Sodium in PDB 6f0z: Glic Mutant D88N
Protein crystallography data
The structure of Glic Mutant D88N, PDB code: 6f0z
was solved by
H.D.Hu,
M.Delarue,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.930,
133.600,
160.220,
90.00,
101.96,
90.00
|
R / Rfree (%)
|
21.7 /
22.6
|
Other elements in 6f0z:
The structure of Glic Mutant D88N also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Glic Mutant D88N
(pdb code 6f0z). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Glic Mutant D88N, PDB code: 6f0z:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 1 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:88.6
occ:1.00
|
O
|
A:ILE71
|
2.6
|
76.1
|
1.0
|
O
|
A:PRO68
|
3.2
|
88.5
|
1.0
|
N
|
A:ILE73
|
3.6
|
66.9
|
1.0
|
C
|
A:ILE71
|
3.7
|
76.5
|
1.0
|
CA
|
A:TRP72
|
3.9
|
69.4
|
1.0
|
CD1
|
A:ILE73
|
4.1
|
73.2
|
1.0
|
C
|
A:TRP72
|
4.1
|
72.3
|
1.0
|
CB
|
A:ILE73
|
4.2
|
65.5
|
1.0
|
C
|
A:PRO68
|
4.2
|
88.9
|
1.0
|
N
|
A:TRP72
|
4.2
|
71.3
|
1.0
|
CG1
|
A:ILE73
|
4.4
|
66.7
|
1.0
|
CA
|
A:ILE73
|
4.5
|
63.9
|
1.0
|
O
|
A:GLU69
|
4.7
|
88.8
|
1.0
|
O
|
A:ILE73
|
4.8
|
64.3
|
1.0
|
CA
|
A:ILE71
|
4.9
|
75.4
|
1.0
|
N
|
A:GLU69
|
5.0
|
85.9
|
1.0
|
CA
|
A:GLU69
|
5.0
|
85.8
|
1.0
|
C
|
A:GLU69
|
5.0
|
88.5
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 2 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na403
b:89.0
occ:1.00
|
O
|
B:ILE71
|
2.5
|
70.6
|
1.0
|
O
|
B:PRO68
|
3.0
|
79.1
|
1.0
|
N
|
B:ILE73
|
3.6
|
64.1
|
1.0
|
C
|
B:ILE71
|
3.6
|
70.0
|
1.0
|
CA
|
B:TRP72
|
3.9
|
65.1
|
1.0
|
C
|
B:TRP72
|
4.1
|
69.0
|
1.0
|
CD1
|
B:ILE73
|
4.1
|
73.8
|
1.0
|
C
|
B:PRO68
|
4.2
|
79.5
|
1.0
|
CB
|
B:ILE73
|
4.2
|
63.0
|
1.0
|
N
|
B:TRP72
|
4.2
|
65.9
|
1.0
|
CG1
|
B:ILE73
|
4.3
|
64.2
|
1.0
|
CA
|
B:ILE73
|
4.4
|
61.1
|
1.0
|
O
|
B:GLU69
|
4.7
|
82.5
|
1.0
|
O
|
B:ILE73
|
4.8
|
63.2
|
1.0
|
CA
|
B:ILE71
|
4.8
|
66.7
|
1.0
|
CA
|
B:GLU69
|
4.9
|
77.4
|
1.0
|
N
|
B:GLU69
|
4.9
|
77.1
|
1.0
|
N
|
B:ILE71
|
4.9
|
68.9
|
1.0
|
C
|
B:GLU69
|
4.9
|
81.0
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 3 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na401
b:0.1
occ:1.00
|
OG1
|
C:THR226
|
3.7
|
73.9
|
1.0
|
OG1
|
D:THR226
|
3.9
|
69.0
|
1.0
|
OG1
|
B:THR226
|
4.1
|
62.9
|
1.0
|
OG1
|
E:THR226
|
4.2
|
70.4
|
1.0
|
OG1
|
A:THR226
|
4.3
|
69.8
|
1.0
|
CG2
|
C:THR226
|
4.7
|
66.2
|
1.0
|
CB
|
C:THR226
|
4.8
|
69.4
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 4 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na404
b:81.9
occ:1.00
|
O
|
C:ILE71
|
2.5
|
75.3
|
1.0
|
O
|
C:PRO68
|
3.0
|
81.8
|
1.0
|
C
|
C:ILE71
|
3.7
|
76.1
|
1.0
|
N
|
C:ILE73
|
3.7
|
66.0
|
1.0
|
CA
|
C:TRP72
|
4.0
|
69.4
|
1.0
|
CD1
|
C:ILE73
|
4.1
|
72.0
|
1.0
|
C
|
C:PRO68
|
4.1
|
82.0
|
1.0
|
CB
|
C:ILE73
|
4.2
|
65.5
|
1.0
|
C
|
C:TRP72
|
4.2
|
71.8
|
1.0
|
N
|
C:TRP72
|
4.3
|
71.0
|
1.0
|
CG1
|
C:ILE73
|
4.3
|
66.4
|
1.0
|
CA
|
C:ILE73
|
4.5
|
63.5
|
1.0
|
O
|
C:GLU69
|
4.7
|
83.4
|
1.0
|
CA
|
C:GLU69
|
4.8
|
79.4
|
1.0
|
N
|
C:GLU69
|
4.8
|
79.1
|
1.0
|
C
|
C:GLU69
|
4.9
|
82.9
|
1.0
|
CA
|
C:ILE71
|
4.9
|
75.1
|
1.0
|
O
|
C:ILE73
|
4.9
|
65.5
|
1.0
|
N
|
C:ILE71
|
5.0
|
76.5
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 5 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na403
b:0.6
occ:1.00
|
O
|
D:ILE71
|
2.5
|
74.5
|
1.0
|
O
|
D:PRO68
|
3.0
|
88.8
|
1.0
|
C
|
D:ILE71
|
3.6
|
76.4
|
1.0
|
N
|
D:ILE73
|
3.7
|
68.7
|
1.0
|
CA
|
D:TRP72
|
3.9
|
71.2
|
1.0
|
C
|
D:PRO68
|
4.1
|
89.2
|
1.0
|
CD1
|
D:ILE73
|
4.1
|
73.2
|
1.0
|
C
|
D:TRP72
|
4.1
|
74.5
|
1.0
|
N
|
D:TRP72
|
4.2
|
72.6
|
1.0
|
CB
|
D:ILE73
|
4.2
|
69.2
|
1.0
|
CG1
|
D:ILE73
|
4.4
|
69.9
|
1.0
|
CA
|
D:ILE73
|
4.5
|
66.5
|
1.0
|
O
|
D:GLU69
|
4.7
|
88.5
|
1.0
|
CA
|
D:GLU69
|
4.8
|
86.0
|
1.0
|
N
|
D:GLU69
|
4.8
|
86.1
|
1.0
|
CA
|
D:ILE71
|
4.9
|
74.5
|
1.0
|
C
|
D:GLU69
|
4.9
|
88.2
|
1.0
|
O
|
D:ILE73
|
4.9
|
66.4
|
1.0
|
N
|
D:ILE71
|
4.9
|
77.8
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6f0z
Go back to
Sodium Binding Sites List in 6f0z
Sodium binding site 6 out
of 6 in the Glic Mutant D88N
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Glic Mutant D88N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na403
b:87.5
occ:1.00
|
O
|
E:ILE71
|
2.6
|
79.4
|
1.0
|
O
|
E:PRO68
|
3.1
|
88.5
|
1.0
|
N
|
E:ILE73
|
3.6
|
67.9
|
1.0
|
C
|
E:ILE71
|
3.7
|
79.1
|
1.0
|
CA
|
E:TRP72
|
4.0
|
70.9
|
1.0
|
CB
|
E:ILE73
|
4.1
|
67.5
|
1.0
|
CD1
|
E:ILE73
|
4.1
|
78.9
|
1.0
|
C
|
E:PRO68
|
4.1
|
89.7
|
1.0
|
C
|
E:TRP72
|
4.2
|
73.6
|
1.0
|
CG1
|
E:ILE73
|
4.3
|
68.8
|
1.0
|
N
|
E:TRP72
|
4.3
|
73.1
|
1.0
|
CA
|
E:ILE73
|
4.4
|
65.3
|
1.0
|
O
|
E:GLU69
|
4.8
|
92.2
|
1.0
|
O
|
E:ILE73
|
4.8
|
67.6
|
1.0
|
N
|
E:GLU69
|
4.9
|
87.4
|
1.0
|
CA
|
E:GLU69
|
4.9
|
87.7
|
1.0
|
CA
|
E:ILE71
|
5.0
|
78.3
|
1.0
|
C
|
E:GLU69
|
5.0
|
91.1
|
1.0
|
|
Reference:
A.Nemecz,
H.Hu,
Z.Fourati,
C.Van Renterghem,
M.Delarue,
P.J.Corringer.
Full Mutational Mapping of Titratable Residues Helps to Identify Proton-Sensors Involved in the Control of Channel Gating in the Gloeobacter Violaceus Pentameric Ligand-Gated Ion Channel. Plos Biol. V. 15 04470 2017.
ISSN: ESSN 1545-7885
PubMed: 29281623
DOI: 10.1371/JOURNAL.PBIO.2004470
Page generated: Tue Oct 8 08:35:56 2024
|