Zinc in PDB 4q30: Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5

The structure of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5, PDB code: 4q30 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)	44.04 / 2.03
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.797, 113.270, 164.321, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23

The binding sites of Zinc atom in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 (pdb code 4q30). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5, PDB code: 4q30:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:29.8 occ:1.00 NE2 B:HIS23 2.5 22.6 1.0 CD2 B:HIS23 3.3 22.3 1.0 CE1 B:HIS23 3.6 24.4 1.0 CG B:HIS23 4.5 22.5 1.0 CB B:MET19 4.6 21.1 1.0 ND1 B:HIS23 4.6 25.1 1.0 CG B:MET19 4.7 19.0 1.0

Zinc binding site 2 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:22.6 occ:1.00 OE1 F:GLU166 2.2 20.3 1.0 NE2 B:HIS46 2.2 21.5 1.0 O F:HOH819 2.4 14.0 1.0 OE1 B:GLU42 2.4 16.0 1.0 OE2 F:GLU166 2.5 25.1 1.0 CD F:GLU166 2.7 22.0 1.0 CD2 B:HIS46 3.1 19.5 1.0 CE1 B:HIS46 3.1 26.9 1.0 CD B:GLU42 3.3 22.6 1.0 OE2 B:GLU42 3.4 19.0 1.0 CG F:GLU166 4.2 22.7 1.0 ND1 B:HIS46 4.2 22.7 1.0 CG B:HIS46 4.2 18.9 1.0 N F:SER168 4.3 21.5 1.0 CD2 B:LEU241 4.7 17.7 1.0 CG B:GLU42 4.7 14.4 1.0 CE B:LYS45 4.8 41.6 1.0 CB F:SER168 4.8 22.8 1.0 CA F:SER168 4.8 21.2 1.0 CB F:GLU166 4.8 25.3 1.0 O F:ALA165 4.8 20.4 1.0 O F:HOH725 4.8 32.8 1.0 CA F:PRO167 4.9 23.9 1.0 C F:PRO167 4.9 22.0 1.0 CD B:LYS45 4.9 35.0 1.0

Zinc binding site 3 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:27.9 occ:1.00 NE2 D:HIS23 2.3 29.8 1.0 O D:HOH701 2.4 28.3 1.0 OE2 D:GLU24 2.5 52.4 1.0 CG D:GLU24 3.1 42.7 1.0 CD D:GLU24 3.2 55.3 1.0 CD2 D:HIS23 3.2 25.4 1.0 CE1 D:HIS23 3.3 33.6 1.0 ND1 D:HIS23 4.3 33.4 1.0 CG D:HIS23 4.4 31.0 1.0 OE1 D:GLU24 4.4 49.7 1.0 CE D:MET19 4.5 32.2 1.0 CB D:GLU24 4.6 40.3 1.0 O D:HOH798 4.9 34.0 1.0

Zinc binding site 4 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:42.7 occ:1.00 NE2 D:HIS46 2.4 33.8 1.0 OE1 D:GLU42 2.4 31.6 1.0 O D:HOH886 2.5 43.6 1.0 O D:HOH898 3.1 44.0 1.0 CD D:GLU42 3.2 33.0 1.0 OE2 D:GLU42 3.3 39.2 1.0 CE1 D:HIS46 3.3 36.4 1.0 CD2 D:HIS46 3.4 27.9 1.0 OE1 D:GLN244 4.0 35.1 1.0 CD2 D:LEU241 4.1 23.1 1.0 ND1 D:HIS46 4.5 34.1 1.0 CG D:HIS46 4.5 31.9 1.0 CG D:GLU42 4.6 24.1 1.0 CE D:LYS45 4.7 56.0 1.0 CD D:LYS45 4.9 38.1 1.0 CG2 D:VAL246 5.0 26.0 1.0 CD D:GLN244 5.0 34.0 1.0

Zinc binding site 5 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 at pH 3.5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn602 b:39.0 occ:1.00 O F:HOH820 2.2 34.4 1.0 NE2 F:HIS46 2.4 30.6 1.0 OE1 F:GLU42 2.5 41.3 1.0 CD2 F:HIS46 3.3 26.5 1.0 CE1 F:HIS46 3.4 36.0 1.0 CD F:GLU42 3.7 44.9 1.0 CD2 F:LEU241 3.7 21.6 1.0 OE1 F:GLN244 3.8 33.0 1.0 CE F:LYS45 4.3 41.5 1.0 CG F:GLU42 4.4 29.2 1.0 CG F:HIS46 4.4 29.5 1.0 ND1 F:HIS46 4.5 34.4 1.0 OE2 F:GLU42 4.7 43.6 1.0 CD F:GLN244 4.7 35.0 1.0 CB F:GLU42 4.7 23.1 1.0 CD F:LYS45 4.8 36.1 1.0 NE2 F:GLN244 4.9 37.0 1.0 CG2 F:VAL246 5.0 22.8 1.0

M.Martinez, A.H.Ahmed, A.P.Loh, R.E.Oswald. Thermodynamics and Mechanism of the Interaction of Willardiine Partial Agonists with A Glutamate Receptor: Implications For Drug Development. Biochemistry V. 53 3790 2014.
ISSN: ISSN 0006-2960
PubMed: 24850223
DOI: 10.1021/BI500511M