Potassium in PDB 5lok: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution:
2.4.2.3;
Protein crystallography data
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok
was solved by
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdoulkhakov,
M.V.Dontsova,
C.Betzel,
A.M.Mikhailov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.68 /
1.11
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.258,
71.772,
89.228,
69.35,
72.17,
85.78
|
R / Rfree (%)
|
11.4 /
13.6
|
Other elements in 5lok:
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
(pdb code 5lok). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the
X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok:
Jump to Potassium binding site number:
1;
2;
3;
Potassium binding site 1 out
of 3 in 5lok
Go back to
Potassium Binding Sites List in 5lok
Potassium binding site 1 out
of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K302
b:11.4
occ:0.43
|
OE2
|
A:GLU48
|
2.7
|
10.0
|
1.0
|
OE2
|
B:GLU48
|
2.8
|
10.2
|
1.0
|
OG
|
B:SER72
|
2.9
|
8.0
|
1.0
|
OG
|
A:SER72
|
2.9
|
8.0
|
1.0
|
O
|
A:ILE68
|
2.9
|
8.7
|
1.0
|
HB3
|
B:SER72
|
2.9
|
9.2
|
1.0
|
HB3
|
A:SER72
|
3.0
|
9.9
|
1.0
|
O
|
B:ILE68
|
3.0
|
7.9
|
1.0
|
H
|
B:ILE68
|
3.2
|
10.1
|
1.0
|
H
|
A:ILE68
|
3.2
|
10.3
|
1.0
|
HA3
|
B:GLY67
|
3.3
|
11.1
|
1.0
|
HA3
|
A:GLY67
|
3.3
|
11.6
|
1.0
|
CB
|
B:SER72
|
3.4
|
7.7
|
1.0
|
CB
|
A:SER72
|
3.4
|
8.3
|
1.0
|
O
|
B:HOH466
|
3.6
|
8.4
|
0.5
|
O
|
B:HOH466
|
3.6
|
7.6
|
0.5
|
N
|
A:ILE68
|
3.6
|
8.6
|
1.0
|
N
|
B:ILE68
|
3.6
|
8.4
|
1.0
|
HB2
|
B:SER72
|
3.7
|
9.2
|
1.0
|
HB2
|
A:SER72
|
3.7
|
9.9
|
1.0
|
HG3
|
B:GLU48
|
3.8
|
13.7
|
1.0
|
CD
|
A:GLU48
|
3.8
|
11.2
|
1.0
|
HG3
|
A:GLU48
|
3.8
|
13.7
|
1.0
|
CD
|
B:GLU48
|
3.9
|
11.1
|
1.0
|
C
|
B:ILE68
|
3.9
|
7.5
|
1.0
|
C
|
A:ILE68
|
3.9
|
7.9
|
1.0
|
HB
|
B:ILE68
|
4.1
|
10.1
|
1.0
|
CA
|
A:GLY67
|
4.1
|
9.7
|
1.0
|
CA
|
B:GLY67
|
4.1
|
9.3
|
1.0
|
HB
|
A:ILE68
|
4.1
|
10.5
|
1.0
|
C
|
A:GLY67
|
4.2
|
9.0
|
1.0
|
C
|
B:GLY67
|
4.2
|
9.0
|
1.0
|
CA
|
B:ILE68
|
4.3
|
8.1
|
1.0
|
CA
|
A:ILE68
|
4.3
|
8.4
|
1.0
|
CG
|
A:GLU48
|
4.3
|
11.4
|
1.0
|
CG
|
B:GLU48
|
4.4
|
11.4
|
1.0
|
H
|
B:SER72
|
4.4
|
8.3
|
1.0
|
HA2
|
A:GLY67
|
4.4
|
11.6
|
1.0
|
H
|
A:SER72
|
4.4
|
9.1
|
1.0
|
HA2
|
B:GLY67
|
4.4
|
11.1
|
1.0
|
HB3
|
A:GLU48
|
4.5
|
15.5
|
1.0
|
CB
|
B:ILE68
|
4.7
|
8.4
|
1.0
|
HB3
|
B:GLU48
|
4.7
|
14.9
|
1.0
|
CB
|
A:ILE68
|
4.8
|
8.8
|
1.0
|
CA
|
B:SER72
|
4.8
|
7.1
|
1.0
|
O
|
A:THR66
|
4.8
|
10.0
|
1.0
|
CA
|
A:SER72
|
4.8
|
8.0
|
1.0
|
O
|
B:THR66
|
4.8
|
9.4
|
1.0
|
OE1
|
A:GLU48
|
4.8
|
12.4
|
1.0
|
OE1
|
B:GLU48
|
4.9
|
12.8
|
1.0
|
CB
|
A:GLU48
|
4.9
|
12.9
|
1.0
|
N
|
B:SER72
|
4.9
|
6.9
|
1.0
|
N
|
A:SER72
|
5.0
|
7.5
|
1.0
|
HB2
|
A:GLU48
|
5.0
|
15.5
|
1.0
|
|
Potassium binding site 2 out
of 3 in 5lok
Go back to
Potassium Binding Sites List in 5lok
Potassium binding site 2 out
of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K302
b:13.3
occ:0.45
|
OE2
|
D:GLU48
|
2.8
|
12.6
|
1.0
|
OE2
|
C:GLU48
|
2.8
|
12.1
|
1.0
|
OG
|
D:SER72
|
2.9
|
10.3
|
1.0
|
OG
|
C:SER72
|
2.9
|
9.6
|
1.0
|
O
|
C:ILE68
|
2.9
|
9.3
|
1.0
|
HB3
|
C:SER72
|
2.9
|
11.9
|
1.0
|
O
|
D:ILE68
|
2.9
|
10.0
|
1.0
|
HB3
|
D:SER72
|
3.0
|
12.3
|
1.0
|
H
|
C:ILE68
|
3.2
|
12.2
|
1.0
|
H
|
D:ILE68
|
3.2
|
12.0
|
1.0
|
HA3
|
D:GLY67
|
3.3
|
13.3
|
1.0
|
HA3
|
C:GLY67
|
3.4
|
13.1
|
1.0
|
CB
|
C:SER72
|
3.4
|
9.9
|
1.0
|
CB
|
D:SER72
|
3.4
|
10.2
|
1.0
|
N
|
C:ILE68
|
3.6
|
10.2
|
1.0
|
N
|
D:ILE68
|
3.6
|
10.0
|
1.0
|
O
|
C:HOH488
|
3.6
|
9.0
|
0.5
|
O
|
C:HOH488
|
3.7
|
9.1
|
0.5
|
HB2
|
C:SER72
|
3.7
|
11.9
|
1.0
|
HB2
|
D:SER72
|
3.7
|
12.3
|
1.0
|
HG3
|
D:GLU48
|
3.8
|
17.1
|
1.0
|
CD
|
D:GLU48
|
3.9
|
13.2
|
1.0
|
HG3
|
C:GLU48
|
3.9
|
16.4
|
1.0
|
CD
|
C:GLU48
|
3.9
|
12.8
|
1.0
|
C
|
D:ILE68
|
3.9
|
9.0
|
1.0
|
C
|
C:ILE68
|
3.9
|
8.8
|
1.0
|
CA
|
D:GLY67
|
4.1
|
11.1
|
1.0
|
HB
|
D:ILE68
|
4.1
|
11.7
|
1.0
|
HB
|
C:ILE68
|
4.1
|
11.7
|
1.0
|
CA
|
C:GLY67
|
4.1
|
10.9
|
1.0
|
C
|
D:GLY67
|
4.2
|
10.1
|
1.0
|
C
|
C:GLY67
|
4.2
|
10.1
|
1.0
|
CA
|
C:ILE68
|
4.3
|
9.5
|
1.0
|
CA
|
D:ILE68
|
4.3
|
9.9
|
1.0
|
CG
|
D:GLU48
|
4.3
|
14.3
|
1.0
|
CG
|
C:GLU48
|
4.4
|
13.7
|
1.0
|
HA2
|
D:GLY67
|
4.4
|
13.3
|
1.0
|
H
|
D:SER72
|
4.4
|
10.4
|
1.0
|
H
|
C:SER72
|
4.4
|
9.9
|
1.0
|
HA2
|
C:GLY67
|
4.4
|
13.1
|
1.0
|
HB3
|
C:GLU48
|
4.6
|
16.8
|
1.0
|
HB3
|
D:GLU48
|
4.7
|
18.5
|
1.0
|
CB
|
D:ILE68
|
4.7
|
9.8
|
1.0
|
CB
|
C:ILE68
|
4.7
|
9.7
|
1.0
|
CA
|
D:SER72
|
4.8
|
9.1
|
1.0
|
CA
|
C:SER72
|
4.8
|
9.2
|
1.0
|
O
|
D:THR66
|
4.8
|
11.2
|
1.0
|
O
|
C:THR66
|
4.8
|
11.1
|
1.0
|
OE1
|
D:GLU48
|
4.8
|
14.3
|
1.0
|
OE1
|
C:GLU48
|
4.9
|
14.3
|
1.0
|
N
|
D:SER72
|
5.0
|
8.7
|
1.0
|
N
|
C:SER72
|
5.0
|
8.3
|
1.0
|
CB
|
C:GLU48
|
5.0
|
14.0
|
1.0
|
|
Potassium binding site 3 out
of 3 in 5lok
Go back to
Potassium Binding Sites List in 5lok
Potassium binding site 3 out
of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K304
b:12.0
occ:0.43
|
OE2
|
F:GLU48
|
2.8
|
11.8
|
1.0
|
OE2
|
E:GLU48
|
2.8
|
12.1
|
1.0
|
OG
|
E:SER72
|
2.9
|
9.6
|
1.0
|
O
|
F:ILE68
|
2.9
|
10.0
|
1.0
|
OG
|
F:SER72
|
2.9
|
9.7
|
1.0
|
O
|
E:ILE68
|
2.9
|
9.7
|
1.0
|
HB3
|
F:SER72
|
2.9
|
11.7
|
1.0
|
HB3
|
E:SER72
|
3.0
|
11.1
|
1.0
|
H
|
F:ILE68
|
3.2
|
12.5
|
1.0
|
H
|
E:ILE68
|
3.2
|
11.2
|
1.0
|
HA3
|
F:GLY67
|
3.3
|
12.8
|
1.0
|
HA3
|
E:GLY67
|
3.4
|
12.3
|
1.0
|
CB
|
F:SER72
|
3.4
|
9.8
|
1.0
|
CB
|
E:SER72
|
3.4
|
9.3
|
1.0
|
O
|
F:HOH464
|
3.6
|
9.9
|
0.6
|
O
|
F:HOH464
|
3.6
|
8.8
|
0.4
|
N
|
F:ILE68
|
3.6
|
10.4
|
1.0
|
N
|
E:ILE68
|
3.6
|
9.3
|
1.0
|
HB2
|
F:SER72
|
3.7
|
11.7
|
1.0
|
HB2
|
E:SER72
|
3.7
|
11.1
|
1.0
|
CD
|
F:GLU48
|
3.9
|
13.3
|
1.0
|
HG3
|
F:GLU48
|
3.9
|
16.4
|
1.0
|
C
|
F:ILE68
|
3.9
|
9.3
|
1.0
|
CD
|
E:GLU48
|
3.9
|
13.0
|
1.0
|
C
|
E:ILE68
|
3.9
|
9.1
|
1.0
|
HG3
|
E:GLU48
|
3.9
|
15.9
|
1.0
|
HB
|
F:ILE68
|
4.1
|
12.5
|
1.0
|
HB
|
E:ILE68
|
4.1
|
11.7
|
1.0
|
CA
|
F:GLY67
|
4.1
|
10.7
|
1.0
|
CA
|
E:GLY67
|
4.1
|
10.3
|
1.0
|
C
|
F:GLY67
|
4.2
|
10.7
|
1.0
|
C
|
E:GLY67
|
4.2
|
9.9
|
1.0
|
CA
|
F:ILE68
|
4.2
|
10.2
|
1.0
|
CA
|
E:ILE68
|
4.3
|
9.5
|
1.0
|
H
|
F:SER72
|
4.3
|
10.7
|
1.0
|
CG
|
F:GLU48
|
4.4
|
13.7
|
1.0
|
H
|
E:SER72
|
4.4
|
10.2
|
1.0
|
CG
|
E:GLU48
|
4.4
|
13.2
|
1.0
|
HA2
|
F:GLY67
|
4.4
|
12.8
|
1.0
|
HA2
|
E:GLY67
|
4.5
|
12.3
|
1.0
|
CB
|
F:ILE68
|
4.7
|
10.4
|
1.0
|
HB3
|
E:GLU48
|
4.7
|
17.1
|
1.0
|
HB3
|
F:GLU48
|
4.7
|
17.9
|
1.0
|
CB
|
E:ILE68
|
4.7
|
9.7
|
1.0
|
CA
|
F:SER72
|
4.7
|
9.0
|
1.0
|
CA
|
E:SER72
|
4.7
|
8.7
|
1.0
|
O
|
F:THR66
|
4.8
|
11.5
|
1.0
|
O
|
E:THR66
|
4.8
|
10.7
|
1.0
|
OE1
|
F:GLU48
|
4.9
|
14.8
|
1.0
|
OE1
|
E:GLU48
|
4.9
|
14.4
|
1.0
|
N
|
F:SER72
|
4.9
|
8.9
|
1.0
|
N
|
E:SER72
|
5.0
|
8.5
|
1.0
|
|
Reference:
I.I.Prokofev,
A.G.Gabdoulkhakov,
A.A.Lashkov,
V.V.Balaev,
C.Betzel,
A.M.Mikhailov.
X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution To Be Published.
Page generated: Mon Aug 12 14:14:53 2024
|