Sodium in PDB 6emx: X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Protein crystallography data
The structure of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform, PDB code: 6emx
was solved by
Z.Fourati,
M.Delarue,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.62 /
3.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
179.790,
133.322,
158.767,
90.00,
101.68,
90.00
|
R / Rfree (%)
|
24.6 /
26.8
|
Other elements in 6emx:
The structure of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
(pdb code 6emx). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform, PDB code: 6emx:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 1 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:1.0
occ:1.00
|
O
|
A:ILE71
|
2.4
|
0.9
|
1.0
|
O
|
A:PRO68
|
3.2
|
0.6
|
1.0
|
C
|
A:ILE71
|
3.5
|
0.1
|
1.0
|
N
|
A:ILE73
|
3.7
|
0.8
|
1.0
|
CA
|
A:TRP72
|
3.8
|
0.6
|
1.0
|
N
|
A:TRP72
|
4.1
|
0.2
|
1.0
|
C
|
A:TRP72
|
4.1
|
0.6
|
1.0
|
C
|
A:PRO68
|
4.3
|
0.2
|
1.0
|
O
|
A:GLU69
|
4.5
|
0.9
|
1.0
|
CB
|
A:ILE73
|
4.5
|
0.1
|
1.0
|
CA
|
A:GLU69
|
4.5
|
0.2
|
1.0
|
CD1
|
A:ILE73
|
4.6
|
0.6
|
1.0
|
CG1
|
A:VAL5
|
4.6
|
0.3
|
1.0
|
C
|
A:GLU69
|
4.6
|
0.1
|
1.0
|
CG1
|
A:ILE73
|
4.6
|
0.8
|
1.0
|
CA
|
A:ILE73
|
4.6
|
0.6
|
1.0
|
CB
|
A:VAL5
|
4.7
|
0.8
|
1.0
|
CA
|
A:ILE71
|
4.8
|
0.4
|
1.0
|
N
|
A:ILE71
|
4.8
|
0.4
|
1.0
|
N
|
A:GLU69
|
4.8
|
0.0
|
1.0
|
O
|
A:ILE73
|
4.9
|
0.3
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 2 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:0.4
occ:1.00
|
O
|
D:HOH503
|
2.6
|
0.8
|
1.0
|
O
|
B:HOH502
|
3.4
|
0.6
|
1.0
|
O
|
E:HOH509
|
3.7
|
0.6
|
1.0
|
OG1
|
A:THR226
|
3.9
|
0.3
|
1.0
|
O
|
E:HOH502
|
3.9
|
0.2
|
1.0
|
O
|
A:HOH502
|
4.0
|
0.5
|
1.0
|
OG1
|
E:THR226
|
4.2
|
0.7
|
1.0
|
CG2
|
E:THR226
|
4.2
|
0.1
|
1.0
|
CG2
|
A:THR226
|
4.3
|
0.6
|
1.0
|
O
|
B:HOH501
|
4.3
|
0.2
|
1.0
|
OG1
|
B:THR226
|
4.3
|
0.8
|
1.0
|
O
|
B:HOH505
|
4.7
|
1.0
|
1.0
|
CB
|
A:THR226
|
4.7
|
0.7
|
1.0
|
CG2
|
B:THR226
|
4.8
|
0.3
|
1.0
|
OG1
|
D:THR226
|
4.8
|
0.4
|
1.0
|
OG1
|
C:THR226
|
4.8
|
0.4
|
1.0
|
CB
|
E:THR226
|
4.9
|
0.7
|
1.0
|
CG2
|
D:THR226
|
5.0
|
0.7
|
1.0
|
O
|
C:HOH501
|
5.0
|
0.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 3 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na402
b:0.6
occ:1.00
|
O
|
B:ILE71
|
2.6
|
0.9
|
1.0
|
N
|
B:ILE73
|
3.3
|
0.1
|
1.0
|
O
|
B:PRO68
|
3.4
|
0.4
|
1.0
|
C
|
B:ILE71
|
3.6
|
0.4
|
1.0
|
CA
|
B:TRP72
|
3.7
|
0.1
|
1.0
|
C
|
B:TRP72
|
3.9
|
0.1
|
1.0
|
N
|
B:TRP72
|
4.1
|
0.4
|
1.0
|
CB
|
B:ILE73
|
4.1
|
0.8
|
1.0
|
CA
|
B:ILE73
|
4.2
|
0.4
|
1.0
|
CG1
|
B:ILE73
|
4.4
|
0.2
|
1.0
|
CD1
|
B:ILE73
|
4.5
|
0.1
|
1.0
|
O
|
B:ILE73
|
4.5
|
0.6
|
1.0
|
C
|
B:PRO68
|
4.5
|
0.2
|
1.0
|
O
|
B:GLU69
|
4.9
|
0.5
|
1.0
|
C
|
B:ILE73
|
4.9
|
0.1
|
1.0
|
CA
|
B:GLU69
|
4.9
|
0.0
|
1.0
|
CA
|
B:ILE71
|
4.9
|
0.5
|
1.0
|
CG1
|
B:VAL5
|
5.0
|
0.3
|
1.0
|
CB
|
B:VAL5
|
5.0
|
0.1
|
1.0
|
CB
|
B:TRP72
|
5.0
|
0.4
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 4 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na401
b:0.2
occ:1.00
|
O
|
C:ILE71
|
2.5
|
0.3
|
1.0
|
O
|
C:PRO68
|
2.7
|
0.2
|
1.0
|
C
|
C:ILE71
|
3.7
|
0.5
|
1.0
|
C
|
C:PRO68
|
3.8
|
0.5
|
1.0
|
CA
|
C:GLU69
|
4.0
|
1.0
|
1.0
|
O
|
C:GLU69
|
4.0
|
0.7
|
1.0
|
C
|
C:GLU69
|
4.1
|
0.9
|
1.0
|
N
|
C:ILE73
|
4.2
|
0.9
|
1.0
|
N
|
C:GLU69
|
4.3
|
0.3
|
1.0
|
CA
|
C:TRP72
|
4.3
|
0.3
|
1.0
|
N
|
C:TRP72
|
4.4
|
0.8
|
1.0
|
CD1
|
C:ILE73
|
4.5
|
0.0
|
1.0
|
C
|
C:TRP72
|
4.6
|
0.6
|
1.0
|
N
|
C:ILE71
|
4.6
|
0.2
|
1.0
|
CB
|
C:ILE73
|
4.7
|
0.3
|
1.0
|
CG1
|
C:ILE73
|
4.7
|
0.7
|
1.0
|
CA
|
C:ILE71
|
4.7
|
0.4
|
1.0
|
CG1
|
C:VAL5
|
4.8
|
0.9
|
1.0
|
N
|
C:ALA70
|
5.0
|
0.1
|
1.0
|
CA
|
C:PRO68
|
5.0
|
0.7
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 5 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na402
b:0.3
occ:1.00
|
O
|
D:ILE71
|
2.5
|
0.7
|
1.0
|
O
|
D:PRO68
|
3.5
|
0.8
|
1.0
|
C
|
D:ILE71
|
3.6
|
0.3
|
1.0
|
N
|
D:ILE73
|
3.7
|
0.1
|
1.0
|
CA
|
D:TRP72
|
3.8
|
0.1
|
1.0
|
N
|
D:TRP72
|
4.1
|
0.5
|
1.0
|
C
|
D:TRP72
|
4.2
|
0.6
|
1.0
|
O
|
D:GLU69
|
4.4
|
0.5
|
1.0
|
CG1
|
D:VAL5
|
4.5
|
0.4
|
1.0
|
CB
|
D:VAL5
|
4.5
|
0.0
|
1.0
|
C
|
D:PRO68
|
4.5
|
0.9
|
1.0
|
CA
|
D:GLU69
|
4.7
|
0.6
|
1.0
|
CB
|
D:ILE73
|
4.7
|
0.9
|
1.0
|
C
|
D:GLU69
|
4.7
|
0.7
|
1.0
|
CG2
|
D:VAL5
|
4.7
|
0.4
|
1.0
|
CA
|
D:ILE73
|
4.8
|
0.3
|
1.0
|
CA
|
D:ILE71
|
4.8
|
0.4
|
1.0
|
CG1
|
D:ILE73
|
4.9
|
0.9
|
1.0
|
N
|
D:ILE71
|
4.9
|
0.6
|
1.0
|
CD1
|
D:ILE73
|
4.9
|
0.5
|
1.0
|
CB
|
D:TRP72
|
5.0
|
1.0
|
1.0
|
O
|
D:ILE73
|
5.0
|
0.5
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6emx
Go back to
Sodium Binding Sites List in 6emx
Sodium binding site 6 out
of 6 in the X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of X-Ray Structure of the N15'C Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na402
b:0.7
occ:1.00
|
O
|
E:ILE71
|
2.3
|
0.3
|
1.0
|
O
|
E:PRO68
|
3.1
|
0.5
|
1.0
|
C
|
E:ILE71
|
3.4
|
0.2
|
1.0
|
N
|
E:ILE73
|
3.7
|
0.6
|
1.0
|
CA
|
E:TRP72
|
3.8
|
0.7
|
1.0
|
N
|
E:TRP72
|
4.0
|
0.9
|
1.0
|
C
|
E:TRP72
|
4.1
|
0.2
|
1.0
|
C
|
E:PRO68
|
4.2
|
0.1
|
1.0
|
O
|
E:GLU69
|
4.3
|
0.5
|
1.0
|
CA
|
E:GLU69
|
4.5
|
0.1
|
1.0
|
C
|
E:GLU69
|
4.5
|
0.6
|
1.0
|
CB
|
E:ILE73
|
4.5
|
0.8
|
1.0
|
CG1
|
E:VAL5
|
4.6
|
0.2
|
1.0
|
CD1
|
E:ILE73
|
4.6
|
0.9
|
1.0
|
CA
|
E:ILE71
|
4.6
|
0.4
|
1.0
|
CG1
|
E:ILE73
|
4.6
|
0.8
|
1.0
|
N
|
E:ILE71
|
4.7
|
0.4
|
1.0
|
CB
|
E:VAL5
|
4.7
|
0.9
|
1.0
|
CA
|
E:ILE73
|
4.7
|
0.5
|
1.0
|
N
|
E:GLU69
|
4.8
|
0.4
|
1.0
|
CG2
|
E:VAL5
|
5.0
|
0.2
|
1.0
|
|
Reference:
Z.Fourati,
R.J.Howard,
S.A.Heusser,
H.Hu,
R.R.Ruza,
L.Sauguet,
E.Lindahl,
M.Delarue.
Structural Basis For A Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep V. 23 993 2018.
ISSN: ESSN 2211-1247
PubMed: 29694907
DOI: 10.1016/J.CELREP.2018.03.108
Page generated: Tue Oct 8 08:26:36 2024
|