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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

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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

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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

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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

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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

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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

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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: Tue Dec 15 11:19:46 2020

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