Chlorine in PDB 5our: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.:
2.4.2.3;
Protein crystallography data
The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A., PDB code: 5our
was solved by
I.I.Prokofev,
V.V.Balaev,
A.G.Gabdoulkhakov,
C.Betzel,
A.A.Lashkov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.60 /
1.35
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.245,
93.245,
152.928,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.1 /
17.1
|
Other elements in 5our:
The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
(pdb code 5our). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A., PDB code: 5our:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 5our
Go back to
Chlorine Binding Sites List in 5our
Chlorine binding site 1 out
of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:59.1
occ:1.00
|
O
|
B:HOH440
|
3.0
|
38.0
|
1.0
|
N
|
B:ASN39
|
3.0
|
13.3
|
1.0
|
O
|
B:HOH689
|
3.2
|
54.0
|
1.0
|
CA
|
B:ASN39
|
3.8
|
13.6
|
1.0
|
OD1
|
B:ASN39
|
3.9
|
22.4
|
1.0
|
C
|
B:ASP38
|
4.0
|
14.1
|
1.0
|
CA
|
B:ASP38
|
4.0
|
13.9
|
1.0
|
CD
|
B:PRO40
|
4.1
|
12.1
|
1.0
|
CG
|
B:ASN39
|
4.4
|
19.6
|
1.0
|
CB
|
B:ASP38
|
4.6
|
15.6
|
1.0
|
O
|
B:MET37
|
4.6
|
14.9
|
1.0
|
CB
|
B:ASN39
|
4.7
|
15.9
|
1.0
|
OD1
|
B:ASP38
|
4.7
|
22.8
|
1.0
|
O
|
B:HOH549
|
4.7
|
26.2
|
1.0
|
O
|
B:HOH484
|
4.8
|
24.3
|
1.0
|
C
|
B:ASN39
|
4.9
|
11.8
|
1.0
|
N
|
B:PRO40
|
4.9
|
10.8
|
1.0
|
O
|
B:HOH709
|
4.9
|
52.7
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 5our
Go back to
Chlorine Binding Sites List in 5our
Chlorine binding site 2 out
of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl305
b:24.2
occ:1.00
|
O
|
B:HOH536
|
2.8
|
10.9
|
1.0
|
N
|
B:PHE133
|
2.9
|
7.4
|
1.0
|
O
|
B:HOH633
|
3.2
|
43.7
|
1.0
|
CB
|
B:PHE133
|
3.5
|
8.6
|
1.0
|
CA
|
B:ASP132
|
3.7
|
7.6
|
1.0
|
O
|
C:HOH635
|
3.7
|
53.0
|
1.0
|
O
|
C:MET152
|
3.7
|
12.7
|
1.0
|
C
|
B:ASP132
|
3.8
|
7.4
|
1.0
|
OD1
|
B:ASP132
|
3.8
|
12.7
|
1.0
|
CA
|
B:PHE133
|
3.8
|
7.6
|
1.0
|
CG2
|
C:THR110
|
3.9
|
9.4
|
1.0
|
O
|
B:HOH435
|
3.9
|
32.4
|
1.0
|
CB
|
C:MET152
|
4.0
|
10.4
|
1.0
|
C
|
C:MET152
|
4.1
|
9.6
|
1.0
|
O
|
B:PRO131
|
4.2
|
7.4
|
1.0
|
O
|
B:HOH696
|
4.2
|
23.9
|
1.0
|
CG
|
B:ASP132
|
4.2
|
11.3
|
1.0
|
OG1
|
C:THR110
|
4.2
|
9.9
|
1.0
|
CB
|
B:ASP132
|
4.5
|
9.0
|
1.0
|
CB
|
C:THR110
|
4.5
|
8.9
|
1.0
|
CA
|
C:GLY153
|
4.5
|
7.8
|
1.0
|
N
|
C:GLY153
|
4.5
|
8.1
|
1.0
|
O
|
B:HOH580
|
4.7
|
10.4
|
1.0
|
N
|
B:ASP132
|
4.7
|
6.7
|
1.0
|
CA
|
C:MET152
|
4.8
|
8.3
|
1.0
|
O
|
C:HOH557
|
4.8
|
25.6
|
1.0
|
C
|
B:PRO131
|
4.9
|
5.9
|
1.0
|
CG
|
B:PHE133
|
4.9
|
9.5
|
1.0
|
OD2
|
B:ASP132
|
4.9
|
11.9
|
1.0
|
C
|
B:PHE133
|
4.9
|
8.3
|
1.0
|
N
|
B:ASP134
|
5.0
|
8.4
|
1.0
|
O
|
B:ASP132
|
5.0
|
7.6
|
1.0
|
O
|
B:HOH523
|
5.0
|
25.4
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 5our
Go back to
Chlorine Binding Sites List in 5our
Chlorine binding site 3 out
of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl301
b:26.9
occ:1.00
|
O
|
B:HOH564
|
2.7
|
12.4
|
1.0
|
O
|
B:HOH653
|
2.8
|
48.1
|
1.0
|
N
|
C:PHE133
|
2.9
|
6.3
|
1.0
|
CB
|
C:PHE133
|
3.5
|
8.6
|
1.0
|
CA
|
C:ASP132
|
3.7
|
7.3
|
1.0
|
CA
|
C:PHE133
|
3.8
|
7.8
|
1.0
|
C
|
C:ASP132
|
3.8
|
6.7
|
1.0
|
OD1
|
C:ASP132
|
3.9
|
12.6
|
1.0
|
CG2
|
B:THR110
|
3.9
|
10.0
|
1.0
|
O
|
B:MET152
|
3.9
|
9.8
|
1.0
|
O
|
C:HOH443
|
4.1
|
38.5
|
1.0
|
OG1
|
B:THR110
|
4.2
|
9.2
|
1.0
|
O
|
C:PRO131
|
4.2
|
7.6
|
1.0
|
CB
|
B:MET152
|
4.2
|
9.3
|
1.0
|
O
|
C:HOH681
|
4.2
|
31.6
|
1.0
|
C
|
B:MET152
|
4.3
|
8.3
|
1.0
|
CG
|
C:ASP132
|
4.3
|
9.8
|
1.0
|
CA
|
B:GLY153
|
4.5
|
8.1
|
1.0
|
CB
|
B:THR110
|
4.5
|
9.2
|
1.0
|
CB
|
C:ASP132
|
4.6
|
8.9
|
1.0
|
N
|
B:GLY153
|
4.6
|
7.4
|
1.0
|
O
|
B:HOH519
|
4.7
|
28.9
|
1.0
|
O
|
C:HOH590
|
4.8
|
11.3
|
1.0
|
N
|
C:ASP132
|
4.8
|
7.0
|
1.0
|
CG
|
C:PHE133
|
4.8
|
9.6
|
1.0
|
C
|
C:PHE133
|
5.0
|
8.6
|
1.0
|
C
|
C:PRO131
|
5.0
|
6.9
|
1.0
|
CA
|
B:MET152
|
5.0
|
8.5
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 5our
Go back to
Chlorine Binding Sites List in 5our
Chlorine binding site 4 out
of 4 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl306
b:25.5
occ:1.00
|
O
|
F:HOH546
|
2.8
|
11.4
|
1.0
|
N
|
F:PHE133
|
2.9
|
7.8
|
1.0
|
O
|
A:HOH655
|
3.1
|
31.0
|
0.4
|
O
|
A:HOH655
|
3.3
|
37.0
|
0.6
|
CB
|
F:PHE133
|
3.5
|
8.0
|
1.0
|
CA
|
F:ASP132
|
3.7
|
7.9
|
1.0
|
CA
|
F:PHE133
|
3.8
|
7.3
|
1.0
|
C
|
F:ASP132
|
3.8
|
7.5
|
1.0
|
OD1
|
F:ASP132
|
3.8
|
11.6
|
1.0
|
CG2
|
A:THR110
|
3.8
|
9.3
|
1.0
|
O
|
A:MET152
|
3.9
|
11.7
|
1.0
|
O
|
F:HOH439
|
3.9
|
33.3
|
1.0
|
CB
|
A:MET152
|
4.1
|
9.6
|
1.0
|
O
|
F:HOH693
|
4.1
|
29.2
|
1.0
|
C
|
A:MET152
|
4.2
|
8.6
|
1.0
|
OG1
|
A:THR110
|
4.2
|
9.2
|
1.0
|
O
|
F:PRO131
|
4.2
|
7.2
|
1.0
|
CG
|
F:ASP132
|
4.3
|
10.3
|
1.0
|
CB
|
A:THR110
|
4.4
|
8.1
|
1.0
|
CA
|
A:GLY153
|
4.5
|
8.0
|
1.0
|
CB
|
F:ASP132
|
4.5
|
9.2
|
1.0
|
N
|
A:GLY153
|
4.5
|
7.8
|
1.0
|
O
|
F:HOH577
|
4.7
|
10.4
|
1.0
|
O
|
A:HOH548
|
4.8
|
27.0
|
1.0
|
CA
|
A:MET152
|
4.8
|
8.5
|
1.0
|
N
|
F:ASP132
|
4.8
|
7.3
|
1.0
|
CG
|
F:PHE133
|
4.9
|
8.9
|
1.0
|
C
|
F:PRO131
|
5.0
|
7.0
|
1.0
|
OD2
|
F:ASP132
|
5.0
|
10.7
|
1.0
|
C
|
F:PHE133
|
5.0
|
7.6
|
1.0
|
N
|
F:ASP134
|
5.0
|
9.3
|
1.0
|
|
Reference:
I.I.Prokofev,
V.V.Balaev,
A.G.Gabdoulkhakov,
C.Betzel,
A.A.Lashkov.
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. To Be Published.
Page generated: Sat Dec 12 12:14:11 2020
|