Sodium in PDB 6z9z: Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
Enzymatic activity of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
All present enzymatic activity of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity:
2.4.2.3;
Protein crystallography data
The structure of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity, PDB code: 6z9z
was solved by
P.A.Eistrikh-Heller,
S.V.Rubinsky,
V.R.Samygina,
A.G.Gabdulkhakov,
A.A.Lashkov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.61 /
1.04
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.186,
97.061,
93.227,
90,
119.97,
90
|
|
R / Rfree (%)
|
12.6 /
14.2
|
Other elements in 6z9z:
The structure of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Sodium atom in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
(pdb code 6z9z). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the
Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity, PDB code: 6z9z:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 1 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:41.5
occ:1.00
|
O
|
C:HOH675
|
1.8
|
54.5
|
1.0
|
|
O
|
A:HOH428
|
2.0
|
43.7
|
1.0
|
|
O
|
A:HOH435
|
2.2
|
38.2
|
1.0
|
|
NE2
|
A:GLN180
|
2.2
|
13.9
|
0.5
|
|
NE2
|
A:GLN180
|
2.2
|
14.2
|
0.5
|
|
O
|
A:HOH423
|
2.3
|
40.0
|
1.0
|
|
O
|
A:HOH551
|
2.5
|
40.8
|
1.0
|
|
HE21
|
A:GLN180
|
2.6
|
17.1
|
0.5
|
|
HE21
|
A:GLN180
|
2.8
|
16.7
|
0.5
|
|
CD
|
A:GLN180
|
3.0
|
13.5
|
0.5
|
|
OE1
|
A:GLN180
|
3.1
|
13.7
|
0.5
|
|
CD
|
A:GLN180
|
3.3
|
14.7
|
0.5
|
|
OE1
|
A:GLN180
|
3.6
|
15.8
|
0.5
|
|
HA
|
A:ARG177
|
4.1
|
13.4
|
1.0
|
|
HG3
|
A:ARG177
|
4.2
|
20.6
|
1.0
|
|
OE1
|
C:GLU185
|
4.2
|
14.4
|
0.7
|
|
O
|
C:HOH693
|
4.3
|
19.1
|
1.0
|
|
HB2
|
A:ARG177
|
4.3
|
17.5
|
1.0
|
|
O
|
C:HOH485
|
4.4
|
21.6
|
1.0
|
|
CG
|
A:GLN180
|
4.5
|
12.5
|
0.5
|
|
O
|
A:HOH596
|
4.5
|
36.9
|
1.0
|
|
O
|
A:HOH414
|
4.6
|
31.5
|
1.0
|
|
O
|
C:HOH520
|
4.6
|
41.2
|
1.0
|
|
HB2
|
A:GLN180
|
4.6
|
14.8
|
0.5
|
|
HB2
|
A:GLN180
|
4.6
|
13.9
|
0.5
|
|
CG
|
A:GLN180
|
4.6
|
13.6
|
0.5
|
|
HB3
|
A:GLN180
|
4.9
|
14.8
|
0.5
|
|
HB3
|
A:GLN180
|
4.9
|
13.9
|
0.5
|
|
CB
|
A:ARG177
|
4.9
|
14.6
|
1.0
|
|
CA
|
A:ARG177
|
4.9
|
11.2
|
1.0
|
|
CB
|
A:GLN180
|
4.9
|
11.6
|
0.5
|
|
CB
|
A:GLN180
|
4.9
|
12.3
|
0.5
|
|
HG3
|
A:GLN180
|
5.0
|
15.0
|
0.5
|
|
HG2
|
A:GLN180
|
5.0
|
15.0
|
0.5
|
|
CG
|
A:ARG177
|
5.0
|
17.2
|
1.0
|
|
HG3
|
A:GLN180
|
5.0
|
16.3
|
0.5
|
|
Sodium binding site 2 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 2 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na305
b:15.4
occ:1.00
|
OE2
|
B:GLU48
|
2.7
|
11.5
|
1.0
|
|
OE2
|
A:GLU48
|
2.7
|
11.5
|
1.0
|
|
OG
|
B:SER72
|
2.9
|
9.3
|
1.0
|
|
OG
|
A:SER72
|
2.9
|
9.1
|
1.0
|
|
O
|
A:ILE68
|
2.9
|
9.5
|
1.0
|
|
HB3
|
B:SER72
|
2.9
|
11.1
|
1.0
|
|
O
|
B:ILE68
|
3.0
|
9.4
|
1.0
|
|
HB3
|
A:SER72
|
3.0
|
10.7
|
1.0
|
|
H
|
A:ILE68
|
3.2
|
11.1
|
1.0
|
|
H
|
B:ILE68
|
3.2
|
10.9
|
1.0
|
|
HA3
|
B:GLY67
|
3.3
|
11.3
|
1.0
|
|
HA3
|
A:GLY67
|
3.4
|
11.3
|
1.0
|
|
CB
|
B:SER72
|
3.4
|
9.3
|
1.0
|
|
CB
|
A:SER72
|
3.4
|
8.9
|
1.0
|
|
N
|
A:ILE68
|
3.6
|
9.2
|
1.0
|
|
O
|
A:HOH479
|
3.6
|
8.9
|
0.5
|
|
N
|
B:ILE68
|
3.6
|
9.1
|
1.0
|
|
O
|
A:HOH479
|
3.6
|
9.6
|
0.5
|
|
HG
|
A:SER72
|
3.6
|
10.9
|
1.0
|
|
HG
|
B:SER72
|
3.6
|
11.2
|
1.0
|
|
HB2
|
B:SER72
|
3.7
|
11.1
|
1.0
|
|
HB2
|
A:SER72
|
3.7
|
10.7
|
1.0
|
|
CD
|
B:GLU48
|
3.8
|
12.5
|
1.0
|
|
CD
|
A:GLU48
|
3.8
|
11.9
|
1.0
|
|
HG3
|
A:GLU48
|
3.8
|
14.2
|
1.0
|
|
HG3
|
B:GLU48
|
3.8
|
15.1
|
1.0
|
|
C
|
A:ILE68
|
3.9
|
8.6
|
1.0
|
|
C
|
B:ILE68
|
3.9
|
8.5
|
1.0
|
|
HB
|
A:ILE68
|
4.0
|
11.6
|
1.0
|
|
HB
|
B:ILE68
|
4.1
|
12.1
|
1.0
|
|
CA
|
B:GLY67
|
4.1
|
9.4
|
1.0
|
|
CA
|
A:GLY67
|
4.1
|
9.4
|
1.0
|
|
C
|
A:GLY67
|
4.2
|
9.1
|
1.0
|
|
C
|
B:GLY67
|
4.2
|
9.0
|
1.0
|
|
CA
|
A:ILE68
|
4.3
|
9.0
|
1.0
|
|
CA
|
B:ILE68
|
4.3
|
8.8
|
1.0
|
|
CG
|
A:GLU48
|
4.3
|
11.9
|
1.0
|
|
CG
|
B:GLU48
|
4.3
|
12.6
|
1.0
|
|
H
|
A:SER72
|
4.4
|
9.4
|
1.0
|
|
H
|
B:SER72
|
4.4
|
9.5
|
1.0
|
|
HA2
|
B:GLY67
|
4.4
|
11.3
|
1.0
|
|
HA2
|
A:GLY67
|
4.4
|
11.3
|
1.0
|
|
HB3
|
A:GLU48
|
4.6
|
14.0
|
1.0
|
|
CB
|
A:ILE68
|
4.7
|
9.7
|
1.0
|
|
HB3
|
B:GLU48
|
4.7
|
15.0
|
1.0
|
|
CB
|
B:ILE68
|
4.7
|
10.1
|
1.0
|
|
CA
|
B:SER72
|
4.8
|
8.3
|
1.0
|
|
CA
|
A:SER72
|
4.8
|
8.3
|
1.0
|
|
OE1
|
B:GLU48
|
4.8
|
13.8
|
1.0
|
|
O
|
B:THR66
|
4.8
|
10.1
|
1.0
|
|
OE1
|
A:GLU48
|
4.8
|
13.4
|
1.0
|
|
O
|
A:THR66
|
4.8
|
10.4
|
1.0
|
|
N
|
B:SER72
|
5.0
|
7.9
|
1.0
|
|
N
|
A:SER72
|
5.0
|
7.8
|
1.0
|
|
CB
|
A:GLU48
|
5.0
|
11.6
|
1.0
|
|
Sodium binding site 3 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 3 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na305
b:16.2
occ:0.47
|
OD1
|
B:ASN102
|
1.9
|
20.1
|
1.0
|
|
O
|
B:HOH469
|
2.4
|
28.6
|
1.0
|
|
O
|
B:HOH654
|
2.7
|
21.5
|
1.0
|
|
CG
|
B:ASN102
|
3.0
|
18.4
|
1.0
|
|
HD21
|
B:ASN102
|
3.3
|
23.4
|
1.0
|
|
HE22
|
B:GLN224
|
3.5
|
17.2
|
0.6
|
|
ND2
|
B:ASN102
|
3.5
|
19.4
|
1.0
|
|
HE22
|
B:GLN224
|
3.7
|
27.3
|
0.4
|
|
O
|
B:HOH555
|
4.1
|
23.4
|
1.0
|
|
HA
|
B:ASN102
|
4.1
|
17.9
|
1.0
|
|
CB
|
B:ASN102
|
4.2
|
16.3
|
1.0
|
|
NE2
|
B:GLN224
|
4.3
|
14.3
|
0.6
|
|
HB3
|
B:ASN102
|
4.3
|
19.5
|
1.0
|
|
O
|
B:PRO99
|
4.3
|
18.6
|
1.0
|
|
O
|
B:HOH660
|
4.4
|
39.6
|
1.0
|
|
HD22
|
B:ASN102
|
4.4
|
23.4
|
1.0
|
|
NE2
|
B:GLN224
|
4.4
|
22.7
|
0.4
|
|
HE21
|
B:GLN224
|
4.5
|
27.3
|
0.4
|
|
HE21
|
B:GLN224
|
4.5
|
17.2
|
0.6
|
|
O
|
B:HOH727
|
4.6
|
36.5
|
1.0
|
|
O
|
B:HOH651
|
4.7
|
50.2
|
1.0
|
|
CA
|
B:ASN102
|
4.7
|
14.9
|
1.0
|
|
HB2
|
B:ASN102
|
4.9
|
19.5
|
1.0
|
|
Sodium binding site 4 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 4 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na304
b:12.6
occ:0.62
|
OE2
|
C:GLU48
|
2.7
|
12.1
|
1.0
|
|
OE2
|
D:GLU48
|
2.8
|
13.4
|
1.0
|
|
OG
|
D:SER72
|
2.9
|
10.5
|
1.0
|
|
O
|
D:ILE68
|
2.9
|
10.1
|
1.0
|
|
O
|
C:ILE68
|
2.9
|
10.4
|
1.0
|
|
HB3
|
C:SER72
|
2.9
|
11.3
|
1.0
|
|
OG
|
C:SER72
|
3.0
|
10.2
|
1.0
|
|
HB3
|
D:SER72
|
3.0
|
12.4
|
1.0
|
|
H
|
D:ILE68
|
3.1
|
11.5
|
1.0
|
|
H
|
C:ILE68
|
3.2
|
12.0
|
1.0
|
|
HA3
|
D:GLY67
|
3.4
|
12.2
|
1.0
|
|
HA3
|
C:GLY67
|
3.4
|
12.1
|
1.0
|
|
CB
|
D:SER72
|
3.4
|
10.3
|
1.0
|
|
CB
|
C:SER72
|
3.4
|
9.4
|
1.0
|
|
N
|
D:ILE68
|
3.6
|
9.6
|
1.0
|
|
O
|
C:HOH489
|
3.6
|
10.2
|
0.5
|
|
N
|
C:ILE68
|
3.6
|
10.0
|
1.0
|
|
HG
|
D:SER72
|
3.6
|
12.6
|
1.0
|
|
O
|
C:HOH489
|
3.6
|
9.4
|
0.5
|
|
HG
|
C:SER72
|
3.7
|
12.2
|
1.0
|
|
HB2
|
C:SER72
|
3.7
|
11.3
|
1.0
|
|
HB2
|
D:SER72
|
3.7
|
12.4
|
1.0
|
|
CD
|
D:GLU48
|
3.8
|
13.8
|
1.0
|
|
HG3
|
D:GLU48
|
3.8
|
16.6
|
1.0
|
|
CD
|
C:GLU48
|
3.8
|
12.5
|
1.0
|
|
HG3
|
C:GLU48
|
3.9
|
15.5
|
1.0
|
|
C
|
D:ILE68
|
3.9
|
9.2
|
1.0
|
|
C
|
C:ILE68
|
3.9
|
9.4
|
1.0
|
|
HB
|
D:ILE68
|
4.0
|
12.7
|
1.0
|
|
HB
|
C:ILE68
|
4.0
|
12.9
|
1.0
|
|
CA
|
D:GLY67
|
4.1
|
10.2
|
1.0
|
|
C
|
D:GLY67
|
4.2
|
9.6
|
1.0
|
|
CA
|
C:GLY67
|
4.2
|
10.1
|
1.0
|
|
C
|
C:GLY67
|
4.2
|
9.7
|
1.0
|
|
CA
|
D:ILE68
|
4.2
|
9.7
|
1.0
|
|
CA
|
C:ILE68
|
4.3
|
10.1
|
1.0
|
|
CG
|
D:GLU48
|
4.3
|
13.8
|
1.0
|
|
CG
|
C:GLU48
|
4.4
|
12.9
|
1.0
|
|
H
|
D:SER72
|
4.4
|
10.4
|
1.0
|
|
H
|
C:SER72
|
4.4
|
10.4
|
1.0
|
|
HA2
|
D:GLY67
|
4.4
|
12.2
|
1.0
|
|
HA2
|
C:GLY67
|
4.5
|
12.1
|
1.0
|
|
CB
|
D:ILE68
|
4.6
|
10.6
|
1.0
|
|
CB
|
C:ILE68
|
4.7
|
10.8
|
1.0
|
|
HB3
|
C:GLU48
|
4.7
|
15.6
|
1.0
|
|
HB3
|
D:GLU48
|
4.7
|
16.3
|
1.0
|
|
CA
|
D:SER72
|
4.8
|
9.2
|
1.0
|
|
CA
|
C:SER72
|
4.8
|
8.6
|
1.0
|
|
OE1
|
D:GLU48
|
4.8
|
15.1
|
1.0
|
|
OE1
|
C:GLU48
|
4.8
|
14.1
|
1.0
|
|
O
|
D:THR66
|
4.8
|
11.0
|
1.0
|
|
O
|
C:THR66
|
4.9
|
10.5
|
1.0
|
|
N
|
D:SER72
|
5.0
|
8.7
|
1.0
|
|
N
|
C:SER72
|
5.0
|
8.7
|
1.0
|
|
Sodium binding site 5 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 5 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na305
b:17.9
occ:0.51
|
O
|
E:HOH606
|
2.2
|
44.4
|
1.0
|
|
OE1
|
C:GLN180
|
2.2
|
17.3
|
1.0
|
|
O
|
C:HOH549
|
2.3
|
43.6
|
1.0
|
|
O
|
C:HOH628
|
2.3
|
44.1
|
1.0
|
|
O
|
E:HOH433
|
2.3
|
35.9
|
1.0
|
|
O
|
C:HOH615
|
2.4
|
73.2
|
1.0
|
|
HE22
|
C:GLN180
|
2.7
|
21.9
|
1.0
|
|
CD
|
C:GLN180
|
3.0
|
16.5
|
1.0
|
|
NE2
|
C:GLN180
|
3.2
|
18.2
|
1.0
|
|
O
|
C:HOH576
|
3.7
|
51.0
|
1.0
|
|
HA
|
C:ARG177
|
4.0
|
13.6
|
1.0
|
|
HE21
|
C:GLN180
|
4.0
|
21.9
|
1.0
|
|
HG3
|
C:ARG177
|
4.1
|
19.8
|
1.0
|
|
OE1
|
E:GLU185
|
4.2
|
16.7
|
1.0
|
|
O
|
E:HOH608
|
4.3
|
19.6
|
1.0
|
|
HB2
|
C:ARG177
|
4.4
|
17.4
|
1.0
|
|
O
|
C:HOH570
|
4.4
|
24.4
|
1.0
|
|
CG
|
C:GLN180
|
4.5
|
13.7
|
1.0
|
|
O
|
C:HOH404
|
4.5
|
39.5
|
1.0
|
|
O
|
E:HOH453
|
4.5
|
18.8
|
1.0
|
|
HB2
|
C:GLN180
|
4.5
|
15.2
|
1.0
|
|
O
|
E:HOH490
|
4.6
|
41.3
|
1.0
|
|
O
|
C:HOH641
|
4.7
|
57.3
|
1.0
|
|
HB3
|
C:GLN180
|
4.8
|
15.2
|
1.0
|
|
CA
|
C:ARG177
|
4.9
|
11.3
|
1.0
|
|
CB
|
C:GLN180
|
4.9
|
12.6
|
1.0
|
|
CB
|
C:ARG177
|
4.9
|
14.5
|
1.0
|
|
CG
|
C:ARG177
|
4.9
|
16.5
|
1.0
|
|
HG2
|
C:GLN180
|
5.0
|
16.5
|
1.0
|
|
HG3
|
C:GLN180
|
5.0
|
16.5
|
1.0
|
|
Sodium binding site 6 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 6 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na306
b:29.4
occ:0.77
|
O
|
C:HOH433
|
2.2
|
30.8
|
1.0
|
|
O
|
C:HOH531
|
2.2
|
19.0
|
1.0
|
|
O
|
C:HOH605
|
2.2
|
19.2
|
1.0
|
|
O
|
C:HOH679
|
2.2
|
16.6
|
1.0
|
|
O
|
B:HOH730
|
2.2
|
50.2
|
1.0
|
|
O
|
B:HOH684
|
2.2
|
43.9
|
1.0
|
|
O
|
C:HOH643
|
2.6
|
39.3
|
1.0
|
|
HA
|
C:ALA206
|
3.5
|
10.7
|
1.0
|
|
O
|
C:HOH695
|
4.0
|
33.3
|
1.0
|
|
O
|
B:HOH473
|
4.1
|
18.5
|
1.0
|
|
O
|
C:HOH511
|
4.2
|
10.3
|
1.0
|
|
O
|
C:ALA206
|
4.2
|
11.0
|
1.0
|
|
O
|
B:HOH546
|
4.3
|
12.1
|
1.0
|
|
O
|
C:LEU210
|
4.4
|
10.4
|
1.0
|
|
O
|
C:HOH539
|
4.4
|
13.4
|
1.0
|
|
CA
|
C:ALA206
|
4.4
|
8.9
|
1.0
|
|
O
|
C:HOH680
|
4.5
|
25.9
|
1.0
|
|
OD1
|
C:ASP132
|
4.6
|
12.0
|
1.0
|
|
HB1
|
C:ALA206
|
4.6
|
11.5
|
1.0
|
|
HB2
|
C:ASP132
|
4.6
|
11.4
|
1.0
|
|
HA
|
C:ASP132
|
4.6
|
10.2
|
1.0
|
|
O
|
B:HOH560
|
4.7
|
12.6
|
1.0
|
|
C
|
C:ALA206
|
4.8
|
9.2
|
1.0
|
|
HA2
|
C:GLY209
|
4.8
|
13.2
|
1.0
|
|
O
|
B:HOH557
|
4.8
|
46.3
|
1.0
|
|
O
|
C:HOH619
|
4.9
|
16.1
|
1.0
|
|
CB
|
C:ALA206
|
4.9
|
9.6
|
1.0
|
|
HA
|
C:LYS211
|
5.0
|
11.4
|
1.0
|
|
Sodium binding site 7 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 7 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na303
b:13.4
occ:1.00
|
O
|
D:HOH561
|
2.9
|
8.5
|
1.0
|
|
O
|
E:HOH560
|
2.9
|
8.5
|
1.0
|
|
O
|
D:MET125
|
2.9
|
8.8
|
1.0
|
|
O
|
E:MET125
|
2.9
|
9.0
|
1.0
|
|
O
|
D:PHE127
|
3.3
|
8.2
|
1.0
|
|
O
|
E:PHE127
|
3.3
|
8.3
|
1.0
|
|
HA
|
E:PRO128
|
3.4
|
9.5
|
1.0
|
|
HA
|
D:PRO128
|
3.4
|
9.4
|
1.0
|
|
HD3
|
D:ARG114
|
3.5
|
9.9
|
1.0
|
|
HD3
|
E:ARG114
|
3.5
|
9.5
|
1.0
|
|
HA
|
E:GLU126
|
3.8
|
10.3
|
0.3
|
|
O
|
D:GLU126
|
3.9
|
7.9
|
1.0
|
|
O
|
E:GLU126
|
3.9
|
8.3
|
0.7
|
|
C
|
D:PHE127
|
4.0
|
7.8
|
1.0
|
|
O
|
E:GLU126
|
4.0
|
8.1
|
0.3
|
|
C
|
E:PHE127
|
4.0
|
8.0
|
1.0
|
|
HA
|
D:GLU126
|
4.0
|
10.5
|
1.0
|
|
C
|
D:GLU126
|
4.0
|
7.9
|
1.0
|
|
C
|
E:GLU126
|
4.0
|
8.3
|
0.3
|
|
C
|
E:GLU126
|
4.1
|
8.4
|
0.7
|
|
HA
|
E:GLU126
|
4.1
|
10.3
|
0.7
|
|
HH11
|
D:ARG114
|
4.1
|
9.6
|
1.0
|
|
C
|
D:MET125
|
4.1
|
8.2
|
1.0
|
|
C
|
E:MET125
|
4.1
|
8.6
|
1.0
|
|
HH11
|
E:ARG114
|
4.1
|
9.5
|
1.0
|
|
HG3
|
D:MET125
|
4.2
|
11.0
|
1.0
|
|
HG3
|
E:MET125
|
4.2
|
11.2
|
1.0
|
|
CA
|
E:PRO128
|
4.2
|
7.9
|
1.0
|
|
CA
|
D:PRO128
|
4.3
|
7.8
|
1.0
|
|
CD
|
D:ARG114
|
4.3
|
8.2
|
1.0
|
|
CD
|
E:ARG114
|
4.3
|
7.9
|
1.0
|
|
HD2
|
D:ARG114
|
4.3
|
9.9
|
1.0
|
|
H
|
D:ALA129
|
4.3
|
9.4
|
1.0
|
|
HD2
|
E:ARG114
|
4.3
|
9.5
|
1.0
|
|
H
|
E:ALA129
|
4.4
|
9.4
|
1.0
|
|
CA
|
E:GLU126
|
4.4
|
8.6
|
0.3
|
|
CA
|
D:GLU126
|
4.4
|
8.7
|
1.0
|
|
N
|
D:PRO128
|
4.5
|
7.3
|
1.0
|
|
N
|
E:PRO128
|
4.5
|
7.8
|
1.0
|
|
CA
|
E:GLU126
|
4.5
|
8.6
|
0.7
|
|
N
|
D:PHE127
|
4.5
|
7.9
|
1.0
|
|
N
|
E:PHE127
|
4.5
|
7.9
|
1.0
|
|
HG3
|
D:ARG114
|
4.6
|
9.1
|
1.0
|
|
HG3
|
E:ARG114
|
4.6
|
9.3
|
1.0
|
|
N
|
E:GLU126
|
4.7
|
8.6
|
0.3
|
|
N
|
D:GLU126
|
4.8
|
8.4
|
1.0
|
|
N
|
E:GLU126
|
4.8
|
8.7
|
0.7
|
|
NH1
|
D:ARG114
|
4.8
|
8.0
|
1.0
|
|
NH1
|
E:ARG114
|
4.8
|
7.9
|
1.0
|
|
H
|
D:PHE127
|
4.9
|
9.4
|
1.0
|
|
H
|
E:PHE127
|
4.9
|
9.5
|
0.3
|
|
HB3
|
E:PRO128
|
4.9
|
10.2
|
1.0
|
|
H
|
E:PHE127
|
4.9
|
9.5
|
0.7
|
|
CA
|
D:PHE127
|
4.9
|
7.8
|
1.0
|
|
HB3
|
D:PRO128
|
4.9
|
10.2
|
1.0
|
|
CA
|
E:PHE127
|
4.9
|
8.2
|
1.0
|
|
N
|
D:ALA129
|
5.0
|
7.8
|
1.0
|
|
N
|
E:ALA129
|
5.0
|
7.8
|
1.0
|
|
Sodium binding site 8 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 8 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na304
b:29.5
occ:1.00
|
O
|
D:HOH547
|
2.2
|
62.0
|
1.0
|
|
OE1
|
D:GLN180
|
2.2
|
15.0
|
0.4
|
|
O
|
D:HOH543
|
2.2
|
46.7
|
1.0
|
|
O
|
B:HOH693
|
2.3
|
39.7
|
1.0
|
|
O
|
B:HOH439
|
2.3
|
28.6
|
1.0
|
|
O
|
D:HOH532
|
2.3
|
38.6
|
1.0
|
|
OE1
|
D:GLN180
|
2.4
|
15.5
|
0.6
|
|
HE22
|
D:GLN180
|
2.8
|
17.2
|
0.6
|
|
CD
|
D:GLN180
|
3.2
|
14.1
|
0.6
|
|
CD
|
D:GLN180
|
3.2
|
14.4
|
0.4
|
|
NE2
|
D:GLN180
|
3.3
|
14.3
|
0.6
|
|
NE2
|
D:GLN180
|
3.5
|
14.9
|
0.4
|
|
HG3
|
D:ARG177
|
3.9
|
18.0
|
1.0
|
|
HA
|
D:ARG177
|
3.9
|
13.0
|
1.0
|
|
HE21
|
D:GLN180
|
4.1
|
17.2
|
0.6
|
|
OE1
|
B:GLU185
|
4.2
|
12.2
|
0.7
|
|
O
|
B:HOH711
|
4.3
|
15.7
|
1.0
|
|
O
|
D:HOH403
|
4.3
|
17.5
|
0.5
|
|
HB2
|
D:ARG177
|
4.3
|
15.7
|
1.0
|
|
O
|
D:HOH524
|
4.3
|
34.1
|
1.0
|
|
O
|
B:HOH511
|
4.4
|
17.3
|
1.0
|
|
CG
|
D:GLN180
|
4.6
|
13.3
|
0.4
|
|
CG
|
D:GLN180
|
4.6
|
13.2
|
0.6
|
|
O
|
B:HOH504
|
4.6
|
31.3
|
1.0
|
|
HB2
|
D:GLN180
|
4.6
|
15.1
|
0.4
|
|
HB2
|
D:GLN180
|
4.6
|
15.2
|
0.6
|
|
CG
|
D:ARG177
|
4.7
|
15.0
|
1.0
|
|
CA
|
D:ARG177
|
4.8
|
10.8
|
1.0
|
|
CB
|
D:ARG177
|
4.8
|
13.1
|
1.0
|
|
HG3
|
D:GLN180
|
4.9
|
16.0
|
0.4
|
|
HB3
|
D:GLN180
|
4.9
|
15.1
|
0.4
|
|
HB3
|
D:GLN180
|
4.9
|
15.2
|
0.6
|
|
HG3
|
D:GLN180
|
4.9
|
15.8
|
0.6
|
|
CB
|
D:GLN180
|
5.0
|
12.6
|
0.4
|
|
CB
|
D:GLN180
|
5.0
|
12.6
|
0.6
|
|
HE
|
D:ARG177
|
5.0
|
18.7
|
1.0
|
|
Sodium binding site 9 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 9 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na304
b:74.5
occ:1.00
|
O
|
E:HOH411
|
2.2
|
29.6
|
1.0
|
|
O
|
E:HOH538
|
2.2
|
33.2
|
1.0
|
|
O
|
E:HOH605
|
2.2
|
18.2
|
1.0
|
|
O
|
E:HOH511
|
2.3
|
22.2
|
1.0
|
|
HA
|
E:ALA206
|
3.6
|
11.7
|
1.0
|
|
O
|
D:HOH483
|
3.9
|
27.6
|
1.0
|
|
O
|
E:HOH503
|
4.1
|
10.9
|
1.0
|
|
O
|
E:ALA206
|
4.3
|
11.8
|
1.0
|
|
O
|
D:HOH507
|
4.3
|
14.2
|
1.0
|
|
O
|
E:LEU210
|
4.3
|
11.5
|
1.0
|
|
O
|
E:HOH588
|
4.3
|
29.3
|
1.0
|
|
O
|
E:HOH523
|
4.4
|
14.5
|
1.0
|
|
CA
|
E:ALA206
|
4.5
|
9.8
|
1.0
|
|
OD1
|
E:ASP132
|
4.6
|
14.3
|
1.0
|
|
HB2
|
E:ASP132
|
4.6
|
13.1
|
1.0
|
|
HA
|
E:ASP132
|
4.6
|
11.8
|
1.0
|
|
HB1
|
E:ALA206
|
4.7
|
12.5
|
1.0
|
|
HA2
|
E:GLY209
|
4.7
|
14.1
|
1.0
|
|
O
|
D:HOH517
|
4.8
|
14.2
|
1.0
|
|
HG2
|
E:LYS211
|
4.8
|
17.9
|
0.5
|
|
C
|
E:ALA206
|
4.8
|
10.6
|
1.0
|
|
O
|
E:HOH563
|
4.9
|
17.7
|
1.0
|
|
HA
|
E:LYS211
|
4.9
|
12.5
|
0.5
|
|
HA
|
E:LYS211
|
4.9
|
12.4
|
0.5
|
|
HG2
|
E:LYS211
|
5.0
|
17.2
|
0.5
|
|
Sodium binding site 10 out
of 11 in 6z9z
Go back to
Sodium Binding Sites List in 6z9z
Sodium binding site 10 out
of 11 in the Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Atomic Resolution X-Ray Structure of the Uridine Phosphorylase From Vibrio Cholerae on Crystals Grown Under Microgravity within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na305
b:26.8
occ:1.00
|
OE1
|
E:GLN180
|
2.2
|
14.8
|
0.4
|
|
O
|
A:HOH685
|
2.2
|
33.6
|
1.0
|
|
O
|
E:HOH567
|
2.3
|
60.9
|
1.0
|
|
O
|
A:HOH447
|
2.3
|
30.1
|
1.0
|
|
O
|
E:HOH579
|
2.3
|
52.8
|
1.0
|
|
O
|
E:HOH510
|
2.4
|
37.7
|
1.0
|
|
OE1
|
E:GLN180
|
2.4
|
16.9
|
0.6
|
|
HE22
|
E:GLN180
|
2.9
|
18.6
|
0.6
|
|
CD
|
E:GLN180
|
3.2
|
14.3
|
0.4
|
|
CD
|
E:GLN180
|
3.2
|
15.7
|
0.6
|
|
NE2
|
E:GLN180
|
3.4
|
15.5
|
0.6
|
|
NE2
|
E:GLN180
|
3.5
|
14.1
|
0.4
|
|
HG3
|
E:ARG177
|
3.9
|
17.7
|
1.0
|
|
HA
|
E:ARG177
|
3.9
|
12.4
|
1.0
|
|
OE1
|
A:GLU185
|
4.2
|
12.4
|
0.7
|
|
HE21
|
E:GLN180
|
4.2
|
18.6
|
0.6
|
|
O
|
E:HOH553
|
4.3
|
32.9
|
1.0
|
|
HB2
|
E:ARG177
|
4.3
|
14.8
|
1.0
|
|
O
|
A:HOH556
|
4.3
|
17.5
|
1.0
|
|
O
|
A:HOH530
|
4.3
|
33.1
|
1.0
|
|
O
|
A:HOH494
|
4.4
|
18.2
|
1.0
|
|
CG
|
E:GLN180
|
4.5
|
13.8
|
0.4
|
|
HB2
|
E:GLN180
|
4.6
|
16.0
|
0.6
|
|
O
|
E:HOH403
|
4.6
|
20.0
|
0.5
|
|
HB2
|
E:GLN180
|
4.6
|
15.4
|
0.4
|
|
CG
|
E:GLN180
|
4.6
|
14.6
|
0.6
|
|
CG
|
E:ARG177
|
4.7
|
14.8
|
1.0
|
|
CA
|
E:ARG177
|
4.8
|
10.4
|
1.0
|
|
CB
|
E:ARG177
|
4.8
|
12.3
|
1.0
|
|
HG3
|
E:GLN180
|
4.8
|
16.6
|
0.4
|
|
HB3
|
E:GLN180
|
4.8
|
15.4
|
0.4
|
|
HB3
|
E:GLN180
|
4.9
|
16.0
|
0.6
|
|
CB
|
E:GLN180
|
4.9
|
12.9
|
0.4
|
|
CB
|
E:GLN180
|
5.0
|
13.3
|
0.6
|
|
HE
|
E:ARG177
|
5.0
|
20.1
|
1.0
|
|
HG3
|
E:GLN180
|
5.0
|
17.5
|
0.6
|
|
Reference:
P.A.Eistrikh-Heller,
S.V.Rubinsky,
V.R.Samygina,
A.G.Gabdulkhakov,
A.S.Mironov,
A.A.Lashkov.
Crystallization Under Microgravity Conditions and Atomic Resolution X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae To Be Published.
Page generated: Mon Jul 12 15:53:07 2021
|
