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Sodium in PDB 4bdr: Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate

Protein crystallography data

The structure of Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate, PDB code: 4bdr was solved by N.Nayeem, O.Mayans, T.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 95.503, 105.331, 112.179, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.7

Other elements in 4bdr:

The structure of Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate (pdb code 4bdr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate, PDB code: 4bdr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4bdr

Go back to Sodium Binding Sites List in 4bdr
Sodium binding site 1 out of 2 in the Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:22.3
occ:1.00
O A:GLU524 2.4 23.2 1.0
OD1 A:ASP528 2.4 24.6 1.0
O A:ILE527 2.4 21.2 1.0
O A:HOH2098 2.4 34.0 1.0
OE2 A:GLU524 2.6 28.8 1.0
C A:ILE527 3.3 19.4 1.0
C A:GLU524 3.4 22.0 1.0
CG A:ASP528 3.5 23.2 1.0
SD A:MET770 3.6 46.4 1.0
CD A:GLU524 3.6 29.3 1.0
CA A:ASP528 3.7 17.3 1.0
N A:ASP528 3.9 20.5 1.0
CG A:GLU524 3.9 31.6 1.0
CA A:GLU524 4.0 20.9 1.0
O A:HOH2096 4.1 21.0 1.0
O A:HOH2097 4.2 32.0 1.0
CG A:MET770 4.2 33.0 1.0
CB A:ASP528 4.2 19.7 1.0
N A:ILE527 4.3 20.9 1.0
CA A:ILE527 4.4 19.7 1.0
OD2 A:ASP528 4.5 28.7 1.0
CB A:GLU524 4.5 26.2 1.0
N A:LYS525 4.6 23.0 1.0
OE1 A:GLU524 4.7 27.0 1.0
C A:LYS525 4.8 28.1 1.0
N A:VAL526 4.8 22.6 1.0
CA A:LYS525 4.8 24.8 1.0
CB A:MET770 4.9 27.2 1.0
C A:ASP528 4.9 22.3 1.0
C A:VAL526 5.0 25.4 1.0

Sodium binding site 2 out of 2 in 4bdr

Go back to Sodium Binding Sites List in 4bdr
Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the GLUK2 R775A Lbd Dimer in Complex with Kainate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:26.3
occ:1.00
O B:GLU524 2.4 24.7 1.0
OD1 B:ASP528 2.4 27.6 1.0
O B:ILE527 2.4 23.4 1.0
O B:HOH2084 2.4 30.4 1.0
OE2 B:GLU524 2.7 33.5 1.0
C B:ILE527 3.3 22.0 1.0
C B:GLU524 3.4 22.6 1.0
CG B:ASP528 3.6 29.7 1.0
SD B:MET770 3.6 49.3 1.0
CD B:GLU524 3.6 29.5 1.0
CA B:ASP528 3.7 21.3 1.0
N B:ASP528 3.8 23.3 1.0
CG B:GLU524 3.9 30.5 1.0
CA B:GLU524 3.9 23.3 1.0
O A:HOH2106 4.1 23.2 1.0
CB B:ASP528 4.2 22.0 1.0
O A:HOH2225 4.3 31.3 1.0
O A:HOH2019 4.3 44.6 1.0
CG B:MET770 4.3 36.2 1.0
N B:ILE527 4.4 24.1 1.0
CA B:ILE527 4.4 21.1 1.0
CB B:GLU524 4.5 23.1 1.0
OD2 B:ASP528 4.5 29.6 1.0
N B:LYS525 4.5 23.6 1.0
C B:LYS525 4.7 30.2 1.0
OE1 B:GLU524 4.8 24.9 1.0
N B:VAL526 4.8 26.1 1.0
CA B:LYS525 4.9 27.2 1.0
C B:ASP528 4.9 23.0 1.0
O B:ARG523 5.0 21.2 1.0

Reference:

N.Nayeem, O.Mayans, T.Green. Correlating Efficacy and Desensitization with GLUK2 Ligand-Binding Domain Movements. Open Biol. V. 3 0051 2013.
ISSN: ESSN 2046-2441
PubMed: 23720540
DOI: 10.1098/RSOB.130051
Page generated: Tue Dec 15 06:33:55 2020

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