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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:

Bromine (Br) 18 atoms
Chlorine (Cl) 4 atoms

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

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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

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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

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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

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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

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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 Dec 15 12:11:18 2020

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