Zinc in PDB 3dp6: Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate

The structure of Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate, PDB code: 3dp6 was solved by A.H.Ahmed, Q.Wang, H.Sondermann, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.840, 163.184, 47.324, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.4

The binding sites of Zinc atom in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate (pdb code 3dp6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate, PDB code: 3dp6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:63.3 occ:1.00 NE2 A:HIS23 2.2 15.0 1.0 O A:HOH465 2.5 25.0 1.0 CE1 A:HIS23 3.1 17.6 1.0 CD2 A:HIS23 3.2 17.1 1.0 ND1 A:HIS23 4.3 16.4 1.0 CG A:HIS23 4.4 15.6 1.0 OE2 A:GLU24 4.7 20.9 1.0 CB A:MET19 4.9 15.1 1.0 CG A:MET19 5.0 18.4 1.0 CG A:GLU24 5.0 20.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:39.4 occ:1.00 OE2 C:GLU166 2.1 13.5 1.0 OE1 A:GLU42 2.1 13.3 1.0 NE2 A:HIS46 2.1 9.6 1.0 NZ A:LYS45 2.2 11.7 1.0 OE1 C:GLU166 2.6 14.6 1.0 CD C:GLU166 2.7 15.1 1.0 CE A:LYS45 2.8 19.6 1.0 CD A:GLU42 3.0 16.6 1.0 CD2 A:HIS46 3.1 14.9 1.0 CE1 A:HIS46 3.1 15.5 1.0 OE2 A:GLU42 3.2 13.9 1.0 CD A:LYS45 4.1 19.9 1.0 CG C:GLU166 4.2 16.7 1.0 CD2 A:LEU241 4.2 14.2 1.0 N C:SER168 4.2 12.1 1.0 ND1 A:HIS46 4.2 15.0 1.0 CG A:HIS46 4.2 12.9 1.0 CG A:GLU42 4.3 12.2 1.0 O C:ALA165 4.6 13.0 1.0 CB C:SER168 4.7 14.2 1.0 CB A:GLU42 4.7 12.6 1.0 CA C:SER168 4.8 12.4 1.0 CB C:GLU166 4.8 15.2 1.0 C C:PRO167 4.9 13.4 1.0 CA C:PRO167 4.9 13.5 1.0 CA C:GLU166 4.9 14.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:79.2 occ:1.00 NE2 B:HIS23 2.7 25.9 1.0 CD2 B:HIS23 3.1 27.1 1.0 CG B:GLU24 3.5 20.9 1.0 OE2 B:GLU24 3.7 20.9 1.0 CE1 B:HIS23 3.9 27.2 1.0 CD B:GLU24 4.0 20.9 1.0 CG B:HIS23 4.4 29.2 1.0 CB B:GLU24 4.5 20.9 1.0 CA B:GLU24 4.6 20.9 1.0 ND1 B:HIS23 4.8 26.8 1.0 N B:GLU24 4.8 20.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.0 occ:1.00 NE2 B:HIS46 2.6 57.4 1.0 OE2 B:GLU42 2.7 55.2 1.0 NZ B:LYS45 3.1 58.9 1.0 CE1 B:HIS46 3.3 58.1 1.0 CD B:GLU42 3.4 50.0 1.0 OE1 B:GLU42 3.6 56.3 1.0 O B:HOH535 3.6 64.8 1.0 CD2 B:HIS46 3.7 54.4 1.0 CE B:LYS45 4.0 55.0 1.0 CD2 B:LEU241 4.1 14.8 1.0 ND1 B:HIS46 4.5 53.0 1.0 CD2 B:LEU246 4.6 22.5 1.0 CG B:HIS46 4.7 51.1 1.0 CG B:GLU42 4.7 46.1 1.0 CG B:LEU246 4.9 19.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Binding Domain of the Ampa Subunit GLUR2 Bound to Glutamate


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:77.1 occ:1.00 NE2 C:HIS23 2.3 12.3 1.0 CD2 C:HIS23 3.0 14.8 1.0 CE1 C:HIS23 3.5 12.5 1.0 NZ C:LYS20 3.7 16.0 1.0 O C:GLU30 3.7 15.3 1.0 CD C:LYS20 4.0 15.1 1.0 CG C:HIS23 4.2 13.6 1.0 CD1 C:LEU26 4.4 19.8 1.0 ND1 C:HIS23 4.5 13.0 1.0 CB C:GLU30 4.5 15.5 1.0 CE C:LYS20 4.5 15.2 1.0 C C:GLU30 4.5 13.3 1.0

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


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 Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:2.3 occ:1.00 OE1 C:GLU42 1.9 9.2 1.0 NE2 C:HIS46 2.0 13.3 1.0 O C:HOH375 2.4 1.9 1.0 CD C:GLU42 2.9 12.4 1.0 CD2 C:HIS46 3.0 12.6 1.0 CE1 C:HIS46 3.0 15.2 1.0 OE2 C:GLU42 3.2 15.8 1.0 CD2 C:LEU241 3.6 16.6 1.0 O C:HOH565 3.8 29.1 1.0 NZ C:LYS45 3.9 13.6 1.0 CE C:LYS45 3.9 13.2 1.0 O C:HOH553 4.1 30.1 1.0 ND1 C:HIS46 4.1 13.5 1.0 CG C:HIS46 4.2 12.9 1.0 OE1 C:GLN244 4.2 21.2 1.0 CG C:GLU42 4.2 12.2 1.0 CB C:GLU42 4.6 12.1 1.0

A.H.Ahmed, Q.Wang, H.Sondermann, R.E.Oswald. Structure of the S1S2 Glutamate Binding Domain of GLUR3. Proteins V. 75 628 2008.
ISSN: ISSN 0887-3585
PubMed: 19003990
DOI: 10.1002/PROT.22274