Atomistry » Sodium » PDB 5mss-5nbj » 5mvm
Atomistry »
  Sodium »
    PDB 5mss-5nbj »
      5mvm »

Sodium in PDB 5mvm: X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol

Protein crystallography data

The structure of X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol, PDB code: 5mvm 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) 20.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.760, 132.510, 160.520, 90.00, 102.72, 90.00
R / Rfree (%) 19.5 / 20.8

Other elements in 5mvm:

The structure of X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol (pdb code 5mvm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol, PDB code: 5mvm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 1 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:74.8
occ:1.00
 O A:ILE71 2.4 82.0 1.0
O A:PRO68 3.2 92.9 1.0
C A:ILE71 3.5 83.7 1.0
N A:ILE73 3.6 75.8 1.0
CA A:TRP72 3.9 78.4 1.0
CG1 A:VAL5 4.0 0.3 1.0
C A:TRP72 4.1 83.1 1.0
N A:TRP72 4.1 78.9 1.0
C A:PRO68 4.2 93.5 1.0
CB A:ILE73 4.2 75.8 1.0
CD1 A:ILE73 4.3 81.9 1.0
CG1 A:ILE73 4.4 75.7 1.0
CA A:ILE73 4.5 73.4 1.0
O A:GLU69 4.5 94.9 1.0
CA A:ILE71 4.7 81.9 1.0
N A:ILE71 4.8 84.1 1.0
CA A:GLU69 4.8 92.1 1.0
C A:GLU69 4.8 95.1 1.0
N A:GLU69 4.8 91.3 1.0
O A:ILE73 4.9 76.5 1.0

Sodium binding site 2 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 2 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:82.1
occ:1.00
 OG1 B:THR226 3.7 0.9 1.0
OG1 A:THR226 4.1 85.2 1.0
OG1 C:THR226 4.2 84.2 1.0
CG2 B:THR226 4.3 85.0 1.0
CG2 A:THR226 4.5 76.9 1.0
CB B:THR226 4.6 89.1 1.0
O C:HOH534 4.9 32.4 1.0
CG2 C:THR226 4.9 70.7 1.0
OG1 E:THR226 4.9 90.9 1.0
CB A:THR226 5.0 82.4 1.0
OG1 D:THR226 5.0 91.2 1.0

Sodium binding site 3 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 3 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:70.6
occ:1.00
 O B:ILE71 2.4 73.7 1.0
O B:PRO68 3.1 84.3 1.0
C B:ILE71 3.6 72.7 1.0
N B:ILE73 3.8 63.7 1.0
C B:PRO68 4.1 84.4 1.0
CA B:TRP72 4.1 67.3 1.0
O B:GLU69 4.3 83.7 1.0
N B:TRP72 4.3 68.3 1.0
C B:TRP72 4.3 71.2 1.0
CB B:ILE73 4.4 63.9 1.0
CD1 B:ILE73 4.4 72.6 1.0
CA B:GLU69 4.5 79.7 1.0
C B:GLU69 4.5 81.5 1.0
CG1 B:ILE73 4.6 63.5 1.0
N B:GLU69 4.6 80.4 1.0
N B:ILE71 4.7 69.0 1.0
CA B:ILE73 4.7 61.9 1.0
CA B:ILE71 4.7 66.5 1.0

Sodium binding site 4 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 4 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:72.8
occ:1.00
 O C:ILE71 2.5 82.2 1.0
O C:PRO68 2.9 86.8 1.0
C C:ILE71 3.7 84.4 1.0
C C:PRO68 3.8 87.0 1.0
N C:ILE73 4.1 73.8 1.0
O C:GLU69 4.2 87.2 1.0
CA C:GLU69 4.3 84.4 1.0
CD1 C:ILE73 4.3 70.9 1.0
N C:GLU69 4.3 84.0 1.0
C C:GLU69 4.4 87.6 1.0
CA C:TRP72 4.4 78.3 1.0
CB C:ILE73 4.5 73.6 1.0
N C:TRP72 4.5 79.4 1.0
C C:TRP72 4.5 80.9 1.0
CG1 C:ILE73 4.6 72.8 1.0
N C:ILE71 4.7 83.3 1.0
CA C:ILE71 4.8 82.9 1.0
CA C:PRO68 4.8 82.2 1.0
CA C:ILE73 4.9 71.5 1.0

Sodium binding site 5 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 5 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:81.8
occ:1.00
 O D:ILE71 2.2 83.3 1.0
O D:PRO68 3.0 98.4 1.0
C D:ILE71 3.4 83.9 1.0
N D:ILE73 3.6 72.8 1.0
CA D:TRP72 3.9 75.4 1.0
C D:PRO68 4.0 99.5 1.0
C D:TRP72 4.0 79.0 1.0
N D:TRP72 4.1 77.5 1.0
CB D:ILE73 4.1 72.7 1.0
CD1 D:ILE73 4.2 79.3 1.0
CG1 D:ILE73 4.3 72.3 1.0
CA D:ILE73 4.4 70.8 1.0
O D:GLU69 4.5 97.4 1.0
CA D:ILE71 4.6 81.8 1.0
N D:ILE71 4.6 83.9 1.0
C D:GLU69 4.7 96.7 1.0
CA D:GLU69 4.7 95.6 1.0
N D:GLU69 4.7 96.5 1.0
O D:TRP72 5.0 79.3 1.0

Sodium binding site 6 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 6 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na405

b:72.2
occ:1.00
 CG E:GLU69 3.1 0.6 1.0
CD E:GLU69 3.4 0.9 1.0
OE2 E:GLU69 3.4 0.8 1.0
N E:GLU69 3.7 93.2 1.0
CA E:GLU69 3.7 92.4 1.0
CB E:GLU69 4.0 94.2 1.0
OE1 E:GLU69 4.1 0.8 1.0
CB E:PRO68 4.2 89.9 1.0
C E:PRO68 4.2 94.9 1.0
NA E:NA410 4.2 92.9 1.0
O E:PRO68 4.8 93.8 1.0
CA E:PRO68 4.8 88.7 1.0

Sodium binding site 7 out of 7 in 5mvm

Go back to Sodium Binding Sites List in 5mvm
Sodium binding site 7 out of 7 in the X-Ray Structure of the F14'A -N15'A Double 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 7 of X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na410

b:92.9
occ:1.00
 O E:PRO68 2.6 93.8 1.0
O E:ILE71 2.8 87.4 1.0
C E:PRO68 3.4 94.9 1.0
CA E:GLU69 3.9 92.4 1.0
N E:GLU69 3.9 93.2 1.0
C E:ILE71 4.1 88.3 1.0
O E:GLU69 4.1 94.6 1.0
C E:GLU69 4.2 94.1 1.0
NA E:NA405 4.2 72.2 1.0
CD1 E:ILE73 4.2 67.9 1.0
CA E:PRO68 4.5 88.7 1.0
N E:ILE73 4.5 74.6 1.0
CB E:ILE73 4.6 72.7 1.0
CG1 E:ILE73 4.7 71.3 1.0
CB E:PRO68 4.7 89.9 1.0
N E:ILE71 4.8 86.4 1.0
CA E:TRP72 4.9 82.6 1.0
N E:TRP72 4.9 83.6 1.0
C E:TRP72 5.0 84.3 1.0

Reference:

Z.Fourati, M.Delarue. X-Ray Structure of the F14'A -N15'A Double Mutant of Glic in Complex with Propofol To Be Published.
Page generated: Mon Oct 7 22:46:34 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy