Zinc in PDB 3rtf: Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2

The structure of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2, PDB code: 3rtf was solved by A.H.Ahmed, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.70 / 1.70
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.137, 113.928, 163.333, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.3

The structure of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 (pdb code 3rtf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2, PDB code: 3rtf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:28.9 occ:1.00 NE2 B:HIS23 2.2 26.1 1.0 CE1 B:HIS23 3.2 29.4 1.0 CD2 B:HIS23 3.2 29.1 1.0 O B:HOH892 3.7 47.3 1.0 O B:HOH454 4.0 40.2 1.0 ND1 B:HIS23 4.3 29.1 1.0 CG B:HIS23 4.4 26.0 1.0 CB B:MET19 4.8 25.4 1.0 CG B:MET19 4.9 27.6 1.0

Zinc binding site 2 out of 5 in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:21.6 occ:1.00 NE2 B:HIS46 2.2 21.1 1.0 OE1 F:GLU166 2.3 18.5 1.0 NZ B:LYS45 2.5 1.6 1.0 OE1 B:GLU42 2.5 20.8 1.0 OE2 F:GLU166 2.8 24.0 1.0 CD F:GLU166 2.9 25.3 1.0 CE B:LYS45 2.9 34.0 1.0 CD B:LYS45 3.0 37.6 1.0 CE1 B:HIS46 3.1 24.2 1.0 CD2 B:HIS46 3.1 21.7 1.0 CD B:GLU42 3.4 22.0 1.0 OE2 B:GLU42 3.5 20.1 1.0 ND1 B:HIS46 4.2 22.0 1.0 CG B:HIS46 4.2 21.4 1.0 N F:SER168 4.2 17.6 1.0 CB F:SER168 4.3 19.2 1.0 CG B:LYS45 4.4 34.8 1.0 CG F:GLU166 4.4 24.4 1.0 CA F:SER168 4.5 16.3 1.0 O F:ALA165 4.6 18.8 1.0 CG B:GLU42 4.8 15.5 1.0 CD2 B:LEU241 4.8 25.7 1.0

Zinc binding site 3 out of 5 in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:62.1 occ:1.00 NE2 D:HIS46 2.4 41.7 1.0 OE1 D:GLU42 2.5 37.9 1.0 O D:HOH531 2.8 55.6 1.0 CD2 D:HIS46 3.3 36.9 1.0 NZ D:LYS45 3.4 54.8 1.0 CE1 D:HIS46 3.4 42.9 1.0 CD D:GLU42 3.5 36.5 1.0 O D:HOH330 3.7 43.9 1.0 OE2 D:GLU42 3.9 42.6 1.0 CD2 D:LEU241 3.9 27.3 1.0 CE D:LYS45 4.2 52.6 1.0 ND1 D:HIS46 4.5 40.3 1.0 CG D:HIS46 4.5 35.1 1.0 CD D:LYS45 4.6 40.4 1.0 CG D:GLU42 4.8 26.3 1.0 CB D:GLU42 4.9 22.6 1.0 CD2 D:LEU246 5.0 36.6 1.0

Zinc binding site 4 out of 5 in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:25.1 occ:1.00 NE2 D:HIS23 2.3 23.9 1.0 OE1 D:GLU24 2.9 49.7 1.0 CD2 D:HIS23 3.1 26.5 1.0 CE1 D:HIS23 3.3 24.2 1.0 CD D:GLU24 4.1 42.7 1.0 CG D:HIS23 4.3 22.3 1.0 CB D:GLU24 4.3 33.4 1.0 ND1 D:HIS23 4.4 23.4 1.0 O D:HOH472 4.7 37.8 1.0 CG D:GLU24 4.8 39.7 1.0 CE D:MET19 4.8 13.9 1.0 O D:HOH278 5.0 32.8 1.0 OE2 D:GLU24 5.0 29.6 1.0

Zinc binding site 5 out of 5 in the Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Chlorowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1 b:22.2 occ:1.00 NE2 F:HIS46 2.3 22.5 1.0 OE1 F:GLU42 2.3 22.4 1.0 CD F:GLU42 3.1 20.9 1.0 CE1 F:HIS46 3.2 25.8 1.0 OE2 F:GLU42 3.3 25.0 1.0 CD2 F:HIS46 3.3 20.5 1.0 CD2 F:LEU241 3.5 23.9 1.0 O F:HOH794 3.6 44.3 1.0 O F:HOH656 3.7 37.8 1.0 OE1 F:GLN244 3.8 34.6 1.0 NZ F:LYS45 4.3 23.1 1.0 CE F:LYS45 4.3 24.3 1.0 ND1 F:HIS46 4.4 26.5 1.0 CG F:GLU42 4.4 17.5 1.0 CG F:HIS46 4.5 18.0 1.0 CB F:GLU42 4.8 15.8 1.0 CG F:LEU241 4.9 19.8 1.0 CD F:GLN244 4.9 38.1 1.0 CD1 F:LEU246 4.9 27.6 1.0

K.Poon, A.H.Ahmed, L.M.Nowak, R.E.Oswald. Mechanisms of Modal Activation of GLUA3 Receptors. Mol.Pharmacol. V. 80 49 2011.
ISSN: ISSN 0026-895X
PubMed: 21464198
DOI: 10.1124/MOL.111.071688