Sodium in PDB 6f0v: Glic Mutant E82Q
Protein crystallography data
The structure of Glic Mutant E82Q, PDB code: 6f0v
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)
|
48.97 /
2.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
179.340,
132.500,
158.310,
90.00,
101.21,
90.00
|
R / Rfree (%)
|
20.1 /
22.1
|
Other elements in 6f0v:
The structure of Glic Mutant E82Q also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Glic Mutant E82Q
(pdb code 6f0v). 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 E82Q, PDB code: 6f0v:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 1 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:84.4
occ:1.00
|
O
|
A:ILE71
|
2.6
|
85.2
|
1.0
|
O
|
A:PRO68
|
3.3
|
0.5
|
1.0
|
N
|
A:ILE73
|
3.6
|
77.8
|
1.0
|
C
|
A:ILE71
|
3.7
|
87.2
|
1.0
|
CD1
|
A:ILE73
|
4.0
|
84.9
|
1.0
|
CA
|
A:TRP72
|
4.0
|
81.2
|
1.0
|
C
|
A:TRP72
|
4.2
|
83.8
|
1.0
|
CB
|
A:ILE73
|
4.2
|
77.7
|
1.0
|
O
|
A:GLU69
|
4.2
|
0.1
|
1.0
|
C
|
A:PRO68
|
4.2
|
0.5
|
1.0
|
N
|
A:TRP72
|
4.3
|
83.0
|
1.0
|
CG1
|
A:ILE73
|
4.4
|
79.0
|
1.0
|
CA
|
A:ILE73
|
4.5
|
75.3
|
1.0
|
O
|
A:ILE73
|
4.8
|
76.3
|
1.0
|
C
|
A:GLU69
|
4.9
|
0.2
|
1.0
|
N
|
A:GLU69
|
5.0
|
98.1
|
1.0
|
CA
|
A:ILE71
|
5.0
|
86.7
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 2 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na404
b:86.3
occ:1.00
|
O
|
B:ILE71
|
2.4
|
82.5
|
1.0
|
O
|
B:PRO68
|
3.1
|
94.6
|
1.0
|
N
|
B:ILE73
|
3.5
|
75.1
|
1.0
|
C
|
B:ILE71
|
3.5
|
82.9
|
1.0
|
CA
|
B:TRP72
|
3.9
|
77.8
|
1.0
|
CG1
|
B:ILE73
|
4.0
|
74.4
|
1.0
|
C
|
B:TRP72
|
4.0
|
82.0
|
1.0
|
CD1
|
B:ILE73
|
4.1
|
78.9
|
1.0
|
CB
|
B:ILE73
|
4.1
|
73.9
|
1.0
|
N
|
B:TRP72
|
4.1
|
78.6
|
1.0
|
C
|
B:PRO68
|
4.2
|
95.6
|
1.0
|
CA
|
B:ILE73
|
4.4
|
72.0
|
1.0
|
O
|
B:ILE73
|
4.7
|
74.8
|
1.0
|
CA
|
B:ILE71
|
4.8
|
81.0
|
1.0
|
O
|
B:GLU69
|
4.8
|
99.7
|
1.0
|
N
|
B:ILE71
|
4.8
|
83.3
|
1.0
|
N
|
B:GLU69
|
5.0
|
94.2
|
1.0
|
CA
|
B:GLU69
|
5.0
|
94.8
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 3 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na401
b:63.4
occ:1.00
|
OG1
|
C:THR226
|
3.7
|
74.2
|
1.0
|
OG1
|
D:THR226
|
3.8
|
67.3
|
1.0
|
OG1
|
B:THR226
|
4.0
|
66.5
|
1.0
|
OG1
|
E:THR226
|
4.2
|
64.5
|
1.0
|
OG1
|
A:THR226
|
4.3
|
77.9
|
1.0
|
CG2
|
C:THR226
|
4.7
|
66.8
|
1.0
|
CB
|
C:THR226
|
4.8
|
70.7
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 4 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na404
b:81.8
occ:1.00
|
O
|
C:ILE71
|
2.6
|
93.2
|
1.0
|
O
|
C:PRO68
|
2.8
|
97.0
|
1.0
|
C
|
C:ILE71
|
3.8
|
94.7
|
1.0
|
N
|
C:ILE73
|
3.8
|
84.4
|
1.0
|
C
|
C:PRO68
|
3.9
|
97.9
|
1.0
|
CD1
|
C:ILE73
|
3.9
|
92.1
|
1.0
|
CA
|
C:TRP72
|
4.1
|
88.6
|
1.0
|
CB
|
C:ILE73
|
4.2
|
83.5
|
1.0
|
C
|
C:TRP72
|
4.3
|
90.9
|
1.0
|
N
|
C:TRP72
|
4.4
|
90.4
|
1.0
|
CG1
|
C:ILE73
|
4.4
|
84.9
|
1.0
|
N
|
C:GLU69
|
4.6
|
95.5
|
1.0
|
CA
|
C:ILE73
|
4.6
|
81.5
|
1.0
|
CA
|
C:GLU69
|
4.6
|
96.4
|
1.0
|
O
|
C:GLU69
|
4.7
|
0.9
|
1.0
|
C
|
C:GLU69
|
4.8
|
0.4
|
1.0
|
CA
|
C:PRO68
|
4.9
|
92.8
|
1.0
|
CA
|
C:ILE71
|
5.0
|
93.5
|
1.0
|
O
|
C:ILE73
|
5.0
|
84.6
|
1.0
|
N
|
C:ILE71
|
5.0
|
94.4
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 5 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na403
b:1.0
occ:1.00
|
O
|
D:ILE71
|
2.3
|
93.4
|
1.0
|
O
|
D:PRO68
|
3.0
|
0.2
|
1.0
|
C
|
D:ILE71
|
3.5
|
94.9
|
1.0
|
N
|
D:ILE73
|
3.7
|
82.5
|
1.0
|
CA
|
D:TRP72
|
3.8
|
88.8
|
1.0
|
N
|
D:TRP72
|
4.1
|
90.6
|
1.0
|
C
|
D:PRO68
|
4.1
|
0.2
|
1.0
|
C
|
D:TRP72
|
4.1
|
90.2
|
1.0
|
CD1
|
D:ILE73
|
4.1
|
93.2
|
1.0
|
CB
|
D:ILE73
|
4.3
|
82.5
|
1.0
|
O
|
D:GLU69
|
4.6
|
0.4
|
1.0
|
CG1
|
D:ILE73
|
4.6
|
84.1
|
1.0
|
CA
|
D:ILE73
|
4.6
|
79.8
|
1.0
|
CA
|
D:ILE71
|
4.8
|
93.2
|
1.0
|
CA
|
D:GLU69
|
4.8
|
0.5
|
1.0
|
C
|
D:GLU69
|
4.8
|
0.9
|
1.0
|
N
|
D:GLU69
|
4.8
|
0.5
|
1.0
|
N
|
D:ILE71
|
4.9
|
95.2
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6f0v
Go back to
Sodium Binding Sites List in 6f0v
Sodium binding site 6 out
of 6 in the Glic Mutant E82Q
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Glic Mutant E82Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na403
b:97.3
occ:1.00
|
O
|
E:ILE71
|
2.9
|
95.2
|
1.0
|
O
|
E:PRO68
|
3.2
|
0.1
|
1.0
|
N
|
E:ILE73
|
3.6
|
82.4
|
1.0
|
CB
|
E:ILE73
|
3.8
|
80.8
|
1.0
|
C
|
E:ILE71
|
4.1
|
95.6
|
1.0
|
CG1
|
E:ILE73
|
4.2
|
81.0
|
1.0
|
CD1
|
E:ILE73
|
4.2
|
83.5
|
1.0
|
CA
|
E:TRP72
|
4.2
|
89.2
|
1.0
|
C
|
E:PRO68
|
4.2
|
0.6
|
1.0
|
C
|
E:TRP72
|
4.2
|
90.0
|
1.0
|
CA
|
E:ILE73
|
4.3
|
79.1
|
1.0
|
O
|
E:ILE73
|
4.5
|
84.1
|
1.0
|
N
|
E:TRP72
|
4.6
|
90.8
|
1.0
|
C
|
E:ILE73
|
4.9
|
84.0
|
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 08:35:50 2024
|