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Sodium in PDB 5mvn: X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol

Protein crystallography data

The structure of X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol, PDB code: 5mvn 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) 49.28 / 3.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.229, 132.474, 159.759, 90.00, 102.50, 90.00
R / Rfree (%) 21.8 / 23.2

Other elements in 5mvn:

The structure of X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol (pdb code 5mvn). 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 M205W Mutant of Glic in Complex with Propofol, PDB code: 5mvn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5mvn

Go back to Sodium Binding Sites List in 5mvn
Sodium binding site 1 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:0.7
occ:1.00
 O A:ILE71 2.4 95.3 1.0
O A:PRO68 2.9 0.8 1.0
N A:ILE73 3.4 87.6 1.0
C A:ILE71 3.6 97.1 1.0
CB A:ILE73 3.8 87.0 1.0
CD1 A:ILE73 4.0 91.8 1.0
CA A:TRP72 4.0 92.5 1.0
C A:PRO68 4.0 0.4 1.0
C A:TRP72 4.0 94.7 1.0
CA A:ILE73 4.2 84.8 1.0
CG1 A:ILE73 4.2 86.6 1.0
N A:TRP72 4.2 93.3 1.0
CA A:GLU69 4.6 0.2 1.0
O A:GLU69 4.6 0.8 1.0
O A:ILE73 4.6 84.8 1.0
N A:GLU69 4.7 0.7 1.0
C A:GLU69 4.7 0.2 1.0
CA A:ILE71 4.8 94.5 1.0
N A:ILE71 4.9 95.7 1.0
CG2 A:VAL5 5.0 0.5 1.0
C A:ILE73 5.0 84.6 1.0

Sodium binding site 2 out of 6 in 5mvn

Go back to Sodium Binding Sites List in 5mvn
Sodium binding site 2 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:89.5
occ:1.00
 O E:HOH506 4.2 48.0 1.0
OG1 B:THR226 4.2 90.4 1.0
OG1 A:THR226 4.3 85.3 1.0
OG1 C:THR226 4.3 95.4 1.0
CG2 B:THR226 4.3 86.4 1.0
CG2 A:THR226 4.4 88.2 1.0
CG2 C:THR226 4.4 90.2 1.0
OG1 E:THR226 4.4 88.0 1.0
OG1 D:THR226 4.4 89.5 1.0
CG2 E:THR226 4.4 82.0 1.0
O B:HOH505 4.4 18.9 1.0
CG2 D:THR226 4.5 83.3 1.0
O A:HOH504 4.6 32.2 1.0
CB B:THR226 5.0 86.4 1.0
CB A:THR226 5.0 87.1 1.0

Sodium binding site 3 out of 6 in 5mvn

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Sodium binding site 3 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:94.5
occ:1.00
 O B:ILE71 2.4 78.3 1.0
O B:PRO68 2.9 87.7 1.0
N B:ILE73 3.5 70.6 1.0
C B:ILE71 3.5 78.3 1.0
CB B:ILE73 3.9 71.0 1.0
C B:PRO68 3.9 88.0 1.0
CA B:TRP72 4.0 74.9 1.0
CD1 B:ILE73 4.0 77.5 1.0
C B:TRP72 4.1 77.1 1.0
N B:TRP72 4.2 75.1 1.0
CG1 B:ILE73 4.2 70.5 1.0
CA B:ILE73 4.3 68.8 1.0
O B:GLU69 4.5 84.5 1.0
CA B:GLU69 4.5 85.1 1.0
C B:GLU69 4.6 85.2 1.0
N B:GLU69 4.6 85.0 1.0
O B:ILE73 4.7 74.1 1.0
CA B:ILE71 4.7 73.0 1.0
N B:ILE71 4.8 74.2 1.0
CG2 B:VAL5 4.9 0.1 1.0

Sodium binding site 4 out of 6 in 5mvn

Go back to Sodium Binding Sites List in 5mvn
Sodium binding site 4 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:59.0
occ:1.00
 O C:ILE71 2.8 89.7 1.0
O C:PRO68 2.9 0.1 1.0
C C:PRO68 3.8 0.8 1.0
CA C:GLU69 3.8 99.8 1.0
O C:GLU69 3.8 98.4 1.0
C C:ILE71 4.0 91.5 1.0
C C:GLU69 4.1 99.8 1.0
N C:GLU69 4.2 99.9 1.0
N C:ILE73 4.4 79.7 1.0
CG2 C:VAL5 4.5 0.7 1.0
CA C:TRP72 4.6 84.7 1.0
CD1 C:ILE73 4.7 82.2 1.0
N C:TRP72 4.7 86.4 1.0
N C:ILE71 4.8 92.5 1.0
CB C:ILE73 4.8 79.8 1.0
C C:TRP72 4.9 87.3 1.0

Sodium binding site 5 out of 6 in 5mvn

Go back to Sodium Binding Sites List in 5mvn
Sodium binding site 5 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na407

b:0.3
occ:1.00
 O D:ILE71 2.3 97.5 1.0
O D:PRO68 3.1 0.9 1.0
C D:ILE71 3.5 98.4 1.0
O D:GLU69 3.9 0.2 1.0
N D:ILE73 3.9 87.3 1.0
CA D:TRP72 4.0 92.5 1.0
C D:PRO68 4.1 0.5 1.0
N D:TRP72 4.2 93.6 1.0
CA D:GLU69 4.2 0.8 1.0
C D:GLU69 4.2 0.6 1.0
CG2 D:VAL5 4.2 0.3 1.0
C D:TRP72 4.4 94.0 1.0
N D:GLU69 4.6 0.5 1.0
N D:ILE71 4.6 97.9 1.0
CB D:ILE73 4.6 87.0 1.0
CA D:ILE71 4.6 96.4 1.0
CD1 D:ILE73 4.6 93.2 1.0
CB D:VAL5 4.8 0.2 1.0
CG1 D:VAL5 4.8 0.8 1.0
CA D:ILE73 4.9 85.0 1.0
CG1 D:ILE73 4.9 87.0 1.0

Sodium binding site 6 out of 6 in 5mvn

Go back to Sodium Binding Sites List in 5mvn
Sodium binding site 6 out of 6 in the X-Ray Structure of the M205W Mutant of Glic in Complex with Propofol


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 M205W Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na405

b:95.4
occ:1.00
 O E:ILE71 2.7 97.4 1.0
O E:PRO68 3.3 0.6 1.0
N E:ILE73 3.8 83.3 1.0
C E:ILE71 3.9 97.7 1.0
CA E:TRP72 4.2 88.9 1.0
C E:PRO68 4.3 0.9 1.0
CB E:ILE73 4.3 84.0 1.0
C E:TRP72 4.4 90.3 1.0
O E:GLU69 4.4 0.0 1.0
N E:TRP72 4.5 90.9 1.0
CA E:GLU69 4.5 0.2 1.0
CG2 E:VAL5 4.5 0.8 1.0
CD1 E:ILE73 4.6 81.9 1.0
CG1 E:ILE73 4.7 83.4 1.0
CA E:ILE73 4.7 81.1 1.0
C E:GLU69 4.7 0.1 1.0
N E:GLU69 4.8 0.8 1.0
O E:ILE73 4.9 81.3 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 11:19:32 2020

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