Atomistry » Sodium » PDB 6dmi-6e8s » 6e7v
Atomistry »
  Sodium »
    PDB 6dmi-6e8s »
      6e7v »

Sodium in PDB 6e7v: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88

Protein crystallography data

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88, PDB code: 6e7v was solved by M.C.Regan, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 268.131, 59.612, 145.526, 90.00, 116.86, 90.00
R / Rfree (%) 19.1 / 23.3

Other elements in 6e7v:

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 also contains other interesting chemical elements:

Chlorine (Cl) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 (pdb code 6e7v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88, PDB code: 6e7v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6e7v

Go back to Sodium Binding Sites List in 6e7v
Sodium binding site 1 out of 2 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:30.4
occ:1.00
O A:PHE137 2.2 32.7 1.0
O A:HOH629 2.3 28.5 1.0
O A:ASP364 2.4 33.9 1.0
O A:HOH636 2.7 33.2 1.0
O A:HOH658 3.3 38.9 1.0
C A:PHE137 3.4 31.0 1.0
O A:HOH690 3.4 17.4 1.0
C A:ASP364 3.5 33.2 1.0
O A:TYR128 3.9 27.6 1.0
CA A:GLY365 4.1 31.4 1.0
CA A:PHE137 4.1 30.3 1.0
CB A:PHE137 4.2 29.1 1.0
N A:GLY365 4.2 33.1 1.0
N A:PHE137 4.3 32.7 1.0
O A:HIS134 4.4 29.3 1.0
N A:LEU138 4.4 29.2 1.0
CA A:ASP364 4.5 34.4 1.0
C A:GLY365 4.5 28.5 1.0
CD1 A:PHE137 4.6 28.6 1.0
CA A:SER129 4.6 29.6 1.0
CA A:LEU138 4.7 29.4 1.0
O A:GLY365 4.8 25.8 1.0
O A:SER129 4.8 34.9 1.0
CG A:PHE137 4.9 30.1 1.0
C A:SER129 4.9 30.1 1.0
C A:TYR128 4.9 26.9 1.0
CB A:ASP364 5.0 34.0 1.0

Sodium binding site 2 out of 2 in 6e7v

Go back to Sodium Binding Sites List in 6e7v
Sodium binding site 2 out of 2 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:37.2
occ:1.00
O C:PHE137 2.2 37.0 1.0
O C:ASP364 2.2 40.1 1.0
O C:HOH651 2.3 49.3 1.0
O C:HOH634 2.4 30.3 1.0
O C:HOH622 2.6 31.2 1.0
C C:ASP364 3.4 42.2 1.0
C C:PHE137 3.4 36.9 1.0
O C:HOH646 3.8 28.0 1.0
O C:TYR128 3.9 31.4 1.0
CA C:GLY365 4.0 39.0 1.0
N C:GLY365 4.1 40.2 1.0
CA C:PHE137 4.2 36.2 1.0
CB C:PHE137 4.2 34.3 1.0
N C:PHE137 4.3 38.6 1.0
C C:GLY365 4.4 36.9 1.0
O C:HIS134 4.4 33.5 1.0
CA C:ASP364 4.4 44.0 1.0
N C:LEU138 4.4 37.7 1.0
CD1 C:PHE137 4.6 31.7 1.0
CA C:LEU138 4.7 38.2 1.0
O C:GLY365 4.7 34.6 1.0
CA C:SER129 4.7 32.0 1.0
O C:SER129 4.9 32.0 1.0
C C:SER129 4.9 33.0 1.0
CB C:ASP364 4.9 45.5 1.0
OD1 C:ASP366 4.9 38.6 1.0
CG C:PHE137 5.0 33.3 1.0
C C:TYR128 5.0 32.0 1.0

Reference:

M.C.Regan, H.Furukawa. Structural Elements of A pH-Sensitive Inhibitor Binding Site in Nmda Receptors Nat Commun V. 10 321 2019.
ISSN: ESSN 2041-1723
Page generated: Tue Dec 15 12:09:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy