Zinc in PDB 3h03: Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277

The structure of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277, PDB code: 3h03 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)	28.10 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.953, 57.719, 105.461, 90.00, 114.88, 90.00
R / Rfree (%)	22.1 / 25.8

The binding sites of Zinc atom in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 (pdb code 3h03). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277, PDB code: 3h03:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:26.5 occ:1.00 NE2 A:HIS46 2.2 21.1 1.0 OE1 A:GLU42 2.2 14.4 1.0 CE1 A:HIS46 3.0 20.6 1.0 CD A:GLU42 3.0 11.4 1.0 CD2 A:HIS46 3.2 20.3 1.0 OE2 A:GLU42 3.2 13.1 1.0 CD2 A:LEU246 4.1 14.7 1.0 ND1 A:HIS46 4.1 20.9 1.0 CD2 A:LEU241 4.2 7.3 1.0 CG A:HIS46 4.2 21.2 1.0 OE1 A:GLN244 4.3 15.4 1.0 CG A:GLU42 4.5 9.5 1.0 CB A:GLU42 4.8 7.6 1.0 O A:GLU42 4.9 8.7 1.0 CA A:GLU42 5.0 7.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn262 b:46.7 occ:1.00 NE2 A:HIS23 2.3 9.7 1.0 CD2 A:HIS23 3.2 8.3 1.0 CE1 A:HIS23 3.4 9.2 1.0 CG A:HIS23 4.4 9.1 1.0 ND1 A:HIS23 4.5 9.4 1.0 OE1 A:GLU24 4.9 22.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:19.5 occ:1.00 NE2 B:HIS46 2.1 12.5 1.0 OE1 B:GLU42 2.4 17.0 1.0 CD B:GLU42 3.0 14.3 1.0 CD2 B:HIS46 3.0 12.8 1.0 CE1 B:HIS46 3.1 13.9 1.0 OE2 B:GLU42 3.1 16.1 1.0 CD B:LYS45 4.0 23.0 1.0 OE1 B:GLN244 4.0 19.2 1.0 CD2 B:LEU241 4.0 7.2 1.0 CE B:LYS45 4.2 24.1 1.0 CG B:HIS46 4.2 14.4 1.0 ND1 B:HIS46 4.2 14.3 1.0 CG B:GLU42 4.4 11.2 1.0 CB B:GLU42 4.7 9.0 1.0 CD B:GLN244 4.9 19.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn262 b:22.9 occ:1.00 OE2 B:GLU24 2.1 25.5 1.0 NE2 B:HIS23 2.2 11.6 1.0 CD B:GLU24 3.0 23.9 1.0 CD2 B:HIS23 3.0 12.8 1.0 CE1 B:HIS23 3.2 13.0 1.0 CG B:GLU24 3.3 21.1 1.0 OE1 B:GLU24 4.2 24.8 1.0 CG B:HIS23 4.2 12.5 1.0 ND1 B:HIS23 4.3 11.1 1.0 CB B:GLU24 4.7 20.3 1.0 O B:HOH281 4.9 15.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:47.3 occ:1.00 NE2 D:HIS23 2.4 13.4 1.0 CD2 D:HIS23 3.2 11.6 1.0 CE1 D:HIS23 3.5 13.3 1.0 OE1 D:GLU24 3.9 32.0 1.0 OD2 G:ASP139 4.3 25.6 1.0 OD1 G:ASP139 4.3 27.5 1.0 CG D:HIS23 4.4 12.0 1.0 ND1 D:HIS23 4.5 12.9 1.0 CD D:GLU24 4.6 28.3 1.0 OE2 D:GLU24 4.6 27.0 1.0 CG G:ASP139 4.7 24.0 1.0 NH1 G:ARG172 4.9 40.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn262 b:24.8 occ:1.00 OE2 D:GLU42 2.1 12.9 1.0 NE2 D:HIS46 2.2 18.4 1.0 CD D:GLU42 3.0 10.2 1.0 CD2 D:HIS46 3.1 18.0 1.0 OE1 D:GLU42 3.1 13.2 1.0 CE1 D:HIS46 3.2 18.3 1.0 O D:HOH489 3.7 36.0 1.0 CD1 D:LEU246 4.2 15.0 1.0 CD2 D:LEU241 4.2 5.5 1.0 CG D:HIS46 4.2 19.2 1.0 ND1 D:HIS46 4.3 18.5 1.0 OE1 D:GLN244 4.3 18.3 1.0 CG D:GLU42 4.4 10.0 1.0 CB D:GLU42 4.8 8.0 1.0 O D:GLU42 4.9 9.9 1.0 CA D:GLU42 5.0 8.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn262 b:20.3 occ:1.00 NE2 G:HIS46 2.1 12.5 1.0 OE1 G:GLU42 2.1 14.8 1.0 CD2 G:HIS46 3.0 12.9 1.0 CD G:GLU42 3.1 12.8 1.0 CE1 G:HIS46 3.1 13.2 1.0 OE2 G:GLU42 3.3 14.0 1.0 OE1 G:GLN244 4.0 18.2 1.0 CD G:LYS45 4.0 21.4 1.0 CD2 G:LEU241 4.1 7.7 1.0 ND1 G:HIS46 4.2 14.6 1.0 CG G:HIS46 4.2 14.9 1.0 CE G:LYS45 4.3 22.5 1.0 CG G:GLU42 4.5 10.2 1.0 CG A:GLU166 4.8 25.1 1.0 CB G:GLU42 4.8 7.6 1.0 CD2 G:LEU246 4.8 13.5 1.0 CD G:GLN244 4.9 19.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn263 b:22.5 occ:1.00 NE2 G:HIS23 2.2 12.5 1.0 OE1 G:GLU24 2.2 22.9 1.0 OD2 D:ASP139 2.2 16.5 1.0 OD1 D:ASP139 2.8 10.9 1.0 CG D:ASP139 2.9 11.4 1.0 CD2 G:HIS23 3.1 10.8 1.0 CE1 G:HIS23 3.2 9.9 1.0 CD G:GLU24 3.4 22.5 1.0 O D:HOH306 3.8 15.8 1.0 CB D:SER140 4.1 17.6 1.0 OE2 G:GLU24 4.2 23.9 1.0 CG G:HIS23 4.2 11.0 1.0 ND1 G:HIS23 4.3 10.3 1.0 CG D:ARG172 4.3 13.2 1.0 CB D:ASP139 4.3 11.5 1.0 CG G:GLU24 4.5 21.4 1.0 CB G:GLU24 4.7 18.8 1.0 C D:ASP139 4.8 11.6 1.0 N D:SER140 4.8 12.6 1.0 CD D:ARG172 4.9 14.9 1.0 O G:HOH414 4.9 16.1 1.0 O D:ASP139 5.0 11.9 1.0

A.H.Ahmed, M.D.Thompson, M.K.Fenwick, B.Romero, A.P.Loh, D.E.Jane, H.Sondermann, R.E.Oswald. Mechanisms of Antagonism of the GLUR2 Ampa Receptor: Structure and Dynamics of the Complex of Two Willardiine Antagonists with the Glutamate Binding Domain. Biochemistry V. 48 3894 2009.
ISSN: ISSN 0006-2960
PubMed: 19284741
DOI: 10.1021/BI900107M