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Sodium in PDB 6hji: Xray Structure of Glic in Complex with Crotonate

Protein crystallography data

The structure of Xray Structure of Glic in Complex with Crotonate, PDB code: 6hji 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) 12.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.943, 133.242, 159.880, 90.00, 101.96, 90.00
R / Rfree (%) 18.9 / 20.4

Other elements in 6hji:

The structure of Xray Structure of Glic in Complex with Crotonate also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Xray Structure of Glic in Complex with Crotonate (pdb code 6hji). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Xray Structure of Glic in Complex with Crotonate, PDB code: 6hji:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6hji

Go back to Sodium Binding Sites List in 6hji
Sodium binding site 1 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:0.4
occ:1.00
O A:ILE71 2.5 0.1 1.0
O A:PRO68 3.3 0.3 1.0
N A:ILE73 3.4 0.1 1.0
C A:ILE71 3.6 0.6 1.0
CA A:TRP72 3.8 0.5 1.0
C A:TRP72 3.9 0.6 1.0
CB A:ILE73 4.0 98.8 1.0
N A:TRP72 4.1 0.9 1.0
CD1 A:ILE73 4.2 0.1 1.0
CG1 A:ILE73 4.2 0.2 1.0
CG2 A:VAL5 4.2 0.9 1.0
CA A:ILE73 4.3 97.1 1.0
C A:PRO68 4.3 0.4 1.0
O A:ILE73 4.6 96.7 1.0
O A:GLU69 4.9 0.4 1.0
CA A:ILE71 4.9 0.2 1.0
CA A:GLU69 4.9 0.4 1.0
O A:TRP72 5.0 0.6 1.0

Sodium binding site 2 out of 6 in 6hji

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Sodium binding site 2 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:0.2
occ:1.00
OG1 A:THR226 4.1 96.9 1.0
OG1 E:THR226 4.1 95.3 1.0
OG1 B:THR226 4.2 87.5 1.0
OG1 C:THR226 4.3 95.0 1.0
OG1 D:THR226 4.3 99.9 1.0
CG2 E:THR226 4.9 88.8 1.0
CG2 A:THR226 4.9 85.5 1.0

Sodium binding site 3 out of 6 in 6hji

Go back to Sodium Binding Sites List in 6hji
Sodium binding site 3 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:98.3
occ:1.00
O B:ILE71 2.4 94.5 1.0
O B:PRO68 2.9 0.7 1.0
C B:ILE71 3.6 95.1 1.0
N B:ILE73 3.8 85.3 1.0
C B:PRO68 4.0 0.8 1.0
CA B:TRP72 4.0 89.0 1.0
CG2 B:VAL5 4.2 0.3 1.0
N B:TRP72 4.2 90.7 1.0
CD1 B:ILE73 4.3 96.8 1.0
C B:TRP72 4.3 91.7 1.0
CB B:ILE73 4.4 83.4 1.0
O B:GLU69 4.4 0.6 1.0
CA B:GLU69 4.4 0.1 1.0
CG1 B:ILE73 4.4 85.6 1.0
C B:GLU69 4.6 0.1 1.0
N B:GLU69 4.6 0.2 1.0
CA B:ILE73 4.7 81.6 1.0
N B:ILE71 4.8 96.3 1.0
CA B:ILE71 4.8 93.8 1.0

Sodium binding site 4 out of 6 in 6hji

Go back to Sodium Binding Sites List in 6hji
Sodium binding site 4 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na405

b:0.4
occ:1.00
O C:ILE71 2.7 0.2 1.0
O C:PRO68 3.2 0.3 1.0
N C:ILE73 3.6 0.1 1.0
C C:ILE71 3.8 0.2 1.0
CA C:TRP72 4.0 0.9 1.0
CB C:ILE73 4.1 99.5 1.0
CD1 C:ILE73 4.2 0.1 1.0
C C:TRP72 4.2 0.7 1.0
C C:PRO68 4.3 0.0 1.0
CG1 C:ILE73 4.3 0.3 1.0
N C:TRP72 4.4 0.8 1.0
CG2 C:VAL5 4.4 0.2 1.0
CA C:ILE73 4.4 97.8 1.0
O C:ILE73 4.8 99.4 1.0
CA C:GLU69 4.8 0.3 1.0
O C:GLU69 4.9 0.9 1.0
N C:GLU69 4.9 0.7 1.0

Sodium binding site 5 out of 6 in 6hji

Go back to Sodium Binding Sites List in 6hji
Sodium binding site 5 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:0.4
occ:1.00
O D:ILE71 2.6 0.9 1.0
O D:PRO68 3.5 0.8 1.0
N D:ILE73 3.7 0.1 1.0
C D:ILE71 3.7 0.4 1.0
CA D:TRP72 3.8 0.4 1.0
CG2 D:VAL5 3.9 0.4 1.0
C D:TRP72 4.2 0.8 1.0
N D:TRP72 4.2 0.7 1.0
CB D:ILE73 4.5 0.1 1.0
C D:PRO68 4.6 0.3 1.0
CA D:ILE73 4.6 99.6 1.0
O D:GLU69 4.7 0.3 1.0
CD1 D:ILE73 4.7 0.1 1.0
CG1 D:ILE73 4.7 0.9 1.0
O D:ILE73 4.9 0.4 1.0
CA D:GLU69 4.9 0.3 1.0
CA D:ILE71 5.0 0.4 1.0
C D:GLU69 5.0 0.9 1.0

Sodium binding site 6 out of 6 in 6hji

Go back to Sodium Binding Sites List in 6hji
Sodium binding site 6 out of 6 in the Xray Structure of Glic in Complex with Crotonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Xray Structure of Glic in Complex with Crotonate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na405

b:0.1
occ:1.00
O E:ILE71 2.7 0.5 1.0
O E:PRO68 3.0 0.3 1.0
N E:ILE73 3.7 0.1 1.0
C E:ILE71 3.9 0.4 1.0
C E:PRO68 4.0 0.2 1.0
CD1 E:ILE73 4.0 0.2 1.0
CB E:ILE73 4.1 99.9 1.0
CG1 E:ILE73 4.2 0.3 1.0
CA E:TRP72 4.2 0.2 1.0
C E:TRP72 4.3 0.1 1.0
CA E:ILE73 4.5 97.8 1.0
N E:TRP72 4.5 0.0 1.0
CA E:GLU69 4.6 0.9 1.0
CG2 E:VAL5 4.6 0.5 1.0
N E:GLU69 4.7 0.9 1.0
O E:GLU69 4.8 0.6 1.0
C E:GLU69 4.9 0.3 1.0
O E:ILE73 4.9 99.2 1.0

Reference:

Z.Fourati, M.Delarue. Xray Structure of Glic in Complex with Crotonate To Be Published.
Page generated: Tue Dec 15 12:21:05 2020

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