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Rubidium in PDB 3c34: Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution, PDB code: 3c34 was solved by M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.10 / 1.82
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.952, 70.952, 234.326, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.9

Other elements in 3c34:

The structure of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution (pdb code 3c34). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution, PDB code: 3c34:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 3c34

Go back to Rubidium Binding Sites List in 3c34
Rubidium binding site 1 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb302

b:24.0
occ:0.65
 O A:GLU96 2.6 11.7 1.0
OD1 A:ASP100 2.7 19.0 1.0
O A:ILE99 2.9 11.1 1.0
O B:HOH671 3.0 27.8 1.0
O B:HOH672 3.0 36.3 1.0
OE2 A:GLU96 3.1 26.2 1.0
O A:HOH559 3.5 35.9 1.0
O A:HOH404 3.5 22.9 1.0
C A:GLU96 3.7 11.3 1.0
CG A:ASP100 3.9 17.2 1.0
C A:ILE99 3.9 10.1 1.0
CA A:ASP100 4.1 12.7 1.0
CA A:GLU96 4.3 10.7 1.0
CD A:GLU96 4.3 24.1 1.0
N A:ASP100 4.4 9.8 1.0
CB A:GLU96 4.5 11.9 1.0
CG1 A:ILE222 4.5 15.6 1.0
O B:HOH773 4.5 22.5 0.3
CB A:ASP100 4.6 13.2 1.0
CD1 B:ILE232 4.7 16.8 1.0
CG B:ASP228 4.8 18.1 1.0
OD2 A:ASP100 4.8 17.9 1.0
N A:LYS97 4.9 10.1 1.0
CD1 A:ILE222 4.9 22.1 1.0
CB B:ASP228 4.9 13.5 1.0
OD2 B:ASP228 4.9 19.2 1.0
CG A:GLU96 5.0 15.8 1.0

Rubidium binding site 2 out of 6 in 3c34

Go back to Rubidium Binding Sites List in 3c34
Rubidium binding site 2 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb303

b:27.7
occ:0.60
 O A:SER22 2.7 18.9 1.0
O A:HOH667 2.8 25.2 1.0
C A:SER22 3.9 19.0 1.0
O A:HOH460 3.9 30.2 1.0
C A:ASP23 4.1 19.1 1.0
O A:ASP23 4.2 21.1 1.0
O A:LYS24 4.3 14.7 1.0
N A:LYS24 4.4 17.8 1.0
CA A:ASP23 4.4 19.8 1.0
C A:LYS24 4.6 14.5 1.0
N A:ASP23 4.6 18.6 1.0
CA A:LYS24 4.8 17.0 1.0
N A:SER22 4.8 18.8 1.0
CA A:SER22 4.9 18.6 1.0

Rubidium binding site 3 out of 6 in 3c34

Go back to Rubidium Binding Sites List in 3c34
Rubidium binding site 3 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb304

b:28.9
occ:0.65
 O A:LEU181 2.7 12.5 1.0
C A:LEU181 4.0 13.4 1.0
CA A:THR182 4.6 14.3 1.0
N A:THR182 4.8 12.4 1.0
O A:HOH496 4.9 27.5 1.0

Rubidium binding site 4 out of 6 in 3c34

Go back to Rubidium Binding Sites List in 3c34
Rubidium binding site 4 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb305

b:45.4
occ:0.60
 O A:LYS150 2.8 17.3 1.0
OE1 A:GLU155 3.1 23.3 1.0
O A:HOH468 3.7 38.5 1.0
N A:SER152 3.7 19.4 1.0
CD A:GLU155 3.9 20.5 1.0
CB A:SER152 3.9 21.4 1.0
O A:HOH540 4.0 40.1 1.0
CA A:SER152 4.0 20.2 1.0
C A:LYS150 4.0 17.3 1.0
OE2 A:GLU155 4.1 21.1 1.0
C A:ILE151 4.3 18.2 1.0
OG A:SER152 4.5 26.5 1.0
CA A:ILE151 4.6 18.0 1.0
N A:ILE151 4.8 16.7 1.0
CA A:LYS150 4.9 17.1 1.0

Rubidium binding site 5 out of 6 in 3c34

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Rubidium binding site 5 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb301

b:25.9
occ:0.70
 O B:GLU96 2.7 12.8 1.0
OD1 B:ASP100 2.8 19.3 1.0
O B:HOH926 2.8 40.5 1.0
O B:ILE99 2.9 12.3 1.0
OE1 B:GLU96 3.1 33.9 1.0
O A:HOH405 3.1 27.9 1.0
O B:HOH774 3.2 37.7 1.0
O B:HOH925 3.7 21.8 0.5
C B:GLU96 3.8 12.7 1.0
CG B:GLU96 3.9 20.1 1.0
C B:ILE99 3.9 11.1 1.0
CD B:GLU96 3.9 28.0 1.0
CG B:ASP100 4.0 18.0 1.0
CA B:ASP100 4.1 14.1 1.0
O B:HOH778 4.3 31.8 1.0
N B:ASP100 4.4 11.4 1.0
CA B:GLU96 4.5 12.8 1.0
CG1 B:ILE222 4.6 14.7 1.0
CB B:ASP100 4.7 14.1 1.0
CB B:GLU96 4.8 16.6 1.0
OD2 A:ASP228 4.8 23.2 1.0
CG A:ASP228 4.8 18.5 1.0
CD1 A:ILE232 4.9 18.3 1.0
N B:LYS97 4.9 11.9 1.0
OD2 B:ASP100 4.9 18.7 1.0
N B:ILE99 4.9 9.6 1.0
C B:LYS97 4.9 12.2 1.0

Rubidium binding site 6 out of 6 in 3c34

Go back to Rubidium Binding Sites List in 3c34
Rubidium binding site 6 out of 6 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Rubidium at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb306

b:37.9
occ:0.60
 O B:HOH769 2.6 30.2 1.0
O B:ILE120 2.7 18.0 1.0
O B:THR118 2.9 20.4 1.0
OD1 B:ASP121 3.0 33.7 1.0
C B:ILE120 3.7 19.8 1.0
O B:HOH691 3.8 27.4 1.0
C B:THR118 4.0 19.8 1.0
N B:ILE120 4.1 20.0 1.0
CG B:ASP121 4.1 29.1 1.0
C B:PRO119 4.2 21.0 1.0
CA B:ASP121 4.4 21.3 1.0
CD1 B:ILE207 4.5 13.6 1.0
CA B:PRO119 4.5 20.8 1.0
OG1 B:THR118 4.5 18.7 1.0
N B:ASP121 4.5 19.9 1.0
O B:PRO119 4.5 21.1 1.0
O B:HOH794 4.6 33.0 1.0
CA B:ILE120 4.6 19.5 1.0
O B:HOH802 4.6 36.2 1.0
O B:HOH845 4.6 41.5 1.0
N B:PRO119 4.7 20.0 1.0
CB B:ASP121 4.8 22.8 1.0
N B:THR118 4.9 20.3 1.0

Reference:

A.J.Plested, R.Vijayan, P.C.Biggin, M.L.Mayer. Molecular Basis of Kainate Receptor Modulation By Sodium. Neuron V. 58 720 2008.
ISSN: ISSN 0896-6273
PubMed: 18549784
DOI: 10.1016/J.NEURON.2008.04.001
Page generated: Thu Oct 10 11:59:42 2024

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