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Sodium in PDB 3bft: Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution

Protein crystallography data

The structure of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution, PDB code: 3bft was solved by M.Beich-Frandsen, O.Mirza, B.Vestergaard, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.27
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.820, 163.333, 47.270, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25

Other elements in 3bft:

The structure of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 5 atoms
Arsenic (As) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution (pdb code 3bft). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution, PDB code: 3bft:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3bft

Go back to Sodium Binding Sites List in 3bft
Sodium binding site 1 out of 2 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:50.1
occ:1.00
O A:HOH1137 2.4 42.8 1.0
OD1 A:ASP156 2.4 51.4 1.0
O A:HOH1119 2.5 45.9 1.0
CG A:ASP156 3.1 49.9 1.0
OD2 A:ASP156 3.2 51.7 1.0
OG1 A:THR160 4.0 45.9 1.0
O A:ASP156 4.6 42.9 1.0
CB A:ASP156 4.6 47.7 1.0
NH1 A:ARG163 4.7 60.5 1.0

Sodium binding site 2 out of 2 in 3bft

Go back to Sodium Binding Sites List in 3bft
Sodium binding site 2 out of 2 in the Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Ligand-Binding Core of GLUR2 in Complex with the Agonist (S)-Tdpa at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:44.2
occ:1.00
O B:HOH1605 2.1 51.6 1.0
OD1 B:ASP156 2.2 43.0 1.0
O B:HOH1541 2.7 53.8 1.0
O B:HOH1574 3.2 45.2 1.0
CG B:ASP156 3.3 40.9 1.0
OD2 B:ASP156 3.8 45.2 1.0
OG1 B:THR160 4.2 28.4 1.0
NH1 B:ARG163 4.2 50.3 1.0
CD1 B:TRP159 4.4 20.2 1.0
O B:ASP156 4.4 34.3 1.0
NH2 B:ARG163 4.4 50.1 1.0
CB B:ASP156 4.5 37.3 1.0
CZ B:ARG163 4.7 48.2 1.0
CA B:ASP156 4.8 34.5 1.0
C B:ASP156 5.0 33.6 1.0

Reference:

M.Beich-Frandsen, D.S.Pickering, O.Mirza, T.N.Johansen, J.Greenwood, B.Vestergaard, A.Schousboe, M.Gajhede, T.Liljefors, J.S.Kastrup. Structures of the Ligand-Binding Core of IGLUR2 in Complex with the Agonists (R)- and (S)-2-Amino-3-(4-Hydroxy-1,2,5-Thiadiazol-3-Yl)Propionic Acid Explain Their Unusual Equipotency. J.Med.Chem. V. 51 1459 2008.
ISSN: ISSN 0022-2623
PubMed: 18269227
DOI: 10.1021/JM701126W
Page generated: Tue Dec 15 06:03:26 2020

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