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

Protein crystallography data

The structure of X-Ray Structure of the M205W Mutant of Glic in Complex with Bromoform, PDB code: 5mzq 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) 19.84 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.969, 131.779, 160.404, 90.00, 102.93, 90.00
R / Rfree (%) 20.2 / 21.9

Other elements in 5mzq:

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

Bromine (Br) 15 atoms
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 Bromoform (pdb code 5mzq). 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 Bromoform, PDB code: 5mzq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5mzq

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Sodium binding site 1 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:79.4
occ:1.00
O A:ILE71 2.8 68.5 1.0
O A:PRO68 3.2 78.4 1.0
N A:ILE73 3.7 59.2 1.0
C A:ILE71 3.9 68.6 1.0
CA A:TRP72 4.1 61.6 1.0
CB A:ILE73 4.2 60.2 1.0
C A:TRP72 4.3 65.0 1.0
C A:PRO68 4.3 79.9 1.0
N A:TRP72 4.5 63.0 1.0
CD1 A:ILE73 4.5 67.5 1.0
CA A:ILE73 4.5 57.5 1.0
CG1 A:ILE73 4.6 60.7 1.0
CA A:GLU69 4.7 77.4 1.0
O A:ILE73 4.7 60.4 1.0
CG2 A:VAL5 4.8 87.5 1.0
O A:GLU69 4.8 79.0 1.0
N A:GLU69 4.9 77.7 1.0
C A:GLU69 5.0 79.0 1.0

Sodium binding site 2 out of 6 in 5mzq

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Sodium binding site 2 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:54.7
occ:1.00
O B:ILE71 2.9 61.2 1.0
N B:ILE73 3.3 51.9 1.0
O B:PRO68 3.7 74.8 1.0
CA B:TRP72 3.8 54.3 1.0
C B:ILE71 3.9 61.2 1.0
C B:TRP72 3.9 58.0 1.0
CB B:ILE73 4.1 53.3 1.0
CA B:ILE73 4.2 50.7 1.0
O B:ILE73 4.2 56.8 1.0
N B:TRP72 4.3 55.6 1.0
CG1 B:ILE73 4.6 53.5 1.0
CD1 B:ILE73 4.6 61.7 1.0
CG2 B:VAL5 4.7 96.8 1.0
C B:ILE73 4.8 55.5 1.0
C B:PRO68 4.8 76.1 1.0
O B:HOH544 4.9 62.7 1.0
CB B:TRP72 5.0 52.8 1.0

Sodium binding site 3 out of 6 in 5mzq

Go back to Sodium Binding Sites List in 5mzq
Sodium binding site 3 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na407

b:65.1
occ:1.00
O C:ILE71 2.7 64.9 1.0
O C:PRO68 3.2 76.6 1.0
C C:ILE71 3.8 65.8 1.0
N C:ILE73 3.8 58.3 1.0
CA C:TRP72 4.0 58.9 1.0
C C:PRO68 4.3 77.7 1.0
C C:TRP72 4.3 64.1 1.0
N C:TRP72 4.4 60.2 1.0
CB C:ILE73 4.5 59.5 1.0
CG2 C:VAL5 4.5 0.3 1.0
CA C:GLU69 4.5 76.1 1.0
O C:GLU69 4.6 78.8 1.0
CD1 C:ILE73 4.6 65.4 1.0
CA C:ILE73 4.7 56.9 1.0
CG1 C:ILE73 4.8 59.7 1.0
C C:GLU69 4.8 78.7 1.0
N C:GLU69 4.8 75.8 1.0
CB C:VAL5 4.9 0.3 1.0
O C:ILE73 4.9 61.9 1.0

Sodium binding site 4 out of 6 in 5mzq

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Sodium binding site 4 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:96.8
occ:1.00
O A:HOH545 3.9 81.2 1.0
O C:HOH557 4.0 82.8 1.0
O D:HOH554 4.1 66.3 1.0
OG1 D:THR226 4.3 63.7 1.0
OG1 E:THR226 4.3 64.9 1.0
OG1 C:THR226 4.4 70.8 1.0
OG1 A:THR226 4.5 68.7 1.0
OG1 B:THR226 4.6 62.1 1.0
CG2 D:THR226 5.0 60.1 1.0
CG2 E:THR226 5.0 61.5 1.0

Sodium binding site 5 out of 6 in 5mzq

Go back to Sodium Binding Sites List in 5mzq
Sodium binding site 5 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na407

b:96.3
occ:1.00
O D:ILE71 3.0 70.4 1.0
N D:ILE73 3.4 62.0 1.0
CA D:TRP72 3.7 66.9 1.0
C D:ILE71 4.0 72.2 1.0
C D:TRP72 4.0 68.9 1.0
O D:PRO68 4.0 81.5 1.0
O D:ILE73 4.3 62.2 1.0
N D:TRP72 4.3 68.0 1.0
CB D:ILE73 4.4 61.8 1.0
CG2 D:VAL5 4.4 95.0 1.0
CA D:ILE73 4.4 59.5 1.0
CB D:VAL5 4.7 95.0 1.0
CD1 D:TRP72 4.8 70.1 1.0
CB D:TRP72 4.8 65.8 1.0
C D:ILE73 4.9 61.8 1.0
CG1 D:ILE73 4.9 61.6 1.0
CG D:TRP72 5.0 66.8 1.0

Sodium binding site 6 out of 6 in 5mzq

Go back to Sodium Binding Sites List in 5mzq
Sodium binding site 6 out of 6 in the X-Ray Structure of the M205W 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 M205W Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na406

b:68.4
occ:1.00
O E:ILE71 2.7 72.8 1.0
O E:PRO68 3.1 80.3 1.0
N E:ILE73 3.8 64.4 1.0
C E:ILE71 3.9 73.3 1.0
C E:PRO68 4.1 81.5 1.0
CA E:TRP72 4.1 66.7 1.0
CB E:ILE73 4.3 66.0 1.0
C E:TRP72 4.3 69.8 1.0
CD1 E:ILE73 4.4 75.2 1.0
N E:TRP72 4.5 68.0 1.0
CA E:GLU69 4.5 80.5 1.0
CG1 E:ILE73 4.5 66.7 1.0
CA E:ILE73 4.6 62.7 1.0
O E:GLU69 4.7 85.2 1.0
N E:GLU69 4.7 80.0 1.0
C E:GLU69 4.8 84.2 1.0
CG2 E:VAL5 4.8 0.2 1.0
O E:ILE73 4.9 64.4 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 11:19:44 2020

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