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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

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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

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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

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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

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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

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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: Tue Dec 15 11:19:26 2020

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