Zinc in PDB 3m3l: Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)

The structure of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3m3l was solved by C.P.Ptak, 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)	25.29 / 1.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.127, 113.924, 164.806, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 24.2

The structure of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) (pdb code 3m3l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3m3l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn262 b:2.5 occ:1.00 NE2 A:HIS46 2.1 21.2 1.0 OE1 G:GLU166 2.1 33.7 1.0 OE2 G:GLU166 2.5 43.9 1.0 CD G:GLU166 2.5 32.6 1.0 OE1 A:GLU42 2.8 21.5 1.0 CE1 A:HIS46 2.9 25.3 1.0 O A:HOH263 3.0 13.8 1.0 CD2 A:HIS46 3.1 23.7 1.0 CD A:GLU42 3.6 21.8 1.0 OE2 A:GLU42 3.7 22.4 1.0 CG G:GLU166 4.0 24.2 1.0 ND1 A:HIS46 4.1 23.6 1.0 CG A:HIS46 4.2 22.1 1.0 CD2 A:LEU241 4.2 23.6 1.0 O G:ALA165 4.4 17.1 1.0 N G:SER168 4.6 20.0 1.0 O G:HOH300 4.7 22.4 1.0 CB G:GLU166 4.7 17.9 1.0 NZ A:LYS45 4.8 36.8 1.0 CE A:LYS45 4.9 38.7 1.0 CA G:GLU166 4.9 20.2 1.0 CG A:GLU42 4.9 16.8 1.0 CD A:LYS45 5.0 37.4 1.0

Zinc binding site 2 out of 5 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:3.0 occ:1.00 OD2 D:ASP65 2.6 33.8 1.0 OD1 D:ASP65 3.0 33.6 1.0 CG D:ASP65 3.1 31.1 1.0 O D:HOH696 3.9 41.6 1.0 OD1 D:ASP67 4.0 44.4 1.0 O D:HOH475 4.1 34.5 1.0 CG D:ASP67 4.5 46.4 1.0 CB D:ASP67 4.5 38.1 1.0 CB D:ASP65 4.6 24.8 1.0 OG1 D:THR68 4.6 38.9 1.0 O D:HOH848 4.7 35.7 1.0 O D:HOH813 4.9 39.1 1.0

Zinc binding site 3 out of 5 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:16.1 occ:1.00 OE1 D:GLU42 2.3 30.1 1.0 NE2 D:HIS46 2.4 32.1 1.0 CD D:GLU42 3.1 31.4 1.0 CD2 D:HIS46 3.3 24.7 1.0 OE2 D:GLU42 3.3 35.6 1.0 CE1 D:HIS46 3.4 30.6 1.0 NE2 D:GLN244 3.9 20.0 1.0 CD2 D:LEU241 4.0 22.5 1.0 CG D:HIS46 4.5 30.2 1.0 ND1 D:HIS46 4.5 36.3 1.0 CD2 D:LEU246 4.5 30.6 1.0 CG D:GLU42 4.5 23.5 1.0 OE1 D:GLN244 4.7 20.0 1.0 CD D:GLN244 4.8 20.0 1.0 CB D:GLU42 4.9 20.0 1.0 CE D:LYS45 4.9 42.4 1.0

Zinc binding site 4 out of 5 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn262 b:40.0 occ:1.00 NE2 D:HIS23 2.1 39.6 1.0 O D:HOH951 2.4 34.5 1.0 CD2 D:HIS23 2.8 46.1 1.0 O D:HOH742 3.0 22.9 1.0 CE1 D:HIS23 3.3 0.7 1.0 CG D:HIS23 4.1 40.2 1.0 ND1 D:HIS23 4.3 46.2 1.0 CE D:MET19 4.5 27.8 1.0 O D:HOH332 4.6 32.6 1.0

Zinc binding site 5 out of 5 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn3 b:23.0 occ:1.00 OE1 G:GLU42 1.7 27.4 1.0 NE2 G:HIS46 2.2 27.2 1.0 CD G:GLU42 2.6 25.1 1.0 OE2 G:GLU42 3.0 26.4 1.0 CD2 G:HIS46 3.0 17.5 1.0 CE1 G:HIS46 3.3 21.8 1.0 CD2 G:LEU241 3.5 24.9 1.0 CD2 G:LEU246 3.6 30.2 1.0 CE G:LYS45 3.7 39.8 1.0 NE2 G:GLN244 3.7 20.0 1.0 NZ G:LYS45 3.8 39.3 1.0 CG G:GLU42 4.0 17.9 1.0 CG G:HIS46 4.2 22.0 1.0 CB G:GLU42 4.3 16.5 1.0 ND1 G:HIS46 4.3 27.4 1.0 CA G:GLU42 4.9 15.4 1.0 CD G:GLN244 4.9 20.0 1.0 O G:GLU42 4.9 16.2 1.0 CG G:LEU241 5.0 21.5 1.0

A.H.Ahmed, C.P.Ptak, R.E.Oswald. Molecular Mechanism of Flop Selectivity and Subsite Recognition For An Ampa Receptor Allosteric Modulator: Structures of GLUA2 and GLUA3 in Complexes with Pepa. Biochemistry V. 49 2843 2010.
ISSN: ISSN 0006-2960
PubMed: 20199107
DOI: 10.1021/BI1000678