|
3.5
|
27.3
|
1.0
|
N
|
B:CYS86
|
3.8
|
19.9
|
1.0
|
C5
|
B:THU138
|
3.8
|
27.5
|
1.0
|
OE2
|
B:GLU55
|
3.9
|
19.5
|
1.0
|
N
|
B:CYS89
|
4.0
|
18.5
|
1.0
|
C6
|
B:THU138
|
4.1
|
27.2
|
1.0
|
CA
|
B:CYS86
|
4.1
|
20.8
|
1.0
|
C2
|
B:THU138
|
4.2
|
28.9
|
1.0
|
OE1
|
B:GLU55
|
4.2
|
21.2
|
1.0
|
NE2
|
B:HIS53
|
4.2
|
23.5
|
1.0
|
CA
|
B:CYS89
|
4.2
|
20.4
|
1.0
|
CD2
|
B:HIS53
|
4.2
|
22.4
|
1.0
|
CD
|
B:GLU55
|
4.3
|
22.6
|
1.0
|
N1
|
B:THU138
|
4.6
|
29.1
|
1.0
|
O
|
B:CYS86
|
4.6
|
19.1
|
1.0
|
C
|
B:CYS86
|
4.6
|
19.2
|
1.0
|
NE2
|
B:GLN56
|
4.6
|
31.7
|
1.0
|
O2
|
B:THU138
|
4.8
|
29.5
|
1.0
|
C
|
B:PRO85
|
4.9
|
21.7
|
1.0
|
CA
|
B:HIS53
|
5.0
|
23.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1ux1
Go back to
Zinc Binding Sites List in 1ux1
Zinc binding site 3 out
of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1131
b:20.7
occ:1.00
|
ND1
|
C:HIS53
|
2.1
|
21.8
|
1.0
|
O4
|
C:THU138
|
2.1
|
20.9
|
1.0
|
SG
|
C:CYS86
|
2.3
|
17.6
|
1.0
|
SG
|
C:CYS89
|
2.4
|
18.3
|
1.0
|
CE1
|
C:HIS53
|
3.1
|
22.9
|
1.0
|
CG
|
C:HIS53
|
3.1
|
20.3
|
1.0
|
C4
|
C:THU138
|
3.1
|
22.8
|
1.0
|
CB
|
C:CYS89
|
3.2
|
20.0
|
1.0
|
N3
|
C:THU138
|
3.2
|
23.8
|
1.0
|
CB
|
C:HIS53
|
3.4
|
20.9
|
1.0
|
CB
|
C:CYS86
|
3.4
|
13.4
|
1.0
|
OE2
|
C:GLU55
|
3.8
|
17.1
|
1.0
|
N
|
C:CYS86
|
3.8
|
16.4
|
1.0
|
C5
|
C:THU138
|
3.9
|
23.0
|
1.0
|
C2
|
C:THU138
|
4.0
|
23.4
|
1.0
|
N
|
C:CYS89
|
4.0
|
19.8
|
1.0
|
CA
|
C:CYS86
|
4.1
|
17.1
|
1.0
|
NE2
|
C:HIS53
|
4.1
|
23.2
|
1.0
|
OE1
|
C:GLU55
|
4.1
|
21.7
|
1.0
|
CA
|
C:CYS89
|
4.2
|
20.5
|
1.0
|
CD2
|
C:HIS53
|
4.2
|
21.4
|
1.0
|
CD
|
C:GLU55
|
4.2
|
21.0
|
1.0
|
C6
|
C:THU138
|
4.3
|
21.9
|
1.0
|
N1
|
C:THU138
|
4.5
|
24.7
|
1.0
|
O
|
C:CYS86
|
4.6
|
15.7
|
1.0
|
O2
|
C:THU138
|
4.6
|
22.6
|
1.0
|
C
|
C:CYS86
|
4.6
|
15.8
|
1.0
|
NE2
|
C:GLN56
|
4.7
|
31.2
|
1.0
|
CA
|
C:HIS53
|
4.9
|
21.4
|
1.0
|
C
|
C:PRO85
|
5.0
|
18.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1ux1
Go back to
Zinc Binding Sites List in 1ux1
Zinc binding site 4 out
of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1132
b:27.7
occ:1.00
|
ND1
|
D:HIS53
|
2.2
|
24.4
|
1.0
|
O4
|
D:THU138
|
2.3
|
30.0
|
1.0
|
SG
|
D:CYS89
|
2.3
|
20.6
|
1.0
|
SG
|
D:CYS86
|
2.4
|
24.3
|
1.0
|
CG
|
D:HIS53
|
3.1
|
26.3
|
1.0
|
CE1
|
D:HIS53
|
3.1
|
27.4
|
1.0
|
CB
|
D:CYS89
|
3.2
|
21.9
|
1.0
|
C4
|
D:THU138
|
3.2
|
31.8
|
1.0
|
CB
|
D:HIS53
|
3.4
|
27.2
|
1.0
|
CB
|
D:CYS86
|
3.5
|
20.6
|
1.0
|
N3
|
D:THU138
|
3.5
|
30.4
|
1.0
|
C5
|
D:THU138
|
3.8
|
32.0
|
1.0
|
N
|
D:CYS86
|
3.8
|
22.0
|
1.0
|
OE2
|
D:GLU55
|
3.9
|
24.6
|
1.0
|
N
|
D:CYS89
|
4.0
|
21.5
|
1.0
|
C6
|
D:THU138
|
4.1
|
33.1
|
1.0
|
CA
|
D:CYS89
|
4.1
|
21.5
|
1.0
|
CA
|
D:CYS86
|
4.1
|
21.8
|
1.0
|
OE1
|
D:GLU55
|
4.2
|
25.1
|
1.0
|
NE2
|
D:HIS53
|
4.2
|
28.6
|
1.0
|
C2
|
D:THU138
|
4.2
|
32.4
|
1.0
|
CD2
|
D:HIS53
|
4.2
|
29.0
|
1.0
|
CD
|
D:GLU55
|
4.3
|
25.4
|
1.0
|
O
|
D:CYS86
|
4.5
|
23.1
|
1.0
|
N1
|
D:THU138
|
4.6
|
32.9
|
1.0
|
C
|
D:CYS86
|
4.6
|
22.0
|
1.0
|
NE2
|
D:GLN56
|
4.6
|
32.1
|
1.0
|
O2
|
D:THU138
|
4.9
|
29.7
|
1.0
|
C
|
D:PRO85
|
4.9
|
23.1
|
1.0
|
CA
|
D:HIS53
|
4.9
|
29.3
|
1.0
|
|
Reference:
E.Johansson,
J.Neuhard,
M.Willemoes,
S.Larsen.
Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetrameric Cytidine Deaminase Biochemistry V. 43 6020 2004.
ISSN: ISSN 0006-2960
PubMed: 15147186
DOI: 10.1021/BI035893X
Page generated: Wed Oct 16 19:39:05 2024
|