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

Sodium in PDB 5mzt: X-Ray Structure of the H235Q Mutant of Glic in Complex with Bromoform

Protein crystallography data

The structure of X-Ray Structure of the H235Q Mutant of Glic in Complex with Bromoform, PDB code: 5mzt 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 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.870, 132.764, 160.292, 90.00, 102.43, 90.00
R / Rfree (%) 19.3 / 21.1

Other elements in 5mzt:

The structure of X-Ray Structure of the H235Q Mutant of Glic in Complex with Bromoform also contains other interesting chemical elements:

Bromine (Br) 30 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the H235Q Mutant of Glic in Complex with Bromoform (pdb code 5mzt). 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 H235Q Mutant of Glic in Complex with Bromoform, PDB code: 5mzt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 1 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:87.4
occ:1.00
O A:ILE71 2.6 64.3 1.0
O A:PRO68 3.1 84.2 1.0
N A:ILE73 3.5 59.4 1.0
C A:ILE71 3.7 65.4 1.0
CA A:TRP72 4.0 61.7 1.0
CB A:ILE73 4.0 59.2 1.0
C A:TRP72 4.1 64.3 1.0
CG2 A:VAL5 4.2 86.0 1.0
C A:PRO68 4.2 84.8 1.0
CG1 A:ILE73 4.2 59.6 1.0
CD1 A:ILE73 4.2 69.4 1.0
N A:TRP72 4.3 62.8 1.0
CA A:ILE73 4.3 57.4 1.0
O A:ILE73 4.7 60.2 1.0
CA A:GLU69 4.8 81.7 1.0
N A:GLU69 4.9 81.6 1.0
O A:GLU69 4.9 81.5 1.0
CA A:ILE71 4.9 64.7 1.0
N A:ILE71 5.0 67.5 1.0
C A:GLU69 5.0 81.3 1.0

Sodium binding site 2 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 2 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:88.9
occ:1.00
OG1 A:THR226 3.9 65.5 1.0
OG1 B:THR226 4.0 73.4 1.0
O A:HOH554 4.2 79.1 1.0
OG1 E:THR226 4.4 81.3 1.0
OG1 C:THR226 4.4 82.3 1.0
O B:HOH546 4.5 92.5 1.0
O C:HOH547 4.6 87.0 1.0
CG2 A:THR226 4.6 66.7 1.0
O D:HOH569 4.6 99.8 1.0
O A:HOH541 4.6 88.8 1.0
OG1 D:THR226 4.7 73.0 1.0
CG2 B:THR226 4.8 65.3 1.0
CG2 E:THR226 4.8 73.1 1.0
CB A:THR226 4.9 68.8 1.0
O E:HOH563 4.9 67.2 1.0

Sodium binding site 3 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 3 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:76.8
occ:1.00
O B:ILE71 2.4 61.3 1.0
O B:PRO68 3.0 76.4 1.0
C B:ILE71 3.5 61.4 1.0
N B:ILE73 3.5 54.1 1.0
CA B:TRP72 3.9 56.3 1.0
C B:TRP72 4.0 58.7 1.0
CB B:ILE73 4.0 54.2 1.0
C B:PRO68 4.1 77.4 1.0
N B:TRP72 4.1 57.4 1.0
CG2 B:VAL5 4.1 0.4 1.0
CG1 B:ILE73 4.2 55.9 1.0
CD1 B:ILE73 4.2 68.2 1.0
CA B:ILE73 4.3 51.9 1.0
CA B:GLU69 4.7 76.1 1.0
CA B:ILE71 4.7 60.6 1.0
O B:ILE73 4.8 58.4 1.0
N B:ILE71 4.8 63.0 1.0
O B:GLU69 4.8 78.5 1.0
N B:GLU69 4.8 75.3 1.0
C B:GLU69 4.8 76.9 1.0
O B:TRP72 5.0 59.5 1.0

Sodium binding site 4 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 4 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:78.0
occ:1.00
O C:ILE71 2.6 67.9 1.0
O C:PRO68 3.0 80.6 1.0
C C:ILE71 3.8 69.1 1.0
N C:ILE73 3.8 60.6 1.0
C C:PRO68 4.0 82.2 1.0
CA C:TRP72 4.2 64.0 1.0
CG2 C:VAL5 4.2 0.8 1.0
CB C:ILE73 4.2 60.9 1.0
CD1 C:ILE73 4.3 70.2 1.0
C C:TRP72 4.3 67.2 1.0
CG1 C:ILE73 4.4 61.7 1.0
N C:TRP72 4.4 64.5 1.0
CA C:GLU69 4.5 81.3 1.0
CA C:ILE73 4.6 58.8 1.0
N C:GLU69 4.7 80.0 1.0
O C:GLU69 4.7 85.8 1.0
C C:GLU69 4.8 83.9 1.0
O B:HOH587 4.8 99.2 1.0
N C:ILE71 4.9 71.2 1.0
CA C:ILE71 5.0 69.2 1.0

Sodium binding site 5 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 5 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na406

b:94.4
occ:1.00
O D:ILE71 2.6 68.2 1.0
O D:PRO68 3.1 86.7 1.0
N D:ILE73 3.6 62.6 1.0
C D:ILE71 3.7 69.6 1.0
CA D:TRP72 4.0 65.2 1.0
CB D:ILE73 4.1 63.3 1.0
C D:TRP72 4.1 68.1 1.0
C D:PRO68 4.1 87.7 1.0
CG2 D:VAL5 4.2 98.6 1.0
CD1 D:ILE73 4.3 70.3 1.0
CG1 D:ILE73 4.3 64.2 1.0
N D:TRP72 4.3 66.3 1.0
CA D:ILE73 4.4 60.9 1.0
CA D:GLU69 4.7 84.6 1.0
O D:ILE73 4.8 63.1 1.0
N D:GLU69 4.8 84.8 1.0
O D:GLU69 4.9 85.4 1.0
C D:GLU69 4.9 85.0 1.0
CA D:ILE71 5.0 70.2 1.0
N D:ILE71 5.0 72.6 1.0

Sodium binding site 6 out of 6 in 5mzt

Go back to Sodium Binding Sites List in 5mzt
Sodium binding site 6 out of 6 in the X-Ray Structure of the H235Q 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 H235Q Mutant of Glic in Complex with Bromoform within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na406

b:84.9
occ:1.00
O E:ILE71 2.5 70.9 1.0
O E:PRO68 2.7 83.1 1.0
C E:ILE71 3.7 72.3 1.0
C E:PRO68 3.8 83.6 1.0
N E:ILE73 3.9 62.5 1.0
CD1 E:ILE73 4.2 70.8 1.0
CA E:TRP72 4.2 65.2 1.0
CB E:ILE73 4.3 61.7 1.0
CG2 E:VAL5 4.3 0.5 1.0
CA E:GLU69 4.3 83.4 1.0
CG1 E:ILE73 4.3 61.9 1.0
C E:TRP72 4.4 66.4 1.0
N E:TRP72 4.4 67.1 1.0
N E:GLU69 4.4 82.4 1.0
O E:GLU69 4.5 85.8 1.0
C E:GLU69 4.6 84.6 1.0
N E:ILE71 4.7 73.4 1.0
CA E:ILE73 4.7 59.9 1.0
CA E:ILE71 4.8 71.9 1.0
CA E:PRO68 4.9 76.5 1.0

Reference:

Z.Fourati, M.Delarue. X-Ray Structure of the H235Q Mutant of Glic in Complex with Bromoform To Be Published.
Page generated: Mon Aug 18 01:14:09 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy