Sodium in PDB 5ue6: Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
Protein crystallography data
The structure of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122, PDB code: 5ue6
was solved by
A.Hamza,
Z.A.Williamson,
R.W.Reed,
A.E.Sikora,
K.V.Korotkov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
83.68 /
2.35
|
|
Space group
|
I 41 2 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.340,
177.340,
449.460,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
23.6 /
25.9
|
Other elements in 5ue6:
The structure of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
(pdb code 5ue6). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the
Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122, PDB code: 5ue6:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Sodium binding site 1 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 1 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:27.5
occ:1.00
|
O
|
A:LYS317
|
2.3
|
32.7
|
1.0
|
|
O
|
A:HOH645
|
2.5
|
27.8
|
1.0
|
|
OE1
|
A:GLU284
|
2.6
|
32.3
|
1.0
|
|
OD2
|
A:ASP319
|
2.7
|
42.2
|
1.0
|
|
O
|
C:HOH614
|
2.8
|
34.6
|
1.0
|
|
OE2
|
A:GLU284
|
3.2
|
36.0
|
1.0
|
|
HG21
|
C:THR142
|
3.3
|
47.8
|
1.0
|
|
CD
|
A:GLU284
|
3.3
|
33.6
|
1.0
|
|
C
|
A:LYS317
|
3.5
|
31.6
|
1.0
|
|
HB3
|
A:LYS317
|
3.5
|
43.7
|
1.0
|
|
H
|
A:LYS317
|
3.5
|
41.5
|
1.0
|
|
HG23
|
C:THR142
|
3.6
|
47.8
|
1.0
|
|
CG
|
A:ASP319
|
3.7
|
45.1
|
1.0
|
|
CG2
|
C:THR142
|
3.9
|
39.7
|
1.0
|
|
HB2
|
A:PHE316
|
4.0
|
37.5
|
1.0
|
|
N
|
A:LYS317
|
4.1
|
34.5
|
1.0
|
|
H
|
A:ASP319
|
4.1
|
47.7
|
1.0
|
|
OD1
|
A:ASP319
|
4.2
|
47.4
|
1.0
|
|
CA
|
A:LYS317
|
4.2
|
34.6
|
1.0
|
|
HA
|
A:VAL318
|
4.2
|
45.2
|
1.0
|
|
CB
|
A:LYS317
|
4.3
|
36.3
|
1.0
|
|
H
|
A:ILE285
|
4.3
|
34.0
|
1.0
|
|
OE1
|
C:GLN167
|
4.3
|
32.9
|
1.0
|
|
OG1
|
C:THR142
|
4.4
|
35.2
|
1.0
|
|
N
|
A:VAL318
|
4.6
|
34.8
|
1.0
|
|
N
|
A:ASP319
|
4.6
|
39.7
|
1.0
|
|
HG22
|
C:THR142
|
4.6
|
47.8
|
1.0
|
|
HG2
|
A:LYS317
|
4.6
|
45.0
|
1.0
|
|
HD12
|
C:LEU166
|
4.7
|
48.2
|
1.0
|
|
HD2
|
A:PHE316
|
4.7
|
34.5
|
1.0
|
|
HD13
|
C:LEU166
|
4.7
|
48.2
|
1.0
|
|
HB2
|
A:ASP319
|
4.7
|
52.6
|
1.0
|
|
HA
|
A:GLU284
|
4.7
|
34.2
|
1.0
|
|
CB
|
A:ASP319
|
4.8
|
43.8
|
1.0
|
|
CG
|
A:GLU284
|
4.8
|
32.1
|
1.0
|
|
CA
|
A:VAL318
|
4.8
|
37.6
|
1.0
|
|
OD2
|
A:ASP287
|
4.8
|
31.2
|
1.0
|
|
O
|
A:ILE285
|
4.8
|
32.5
|
1.0
|
|
O
|
A:HOH653
|
4.8
|
35.7
|
1.0
|
|
CB
|
C:THR142
|
4.8
|
37.1
|
1.0
|
|
OD1
|
A:ASP287
|
4.9
|
33.3
|
1.0
|
|
CB
|
A:PHE316
|
4.9
|
31.1
|
1.0
|
|
HB2
|
A:LYS317
|
5.0
|
43.7
|
1.0
|
|
Sodium binding site 2 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 2 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:32.4
occ:1.00
|
O
|
B:HOH706
|
2.3
|
36.1
|
1.0
|
|
O
|
B:LYS317
|
2.4
|
43.0
|
1.0
|
|
O
|
A:HOH615
|
2.5
|
42.6
|
1.0
|
|
OE1
|
B:GLU284
|
2.5
|
41.5
|
1.0
|
|
O
|
B:HOH688
|
2.6
|
39.7
|
1.0
|
|
OD2
|
B:ASP319
|
2.6
|
52.6
|
1.0
|
|
HG21
|
A:THR142
|
2.9
|
48.1
|
1.0
|
|
OE2
|
B:GLU284
|
3.1
|
43.4
|
1.0
|
|
CD
|
B:GLU284
|
3.2
|
41.0
|
1.0
|
|
HG23
|
A:THR142
|
3.3
|
48.1
|
1.0
|
|
CG2
|
A:THR142
|
3.6
|
40.0
|
1.0
|
|
CG
|
B:ASP319
|
3.6
|
57.9
|
1.0
|
|
C
|
B:LYS317
|
3.6
|
39.4
|
1.0
|
|
H
|
B:LYS317
|
3.8
|
42.5
|
1.0
|
|
H
|
B:ASP319
|
3.8
|
53.0
|
1.0
|
|
HA
|
B:VAL318
|
4.0
|
52.0
|
1.0
|
|
HB2
|
B:PHE316
|
4.1
|
40.7
|
1.0
|
|
OD1
|
B:ASP319
|
4.2
|
59.9
|
1.0
|
|
HB3
|
B:LYS317
|
4.2
|
48.9
|
1.0
|
|
H
|
B:ILE285
|
4.2
|
43.1
|
1.0
|
|
OG1
|
A:THR142
|
4.2
|
40.1
|
1.0
|
|
HG22
|
A:THR142
|
4.3
|
48.1
|
1.0
|
|
N
|
B:LYS317
|
4.3
|
35.4
|
1.0
|
|
OE1
|
A:GLN167
|
4.3
|
44.8
|
1.0
|
|
N
|
B:ASP319
|
4.4
|
44.1
|
1.0
|
|
CA
|
B:LYS317
|
4.5
|
37.0
|
1.0
|
|
HB2
|
B:ASP319
|
4.5
|
58.5
|
1.0
|
|
HD12
|
A:LEU166
|
4.5
|
43.9
|
1.0
|
|
O
|
B:HOH621
|
4.5
|
37.9
|
1.0
|
|
CB
|
A:THR142
|
4.6
|
36.9
|
1.0
|
|
N
|
B:VAL318
|
4.6
|
40.0
|
1.0
|
|
HA
|
B:GLU284
|
4.6
|
42.4
|
1.0
|
|
HD13
|
A:LEU166
|
4.6
|
43.9
|
1.0
|
|
HD2
|
B:PHE316
|
4.6
|
42.6
|
1.0
|
|
CB
|
B:ASP319
|
4.6
|
48.7
|
1.0
|
|
CA
|
B:VAL318
|
4.7
|
43.3
|
1.0
|
|
CG
|
B:GLU284
|
4.7
|
42.0
|
1.0
|
|
CB
|
B:LYS317
|
4.9
|
40.7
|
1.0
|
|
O
|
B:ILE285
|
4.9
|
31.8
|
1.0
|
|
CD1
|
A:LEU166
|
5.0
|
36.5
|
1.0
|
|
HB3
|
B:GLU284
|
5.0
|
44.5
|
1.0
|
|
Sodium binding site 3 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 3 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:30.4
occ:1.00
|
OE1
|
C:GLU284
|
2.4
|
35.3
|
1.0
|
|
O
|
C:HOH644
|
2.5
|
32.6
|
1.0
|
|
O
|
C:LYS317
|
2.5
|
40.9
|
1.0
|
|
OD2
|
C:ASP319
|
2.9
|
44.2
|
1.0
|
|
OE2
|
C:GLU284
|
3.0
|
38.5
|
1.0
|
|
CD
|
C:GLU284
|
3.1
|
34.5
|
1.0
|
|
HG21
|
B:THR142
|
3.2
|
48.0
|
1.0
|
|
HG23
|
B:THR142
|
3.4
|
48.0
|
1.0
|
|
H
|
C:LYS317
|
3.6
|
42.9
|
1.0
|
|
C
|
C:LYS317
|
3.7
|
38.3
|
1.0
|
|
CG2
|
B:THR142
|
3.8
|
39.9
|
1.0
|
|
HB2
|
C:PHE316
|
3.8
|
39.1
|
1.0
|
|
CG
|
C:ASP319
|
3.9
|
45.3
|
1.0
|
|
H
|
C:ILE285
|
4.1
|
35.6
|
1.0
|
|
H
|
C:ASP319
|
4.1
|
49.4
|
1.0
|
|
HB3
|
C:LYS317
|
4.1
|
49.1
|
1.0
|
|
HA
|
C:VAL318
|
4.2
|
49.4
|
1.0
|
|
N
|
C:LYS317
|
4.2
|
35.7
|
1.0
|
|
OE1
|
B:GLN167
|
4.3
|
34.0
|
1.0
|
|
OG1
|
B:THR142
|
4.3
|
42.8
|
1.0
|
|
OD1
|
C:ASP319
|
4.4
|
47.2
|
1.0
|
|
CA
|
C:LYS317
|
4.4
|
40.2
|
1.0
|
|
HG22
|
B:THR142
|
4.4
|
48.0
|
1.0
|
|
HD2
|
C:PHE316
|
4.5
|
39.2
|
1.0
|
|
HA
|
C:GLU284
|
4.5
|
37.6
|
1.0
|
|
CG
|
C:GLU284
|
4.6
|
34.6
|
1.0
|
|
O
|
C:ILE285
|
4.6
|
31.5
|
1.0
|
|
N
|
C:VAL318
|
4.7
|
36.2
|
1.0
|
|
N
|
C:ASP319
|
4.7
|
41.1
|
1.0
|
|
CB
|
B:THR142
|
4.7
|
40.8
|
1.0
|
|
HD12
|
B:LEU166
|
4.7
|
47.4
|
1.0
|
|
CB
|
C:PHE316
|
4.8
|
32.5
|
1.0
|
|
HB2
|
C:ASP319
|
4.8
|
53.4
|
1.0
|
|
CB
|
C:LYS317
|
4.8
|
40.8
|
1.0
|
|
CA
|
C:VAL318
|
4.8
|
41.1
|
1.0
|
|
OD2
|
C:ASP287
|
4.8
|
34.6
|
1.0
|
|
HB3
|
C:GLU284
|
4.8
|
44.0
|
1.0
|
|
HD13
|
B:LEU166
|
4.9
|
47.4
|
1.0
|
|
OD1
|
C:ASP287
|
4.9
|
37.0
|
1.0
|
|
CB
|
C:ASP319
|
4.9
|
44.5
|
1.0
|
|
N
|
C:ILE285
|
4.9
|
29.6
|
1.0
|
|
HG3
|
C:GLU284
|
4.9
|
41.6
|
1.0
|
|
O
|
C:HOH610
|
5.0
|
35.9
|
1.0
|
|
Sodium binding site 4 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 4 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na503
b:45.4
occ:1.00
|
O
|
D:HOH644
|
2.3
|
42.7
|
1.0
|
|
O
|
D:LYS317
|
2.3
|
49.8
|
1.0
|
|
OE1
|
D:GLU284
|
2.6
|
46.4
|
1.0
|
|
OD2
|
D:ASP319
|
2.7
|
62.0
|
1.0
|
|
HG21
|
F:THR142
|
2.9
|
61.5
|
1.0
|
|
OE2
|
D:GLU284
|
3.0
|
49.6
|
1.0
|
|
HG23
|
F:THR142
|
3.2
|
61.5
|
1.0
|
|
CD
|
D:GLU284
|
3.2
|
47.9
|
1.0
|
|
CG2
|
F:THR142
|
3.5
|
51.2
|
1.0
|
|
C
|
D:LYS317
|
3.5
|
47.5
|
1.0
|
|
CG
|
D:ASP319
|
3.6
|
62.2
|
1.0
|
|
H
|
D:ASP319
|
3.8
|
64.7
|
1.0
|
|
H
|
D:LYS317
|
3.8
|
57.1
|
1.0
|
|
HA
|
D:VAL318
|
3.9
|
62.3
|
1.0
|
|
HG22
|
F:THR142
|
4.1
|
61.5
|
1.0
|
|
HB3
|
D:LYS317
|
4.2
|
55.4
|
1.0
|
|
HB2
|
D:PHE316
|
4.2
|
50.1
|
1.0
|
|
OD1
|
D:ASP319
|
4.2
|
59.9
|
1.0
|
|
OG1
|
F:THR142
|
4.3
|
47.8
|
1.0
|
|
N
|
D:LYS317
|
4.3
|
47.5
|
1.0
|
|
N
|
D:ASP319
|
4.3
|
53.8
|
1.0
|
|
H
|
D:ILE285
|
4.4
|
44.3
|
1.0
|
|
CA
|
D:LYS317
|
4.4
|
46.6
|
1.0
|
|
HB2
|
D:ASP319
|
4.4
|
75.3
|
1.0
|
|
HD12
|
F:LEU166
|
4.5
|
52.5
|
1.0
|
|
N
|
D:VAL318
|
4.5
|
48.5
|
1.0
|
|
CB
|
F:THR142
|
4.5
|
45.9
|
1.0
|
|
HD13
|
F:LEU166
|
4.6
|
52.5
|
1.0
|
|
CA
|
D:VAL318
|
4.6
|
51.8
|
1.0
|
|
HA
|
D:GLU284
|
4.6
|
48.0
|
1.0
|
|
CB
|
D:ASP319
|
4.6
|
62.7
|
1.0
|
|
HD2
|
D:PHE316
|
4.6
|
54.4
|
1.0
|
|
CG
|
D:GLU284
|
4.7
|
44.9
|
1.0
|
|
OE1
|
F:GLN167
|
4.8
|
46.8
|
1.0
|
|
CB
|
D:LYS317
|
4.8
|
46.1
|
1.0
|
|
C
|
D:VAL318
|
4.9
|
51.5
|
1.0
|
|
CD1
|
F:LEU166
|
4.9
|
43.7
|
1.0
|
|
Sodium binding site 5 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 5 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na503
b:42.4
occ:1.00
|
O
|
E:HOH636
|
2.4
|
43.1
|
1.0
|
|
O
|
E:LYS317
|
2.5
|
47.7
|
1.0
|
|
OE1
|
E:GLU284
|
2.8
|
46.4
|
1.0
|
|
OD2
|
E:ASP319
|
2.9
|
65.6
|
1.0
|
|
HG21
|
D:THR142
|
3.0
|
69.2
|
1.0
|
|
HG23
|
D:THR142
|
3.5
|
69.2
|
1.0
|
|
OE2
|
E:GLU284
|
3.5
|
48.2
|
1.0
|
|
CD
|
E:GLU284
|
3.6
|
45.1
|
1.0
|
|
H
|
E:LYS317
|
3.6
|
49.4
|
1.0
|
|
HG1
|
D:THR142
|
3.7
|
66.7
|
1.0
|
|
C
|
E:LYS317
|
3.7
|
44.1
|
1.0
|
|
CG2
|
D:THR142
|
3.7
|
57.6
|
1.0
|
|
CG
|
E:ASP319
|
3.9
|
64.7
|
1.0
|
|
HB2
|
E:PHE316
|
4.0
|
51.6
|
1.0
|
|
HB3
|
E:LYS317
|
4.0
|
49.0
|
1.0
|
|
OE1
|
D:GLN167
|
4.1
|
45.7
|
1.0
|
|
N
|
E:LYS317
|
4.2
|
41.1
|
1.0
|
|
H
|
E:ASP319
|
4.2
|
58.9
|
1.0
|
|
OG1
|
D:THR142
|
4.2
|
55.5
|
1.0
|
|
H
|
E:ILE285
|
4.2
|
51.5
|
1.0
|
|
HA
|
E:VAL318
|
4.3
|
55.8
|
1.0
|
|
CA
|
E:LYS317
|
4.4
|
42.0
|
1.0
|
|
HG22
|
D:THR142
|
4.4
|
69.2
|
1.0
|
|
HD12
|
D:LEU166
|
4.5
|
65.5
|
1.0
|
|
OD1
|
E:ASP319
|
4.5
|
62.0
|
1.0
|
|
HD13
|
D:LEU166
|
4.5
|
65.5
|
1.0
|
|
CB
|
D:THR142
|
4.6
|
57.9
|
1.0
|
|
N
|
E:VAL318
|
4.7
|
44.3
|
1.0
|
|
CB
|
E:LYS317
|
4.7
|
40.8
|
1.0
|
|
O
|
E:ILE285
|
4.7
|
41.1
|
1.0
|
|
N
|
E:ASP319
|
4.7
|
49.0
|
1.0
|
|
HA
|
E:GLU284
|
4.7
|
50.6
|
1.0
|
|
HD2
|
E:PHE316
|
4.8
|
50.0
|
1.0
|
|
HB2
|
E:ASP319
|
4.8
|
73.3
|
1.0
|
|
OD2
|
E:ASP287
|
4.8
|
43.7
|
1.0
|
|
OD1
|
E:ASP287
|
4.8
|
46.5
|
1.0
|
|
CA
|
E:VAL318
|
4.9
|
46.4
|
1.0
|
|
CB
|
E:PHE316
|
4.9
|
42.9
|
1.0
|
|
CB
|
E:ASP319
|
5.0
|
61.0
|
1.0
|
|
CD1
|
D:LEU166
|
5.0
|
54.5
|
1.0
|
|
Sodium binding site 6 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 6 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na502
b:39.7
occ:1.00
|
O
|
F:HOH629
|
2.3
|
36.8
|
1.0
|
|
O
|
F:LYS317
|
2.5
|
49.5
|
1.0
|
|
OE1
|
F:GLU284
|
2.5
|
43.6
|
1.0
|
|
OD2
|
F:ASP319
|
2.8
|
51.5
|
1.0
|
|
HG21
|
E:THR142
|
3.0
|
61.1
|
1.0
|
|
OE2
|
F:GLU284
|
3.1
|
50.5
|
1.0
|
|
CD
|
F:GLU284
|
3.2
|
44.8
|
1.0
|
|
HG23
|
E:THR142
|
3.4
|
61.1
|
1.0
|
|
CG2
|
E:THR142
|
3.6
|
50.9
|
1.0
|
|
C
|
F:LYS317
|
3.7
|
49.1
|
1.0
|
|
HG1
|
E:THR142
|
3.7
|
61.7
|
1.0
|
|
H
|
F:LYS317
|
3.7
|
53.7
|
1.0
|
|
CG
|
F:ASP319
|
3.7
|
53.4
|
1.0
|
|
HB2
|
F:PHE316
|
3.9
|
50.4
|
1.0
|
|
H
|
F:ASP319
|
4.0
|
62.0
|
1.0
|
|
HA
|
F:VAL318
|
4.1
|
60.6
|
1.0
|
|
H
|
F:ILE285
|
4.1
|
42.4
|
1.0
|
|
HB3
|
F:LYS317
|
4.2
|
67.8
|
1.0
|
|
OG1
|
E:THR142
|
4.2
|
51.3
|
1.0
|
|
N
|
F:LYS317
|
4.3
|
44.7
|
1.0
|
|
OD1
|
F:ASP319
|
4.3
|
55.4
|
1.0
|
|
HG22
|
E:THR142
|
4.3
|
61.1
|
1.0
|
|
OE1
|
E:GLN167
|
4.4
|
42.0
|
1.0
|
|
CA
|
F:LYS317
|
4.5
|
49.5
|
1.0
|
|
HA
|
F:GLU284
|
4.5
|
49.7
|
1.0
|
|
N
|
F:ASP319
|
4.6
|
51.6
|
1.0
|
|
CB
|
E:THR142
|
4.6
|
49.1
|
1.0
|
|
HD13
|
E:LEU166
|
4.6
|
55.8
|
1.0
|
|
HD2
|
F:PHE316
|
4.6
|
48.9
|
1.0
|
|
HD12
|
E:LEU166
|
4.6
|
55.8
|
1.0
|
|
N
|
F:VAL318
|
4.7
|
48.2
|
1.0
|
|
CG
|
F:GLU284
|
4.7
|
43.5
|
1.0
|
|
HB2
|
F:ASP319
|
4.7
|
66.0
|
1.0
|
|
CA
|
F:VAL318
|
4.8
|
50.5
|
1.0
|
|
CB
|
F:ASP319
|
4.8
|
54.9
|
1.0
|
|
O
|
F:ILE285
|
4.8
|
38.6
|
1.0
|
|
CB
|
F:LYS317
|
4.8
|
56.4
|
1.0
|
|
CB
|
F:PHE316
|
4.9
|
41.9
|
1.0
|
|
O
|
F:HOH607
|
4.9
|
49.5
|
1.0
|
|
HB3
|
F:GLU284
|
4.9
|
53.0
|
1.0
|
|
N
|
F:ILE285
|
5.0
|
35.3
|
1.0
|
|
Sodium binding site 7 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 7 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na503
b:37.3
occ:1.00
|
O
|
G:HOH667
|
2.3
|
38.4
|
1.0
|
|
OE1
|
G:GLU284
|
2.5
|
36.4
|
1.0
|
|
O
|
G:HOH687
|
2.6
|
43.1
|
1.0
|
|
O
|
G:LYS317
|
2.6
|
41.6
|
1.0
|
|
OD2
|
G:ASP319
|
2.7
|
48.3
|
1.0
|
|
HG21
|
I:THR142
|
3.1
|
56.7
|
1.0
|
|
OE2
|
G:GLU284
|
3.2
|
43.8
|
1.0
|
|
CD
|
G:GLU284
|
3.2
|
39.1
|
1.0
|
|
HG23
|
I:THR142
|
3.5
|
56.7
|
1.0
|
|
H
|
G:LYS317
|
3.6
|
45.4
|
1.0
|
|
CG
|
G:ASP319
|
3.7
|
50.0
|
1.0
|
|
CG2
|
I:THR142
|
3.8
|
47.2
|
1.0
|
|
C
|
G:LYS317
|
3.8
|
40.5
|
1.0
|
|
HB3
|
G:LYS317
|
3.8
|
49.3
|
1.0
|
|
HB2
|
G:PHE316
|
4.1
|
42.3
|
1.0
|
|
OG1
|
I:THR142
|
4.2
|
44.6
|
1.0
|
|
OE1
|
I:GLN167
|
4.2
|
36.6
|
1.0
|
|
H
|
G:ILE285
|
4.2
|
41.2
|
1.0
|
|
N
|
G:LYS317
|
4.2
|
37.7
|
1.0
|
|
OD1
|
G:ASP319
|
4.2
|
52.5
|
1.0
|
|
H
|
G:ASP319
|
4.3
|
55.2
|
1.0
|
|
HD12
|
I:LEU166
|
4.4
|
64.2
|
1.0
|
|
HA
|
G:VAL318
|
4.4
|
51.8
|
1.0
|
|
CA
|
G:LYS317
|
4.4
|
39.3
|
1.0
|
|
HD13
|
I:LEU166
|
4.5
|
64.2
|
1.0
|
|
HG22
|
I:THR142
|
4.5
|
56.7
|
1.0
|
|
CB
|
G:LYS317
|
4.6
|
41.0
|
1.0
|
|
CB
|
I:THR142
|
4.6
|
46.0
|
1.0
|
|
HA
|
G:GLU284
|
4.6
|
36.6
|
1.0
|
|
HE2
|
G:LYS317
|
4.7
|
59.1
|
1.0
|
|
CG
|
G:GLU284
|
4.7
|
34.6
|
1.0
|
|
HB2
|
G:ASP319
|
4.8
|
60.2
|
1.0
|
|
O
|
G:ILE285
|
4.8
|
35.5
|
1.0
|
|
N
|
G:ASP319
|
4.8
|
45.9
|
1.0
|
|
OD1
|
G:ASP287
|
4.8
|
35.4
|
1.0
|
|
OD2
|
G:ASP287
|
4.8
|
34.2
|
1.0
|
|
N
|
G:VAL318
|
4.8
|
45.3
|
1.0
|
|
HD2
|
G:PHE316
|
4.8
|
41.1
|
1.0
|
|
CB
|
G:ASP319
|
4.9
|
50.1
|
1.0
|
|
CD1
|
I:LEU166
|
4.9
|
53.4
|
1.0
|
|
HG1
|
I:THR142
|
4.9
|
53.6
|
1.0
|
|
HB3
|
G:GLU284
|
5.0
|
38.5
|
1.0
|
|
Sodium binding site 8 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 8 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na503
b:34.8
occ:1.00
|
O
|
H:HOH656
|
2.3
|
34.5
|
1.0
|
|
O
|
H:LYS317
|
2.4
|
46.1
|
1.0
|
|
O
|
G:HOH619
|
2.5
|
39.0
|
1.0
|
|
OE1
|
H:GLU284
|
2.6
|
41.1
|
1.0
|
|
OD2
|
H:ASP319
|
2.7
|
50.5
|
1.0
|
|
HG21
|
G:THR142
|
2.8
|
52.1
|
1.0
|
|
OE2
|
H:GLU284
|
3.2
|
48.2
|
1.0
|
|
CD
|
H:GLU284
|
3.3
|
41.5
|
1.0
|
|
HG23
|
G:THR142
|
3.3
|
52.1
|
1.0
|
|
CG2
|
G:THR142
|
3.5
|
43.4
|
1.0
|
|
C
|
H:LYS317
|
3.6
|
42.3
|
1.0
|
|
HG1
|
G:THR142
|
3.6
|
47.4
|
1.0
|
|
CG
|
H:ASP319
|
3.7
|
54.9
|
1.0
|
|
H
|
H:LYS317
|
3.7
|
47.5
|
1.0
|
|
H
|
H:ASP319
|
3.9
|
57.9
|
1.0
|
|
HA
|
H:VAL318
|
4.0
|
53.9
|
1.0
|
|
HB3
|
H:LYS317
|
4.0
|
54.3
|
1.0
|
|
HB2
|
H:PHE316
|
4.0
|
42.9
|
1.0
|
|
OG1
|
G:THR142
|
4.1
|
39.5
|
1.0
|
|
H
|
H:ILE285
|
4.1
|
42.1
|
1.0
|
|
HG22
|
G:THR142
|
4.2
|
52.1
|
1.0
|
|
OD1
|
H:ASP319
|
4.2
|
58.0
|
1.0
|
|
N
|
H:LYS317
|
4.2
|
39.5
|
1.0
|
|
OE1
|
G:GLN167
|
4.3
|
38.2
|
1.0
|
|
CA
|
H:LYS317
|
4.4
|
41.8
|
1.0
|
|
CB
|
G:THR142
|
4.4
|
39.5
|
1.0
|
|
N
|
H:ASP319
|
4.5
|
48.2
|
1.0
|
|
N
|
H:VAL318
|
4.5
|
40.0
|
1.0
|
|
HA
|
H:GLU284
|
4.5
|
41.7
|
1.0
|
|
HD2
|
H:PHE316
|
4.6
|
47.8
|
1.0
|
|
HD12
|
G:LEU166
|
4.6
|
49.6
|
1.0
|
|
HB2
|
H:ASP319
|
4.6
|
62.2
|
1.0
|
|
CA
|
H:VAL318
|
4.7
|
44.8
|
1.0
|
|
CB
|
H:LYS317
|
4.7
|
45.2
|
1.0
|
|
HD13
|
G:LEU166
|
4.7
|
49.6
|
1.0
|
|
CB
|
H:ASP319
|
4.7
|
51.8
|
1.0
|
|
O
|
H:ILE285
|
4.7
|
33.7
|
1.0
|
|
CG
|
H:GLU284
|
4.8
|
39.6
|
1.0
|
|
HB
|
G:THR142
|
4.9
|
47.5
|
1.0
|
|
N
|
H:ILE285
|
5.0
|
35.0
|
1.0
|
|
OD1
|
H:ASP287
|
5.0
|
35.1
|
1.0
|
|
OD2
|
H:ASP287
|
5.0
|
34.6
|
1.0
|
|
CB
|
H:PHE316
|
5.0
|
35.7
|
1.0
|
|
Sodium binding site 9 out
of 9 in 5ue6
Go back to
Sodium Binding Sites List in 5ue6
Sodium binding site 9 out
of 9 in the Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of Nitrite Reductase Ania From Neisseria Gonorrhoeae, Space Group I4122 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na502
b:41.0
occ:1.00
|
OE1
|
I:GLU284
|
2.4
|
41.1
|
1.0
|
|
O
|
I:LYS317
|
2.4
|
46.0
|
1.0
|
|
O
|
I:HOH619
|
2.5
|
36.8
|
1.0
|
|
CD
|
I:GLU284
|
3.1
|
44.7
|
1.0
|
|
OE2
|
I:GLU284
|
3.1
|
49.6
|
1.0
|
|
OD2
|
I:ASP319
|
3.2
|
53.1
|
1.0
|
|
HG21
|
H:THR142
|
3.3
|
55.9
|
1.0
|
|
H
|
I:LYS317
|
3.4
|
46.3
|
1.0
|
|
HG23
|
H:THR142
|
3.5
|
55.9
|
1.0
|
|
C
|
I:LYS317
|
3.6
|
45.2
|
1.0
|
|
HB2
|
I:PHE316
|
3.7
|
42.2
|
1.0
|
|
CG2
|
H:THR142
|
3.9
|
46.5
|
1.0
|
|
N
|
I:LYS317
|
4.0
|
38.5
|
1.0
|
|
H
|
I:ILE285
|
4.0
|
45.1
|
1.0
|
|
HB3
|
I:LYS317
|
4.1
|
55.5
|
1.0
|
|
CG
|
I:ASP319
|
4.1
|
55.4
|
1.0
|
|
HA
|
I:VAL318
|
4.2
|
57.3
|
1.0
|
|
OE1
|
H:GLN167
|
4.3
|
38.7
|
1.0
|
|
H
|
I:ASP319
|
4.3
|
58.7
|
1.0
|
|
CA
|
I:LYS317
|
4.3
|
44.9
|
1.0
|
|
OG1
|
H:THR142
|
4.4
|
48.0
|
1.0
|
|
HD2
|
I:PHE316
|
4.4
|
45.0
|
1.0
|
|
OD1
|
I:ASP319
|
4.5
|
58.0
|
1.0
|
|
O
|
I:ILE285
|
4.5
|
35.0
|
1.0
|
|
HA
|
I:GLU284
|
4.5
|
48.2
|
1.0
|
|
HG22
|
H:THR142
|
4.6
|
55.9
|
1.0
|
|
CG
|
I:GLU284
|
4.6
|
42.7
|
1.0
|
|
N
|
I:VAL318
|
4.6
|
44.2
|
1.0
|
|
CB
|
I:PHE316
|
4.6
|
35.1
|
1.0
|
|
CB
|
I:LYS317
|
4.7
|
46.1
|
1.0
|
|
OD2
|
I:ASP287
|
4.8
|
37.5
|
1.0
|
|
HB3
|
I:GLU284
|
4.8
|
48.2
|
1.0
|
|
CB
|
H:THR142
|
4.8
|
44.7
|
1.0
|
|
OD1
|
I:ASP287
|
4.8
|
39.0
|
1.0
|
|
N
|
I:ASP319
|
4.8
|
48.9
|
1.0
|
|
CA
|
I:VAL318
|
4.8
|
47.7
|
1.0
|
|
HD12
|
H:LEU166
|
4.9
|
55.9
|
1.0
|
|
N
|
I:ILE285
|
4.9
|
37.5
|
1.0
|
|
HD13
|
H:LEU166
|
4.9
|
55.9
|
1.0
|
|
C
|
I:PHE316
|
4.9
|
36.4
|
1.0
|
|
HG3
|
I:GLU284
|
5.0
|
51.3
|
1.0
|
|
Reference:
A.E.Sikora,
R.H.Mills,
J.V.Weber,
A.Hamza,
B.W.Passow,
A.Romaine,
Z.A.Williamson,
R.W.Reed,
R.A.Zielke,
K.V.Korotkov.
Peptide Inhibitors Targeting the Neisseria Gonorrhoeae Pivotal Anaerobic Respiration Factor Ania. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28584144
DOI: 10.1128/AAC.00186-17
Page generated: Tue Oct 8 00:30:38 2024
|
