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Sodium in PDB 3om1: Crystal Structure of the GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of the GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution, PDB code: 3om1 was solved by J.Kumar, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.344, 65.635, 113.772, 90.00, 95.72, 90.00
R / Rfree (%) 16.8 / 19.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution (pdb code 3om1). 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 GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution, PDB code: 3om1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3om1

Go back to Sodium Binding Sites List in 3om1
Sodium binding site 1 out of 2 in the Crystal Structure of the GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution


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 GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:36.2
occ:1.00
O A:PHE162 2.5 27.7 1.0
O A:GLU167 2.5 30.8 1.0
O A:SER165 2.6 35.2 1.0
O B:HOH427 2.8 43.0 1.0
O A:HOH429 2.9 44.8 1.0
NA B:NA401 3.5 33.2 1.0
C A:SER165 3.5 25.9 1.0
O A:HOH428 3.5 40.0 1.0
HA A:THR168 3.6 28.7 1.0
C A:GLU167 3.6 31.8 1.0
HB3 A:SER165 3.6 41.5 1.0
H A:SER165 3.6 33.8 1.0
C A:PHE162 3.6 22.5 1.0
O B:HOH542 3.8 56.7 1.0
N A:SER165 4.0 28.1 1.0
HA A:LEU163 4.0 25.8 1.0
CA A:SER165 4.1 31.5 1.0
N A:GLU167 4.1 29.4 1.0
C A:LYS166 4.2 31.0 1.0
O B:LEU163 4.2 32.7 1.0
H A:GLU167 4.2 35.3 1.0
CB A:SER165 4.3 34.6 1.0
HB3 A:PHE162 4.3 26.3 1.0
HA A:PHE162 4.3 28.6 1.0
HA B:LEU163 4.3 31.6 1.0
HA A:LYS166 4.4 42.4 1.0
C A:LEU163 4.4 24.1 1.0
CA A:THR168 4.4 23.9 1.0
N A:LYS166 4.4 33.9 1.0
N A:THR168 4.4 27.6 1.0
O A:LEU163 4.4 26.6 1.0
HD1 A:PHE162 4.4 29.2 1.0
CA A:GLU167 4.5 29.5 1.0
HG22 A:THR168 4.5 37.8 1.0
O A:LYS166 4.5 39.1 1.0
CA A:PHE162 4.5 23.8 1.0
CA A:LEU163 4.5 21.5 1.0
N A:LEU163 4.5 23.2 1.0
CA A:LYS166 4.6 35.4 1.0
O B:PHE162 4.7 28.5 1.0
HD23 B:LEU163 4.7 32.2 1.0
N A:ILE164 4.8 26.2 1.0
C A:ILE164 4.8 37.4 1.0
HG22 B:THR168 4.8 53.3 1.0
O B:SER165 4.8 40.5 1.0
OG A:SER165 4.9 46.2 1.0
C B:LEU163 4.9 31.5 1.0
CB A:PHE162 4.9 21.9 1.0

Sodium binding site 2 out of 2 in 3om1

Go back to Sodium Binding Sites List in 3om1
Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution


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 GLUK5 (KA2) Atd Dimer at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:33.2
occ:1.00
O B:PHE162 2.4 28.5 1.0
O B:SER165 2.5 40.5 1.0
O B:GLU167 2.5 36.5 1.0
O B:HOH427 2.9 43.0 1.0
O A:HOH429 2.9 44.8 1.0
O B:HOH542 3.3 56.7 1.0
C B:SER165 3.4 39.0 1.0
NA A:NA401 3.5 36.2 1.0
H B:SER165 3.5 37.0 1.0
HA B:THR168 3.6 36.0 1.0
C B:PHE162 3.6 25.4 1.0
C B:GLU167 3.6 37.3 1.0
N B:SER165 3.8 30.9 1.0
O A:HOH428 3.8 40.0 1.0
HB3 B:SER165 3.9 55.3 1.0
CA B:SER165 4.1 36.1 1.0
C B:LYS166 4.1 38.6 1.0
HA B:PHE162 4.1 27.4 1.0
HA B:LEU163 4.1 31.6 1.0
N B:GLU167 4.2 41.9 1.0
O B:LYS166 4.3 35.6 1.0
HB3 B:PHE162 4.3 31.6 1.0
N B:LYS166 4.3 37.8 1.0
C B:LEU163 4.3 31.5 1.0
O A:LEU163 4.4 26.6 1.0
HA B:LYS166 4.4 58.1 1.0
H B:GLU167 4.4 50.2 1.0
HD1 B:PHE162 4.4 32.9 1.0
CA B:PHE162 4.4 22.9 1.0
CB B:SER165 4.4 46.1 1.0
CA B:THR168 4.4 30.0 1.0
O B:LEU163 4.4 32.7 1.0
N B:THR168 4.5 30.4 1.0
HG22 B:THR168 4.5 53.3 1.0
CA B:LYS166 4.5 48.5 1.0
N B:LEU163 4.5 24.4 1.0
CA B:GLU167 4.6 37.1 1.0
CA B:LEU163 4.6 26.3 1.0
C B:ILE164 4.6 37.6 1.0
N B:ILE164 4.6 30.1 1.0
HA A:LEU163 4.6 25.8 1.0
O A:SER165 4.7 35.2 1.0
H B:ILE164 4.8 36.1 1.0
OG B:SER165 4.9 58.9 1.0
CB B:PHE162 4.9 26.3 1.0
HG22 A:THR168 4.9 37.8 1.0
HD23 A:LEU163 5.0 29.6 1.0
HA B:SER165 5.0 43.3 1.0

Reference:

J.Kumar, M.L.Mayer. Crystal Structures of the Glutamate Receptor Ion Channel GLUK3 and GLUK5 Amino-Terminal Domains. J.Mol.Biol. V. 404 680 2010.
ISSN: ISSN 0022-2836
PubMed: 20951142
DOI: 10.1016/J.JMB.2010.10.006
Page generated: Tue Dec 15 06:20:09 2020

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