Zinc in PDB 4o3a: Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution, PDB code: 4o3a was solved by C.Krintel, F.Frydenvang, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.25 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.661, 162.211, 47.346, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.8

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution (pdb code 4o3a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution, PDB code: 4o3a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:18.1 occ:1.00 OE2 A:GLU30 1.9 21.2 1.0 OXT A:ACT308 2.0 26.8 1.0 NE2 C:HIS23 2.0 20.4 1.0 NE2 A:HIS23 2.0 18.7 1.0 O A:ACT308 2.5 39.9 1.0 C A:ACT308 2.6 30.3 1.0 CD A:GLU30 2.8 22.7 1.0 OE1 A:GLU30 2.9 20.0 1.0 CE1 C:HIS23 3.0 20.2 1.0 CE1 A:HIS23 3.0 19.3 1.0 CD2 C:HIS23 3.0 20.0 1.0 CD2 A:HIS23 3.0 18.2 1.0 CG C:GLU24 3.9 38.3 1.0 NZ A:LYS20 4.0 19.9 1.0 CD A:LYS20 4.0 15.3 1.0 ND1 C:HIS23 4.1 19.7 1.0 CH3 A:ACT308 4.1 42.6 1.0 ND1 A:HIS23 4.1 19.1 1.0 CG C:HIS23 4.2 19.6 1.0 CG A:GLU30 4.2 32.5 1.0 CG A:HIS23 4.2 18.4 1.0 SD C:MET19 4.3 23.1 0.7 O A:GLU30 4.3 17.6 1.0 CD C:GLU24 4.5 41.9 1.0 OE2 C:GLU24 4.6 47.4 1.0 CE A:LYS20 4.6 15.2 1.0 CE C:MET19 4.9 28.9 0.3

Zinc binding site 2 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:19.2 occ:1.00 O A:HOH635 1.9 19.3 1.0 NE2 A:HIS46 2.0 14.5 1.0 OE1 A:GLU42 2.0 18.5 1.0 CD A:GLU42 2.9 15.6 1.0 CD2 A:HIS46 2.9 13.7 1.0 CE1 A:HIS46 3.0 25.5 1.0 OE2 A:GLU42 3.2 19.4 1.0 CD2 A:LEU241 3.7 15.1 1.0 OE1 A:GLN244 3.7 37.4 1.0 CE A:LYS45 3.8 21.3 1.0 NZ A:LYS45 3.9 19.2 1.0 ND1 A:HIS46 4.1 24.2 1.0 CG A:HIS46 4.1 14.2 1.0 O A:HOH629 4.1 42.5 1.0 CG A:GLU42 4.2 12.0 1.0 NE2 A:GLN244 4.5 33.6 1.0 CD A:GLN244 4.5 36.4 1.0 CB A:GLU42 4.6 12.7 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:71.4 occ:0.76 OD2 A:ASP156 2.2 47.7 1.0 CG A:ASP156 3.2 40.5 1.0 OD1 A:ASP156 3.5 42.4 1.0 O A:HOH415 4.0 23.6 1.0 NH1 A:ARG163 4.1 51.3 1.0 OG1 A:THR160 4.1 26.3 1.0 CB A:ASP156 4.4 29.9 1.0 O A:ASP156 4.6 23.5 1.0 CD1 A:TRP159 4.8 21.4 1.0 CA A:ASP156 4.9 22.6 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.2 occ:1.00 O C:ACT309 1.8 32.4 1.0 O C:HOH559 1.8 29.4 1.0 NE2 B:HIS23 2.1 25.0 1.0 OD2 C:ASP65 2.1 21.7 1.0 C C:ACT309 2.5 44.8 1.0 OXT C:ACT309 2.5 53.4 1.0 CG C:ASP65 2.7 21.6 1.0 OD1 C:ASP65 2.7 26.1 1.0 CE1 B:HIS23 3.0 31.2 1.0 CD2 B:HIS23 3.0 25.5 1.0 OD2 C:ASP67 3.5 62.0 1.0 CH3 C:ACT309 4.0 44.7 1.0 ND1 B:HIS23 4.1 24.0 1.0 CB C:ASP65 4.2 20.0 1.0 CG B:HIS23 4.2 24.7 1.0 CG C:ASP67 4.5 47.9 1.0 CB C:ASP67 4.6 38.4 1.0 O B:HOH487 4.9 31.1 1.0 CB B:MET19 4.9 19.7 1.0 CG2 C:THR68 4.9 30.0 1.0 N C:ASP67 5.0 34.2 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:20.5 occ:1.00 OE1 A:GLU166 1.9 26.6 1.0 OE1 B:GLU42 2.0 18.2 1.0 O B:HOH573 2.1 25.2 1.0 NE2 B:HIS46 2.1 21.2 1.0 CD A:GLU166 2.5 27.0 1.0 OE2 A:GLU166 2.6 27.6 1.0 CD B:GLU42 2.9 21.4 1.0 CD2 B:HIS46 3.0 19.3 1.0 CE1 B:HIS46 3.1 25.4 1.0 OE2 B:GLU42 3.2 20.7 1.0 CD2 B:LEU241 3.9 26.5 1.0 CG A:GLU166 4.0 27.1 1.0 CG B:HIS46 4.2 17.9 1.0 ND1 B:HIS46 4.2 22.8 1.0 O A:HOH634 4.2 35.3 1.0 N A:SER168 4.3 21.2 1.0 CG B:GLU42 4.3 20.9 1.0 CB B:GLU42 4.6 15.1 1.0 O A:ALA165 4.6 21.7 1.0 CB A:GLU166 4.7 26.2 1.0 CB A:SER168 4.8 20.2 1.0 CA A:SER168 4.8 19.7 1.0 CA A:GLU166 4.9 23.8 1.0 C A:PRO167 5.0 22.0 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:48.2 occ:1.00 OE1 C:GLU42 2.3 31.2 1.0 NE2 C:HIS46 2.3 30.8 1.0 CD2 C:HIS46 3.1 28.6 1.0 CD C:GLU42 3.2 26.9 1.0 NZ C:LYS45 3.3 54.1 1.0 CE C:LYS45 3.3 50.3 1.0 CE1 C:HIS46 3.3 30.5 1.0 OE2 C:GLU42 3.6 38.3 1.0 CD2 C:LEU241 3.9 24.3 1.0 OE1 C:GLN244 4.3 46.8 1.0 CG C:HIS46 4.3 29.4 1.0 ND1 C:HIS46 4.4 33.0 1.0 CG C:GLU42 4.5 21.4 1.0 CB C:GLU42 4.8 19.5 1.0 CD C:LYS45 4.8 39.7 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:35.8 occ:0.67 OD2 C:ASP139 2.1 48.0 1.0 O C:HOH553 2.1 42.8 1.0 O C:ACT307 2.2 42.3 1.0 OE2 B:GLU24 2.3 50.6 1.0 CG C:ASP139 2.7 37.0 1.0 OD1 C:ASP139 2.7 37.0 1.0 OE1 B:GLU24 2.8 47.6 1.0 CD B:GLU24 2.8 45.6 1.0 C C:ACT307 3.1 36.4 1.0 OXT C:ACT307 3.4 27.7 1.0 O C:HOH511 3.4 36.4 1.0 OG C:SER140 3.5 25.8 1.0 CB C:ASP139 4.1 24.3 1.0 O B:HOH594 4.1 37.6 1.0 CG B:GLU24 4.3 48.0 1.0 NZ C:LYS60 4.3 24.9 1.0 NZ C:LYS144 4.4 31.9 1.0 CH3 C:ACT307 4.5 38.5 1.0 N C:SER140 4.5 19.4 1.0 O C:HOH528 4.6 41.4 1.0 CB C:SER140 4.8 21.1 1.0 O1 C:GOL313 4.8 47.4 1.0 C1 C:GOL313 4.8 47.5 1.0 O C:HOH576 4.9 53.2 1.0 O B:HOH446 5.0 31.4 1.0 CA C:ASP139 5.0 18.4 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


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 GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn304 b:65.2 occ:1.00 O C:HOH552 2.4 43.3 1.0 ND1 C:HIS46 2.5 33.0 1.0 O C:HOH480 2.9 34.0 1.0 CE1 C:HIS46 3.4 30.5 1.0 CG C:HIS46 3.5 29.4 1.0 CD C:LYS240 3.7 36.3 1.0 CB C:HIS46 3.7 34.2 1.0 NZ C:LYS240 3.7 51.9 1.0 O C:HIS46 4.0 36.0 1.0 CA C:HIS46 4.1 31.3 1.0 O C:HOH525 4.2 38.7 1.0 CE C:LYS240 4.3 48.0 1.0 C C:HIS46 4.5 29.6 1.0 NE2 C:HIS46 4.6 30.8 1.0 CD2 C:HIS46 4.6 28.6 1.0 CG C:LYS240 5.0 27.5 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the GLUA2 Ligand-Binding Domain in Complex with L-Apartate at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn305 b:0.0 occ:0.90 OD2 C:ASP156 2.0 54.2 1.0 O C:HOH560 2.4 55.0 1.0 CG C:ASP156 3.0 50.2 1.0 O C:HOH503 3.1 36.5 1.0 OD1 C:ASP156 3.6 56.8 1.0 CB C:ASP156 4.2 44.0 1.0 OG1 C:THR160 4.4 47.3 1.0 O C:ASP156 4.4 39.6 1.0 CA C:ASP156 4.6 39.1 1.0 CD1 C:TRP159 4.6 46.7 1.0 O C:SER150 4.7 44.1 1.0 C C:ASP156 4.9 41.7 1.0

C.Krintel, K.Frydenvang, A.Ceravalls De Rabassa, A.M.Kaern, M.Gajhede, D.S.Pickering, J.S.Kastrup. L-Asp Is A Useful Tool in the Purification of the Ionotropic Glutamate Receptor A2 Ligand-Binding Domain. Febs J. V. 281 2422 2014.
ISSN: ISSN 1742-464X
PubMed: 24673938
DOI: 10.1111/FEBS.12795