Zinc in PDB 6jmv: Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc, PDB code: 6jmv was solved by J.Kumari, J.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.97 / 1.83
Space group	P 2 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.460, 88.030, 130.470, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.2

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc (pdb code 6jmv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc, PDB code: 6jmv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc


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 GLUK3 Ligand Binding Domain Complex with Sym and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:33.3 occ:1.00 OE2 A:GLU247 1.8 25.9 1.0 NE2 A:HIS243 2.0 35.2 1.0 CD A:GLU247 2.7 31.0 1.0 CE1 A:HIS243 2.8 27.9 1.0 HE1 A:HIS243 2.8 33.5 1.0 OE1 A:GLU247 3.0 37.9 1.0 CD2 A:HIS243 3.2 28.1 1.0 HD2 A:HIS243 3.5 33.8 1.0 ND1 A:HIS243 4.0 29.1 1.0 CG A:GLU247 4.1 30.6 1.0 CG A:HIS243 4.2 39.7 1.0 HG3 A:GLU247 4.2 36.8 1.0 HG2 A:GLU247 4.4 36.8 1.0 HD1 A:HIS243 4.7 35.0 1.0 O A:HOH562 4.8 57.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc


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 GLUK3 Ligand Binding Domain Complex with Sym and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:75.7 occ:1.00 HD1 A:HIS80 1.3 77.3 1.0 ND1 A:HIS80 2.0 64.3 1.0 O A:HOH557 2.3 69.6 1.0 HB3 A:HIS80 2.9 61.2 1.0 CE1 A:HIS80 2.9 61.5 1.0 CG A:HIS80 3.0 63.8 1.0 HE1 A:HIS80 3.1 73.8 1.0 CB A:HIS80 3.4 51.0 1.0 O A:HOH587 3.7 58.5 1.0 HB2 A:HIS80 4.0 61.2 1.0 NE2 A:HIS80 4.0 72.4 1.0 CD2 A:HIS80 4.1 82.0 1.0 HA A:HIS80 4.5 40.5 1.0 HG2 A:PRO220 4.5 35.5 1.0 CA A:HIS80 4.6 33.7 1.0 O A:HOH524 4.8 45.2 1.0 HD2 A:HIS80 5.0 98.5 1.0 HB2 A:PRO220 5.0 39.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc


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 GLUK3 Ligand Binding Domain Complex with Sym and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:28.9 occ:1.00 ND1 A:HIS93 1.8 22.9 1.0 OD1 B:ASP240 1.9 35.8 1.0 ND1 B:HIS243 2.1 32.8 1.0 OE1 A:GLU96 2.1 39.9 1.0 OD2 B:ASP240 2.5 33.1 1.0 CE1 A:HIS93 2.5 35.4 1.0 HE1 A:HIS93 2.5 42.5 1.0 CG B:ASP240 2.6 26.6 1.0 CD A:GLU96 3.0 24.6 1.0 CG B:HIS243 3.0 26.4 1.0 HA A:HIS93 3.1 40.2 1.0 HB3 B:HIS243 3.1 36.7 1.0 CG A:HIS93 3.1 26.8 1.0 CE1 B:HIS243 3.1 32.7 1.0 HB2 B:HIS243 3.2 36.7 1.0 OE2 A:GLU96 3.2 27.9 1.0 CB B:HIS243 3.3 30.5 1.0 HE1 B:HIS243 3.4 39.4 1.0 HB3 A:HIS93 3.6 36.5 1.0 CB A:HIS93 3.7 30.4 1.0 NE2 A:HIS93 3.7 32.0 1.0 CA A:HIS93 3.8 33.4 1.0 H31 B:GOL307 3.9 70.0 1.0 CD2 A:HIS93 4.0 28.1 1.0 CB B:ASP240 4.1 30.0 1.0 HB2 A:GLU96 4.1 29.8 1.0 O A:HOH474 4.2 42.0 1.0 CD2 B:HIS243 4.2 33.6 1.0 NE2 B:HIS243 4.2 36.3 1.0 HA B:ASP240 4.2 38.6 1.0 CG A:GLU96 4.4 31.6 1.0 O B:HOH474 4.4 54.1 1.0 HB2 B:ASP240 4.5 36.1 1.0 HE2 A:HIS93 4.5 38.5 1.0 H32 B:GOL307 4.6 70.0 1.0 HB3 B:ASP240 4.6 36.1 1.0 CB A:GLU96 4.6 24.8 1.0 HB2 A:HIS93 4.7 36.5 1.0 N A:HIS93 4.7 31.0 1.0 HB3 A:GLU96 4.7 29.8 1.0 C3 B:GOL307 4.7 58.3 1.0 CA B:ASP240 4.7 32.1 1.0 HG3 A:GLU96 4.8 38.1 1.0 O A:HIS93 4.8 32.6 1.0 O B:ASP240 4.8 34.3 1.0 CA B:HIS243 4.8 27.3 1.0 C A:HIS93 4.9 21.9 1.0 HD2 A:HIS93 4.9 33.8 1.0 H A:HIS93 4.9 37.3 1.0 HG2 A:GLU96 5.0 38.1 1.0 HE2 B:HIS243 5.0 43.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Sym and Zinc


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 GLUK3 Ligand Binding Domain Complex with Sym and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:60.6 occ:0.50 ND1 B:HIS80 2.0 80.1 1.0 O B:HOH458 2.4 58.1 1.0 CE1 B:HIS80 3.0 64.0 1.0 CG B:HIS80 3.0 56.3 1.0 HB2 B:HIS80 3.1 48.9 1.0 HB3 B:HIS80 3.2 48.9 1.0 HE1 B:HIS80 3.2 76.8 1.0 CB B:HIS80 3.3 40.7 1.0 NE2 B:HIS80 4.1 63.5 1.0 CD2 B:HIS80 4.1 51.4 1.0 O B:HOH514 4.7 55.5 1.0 CA B:HIS80 4.8 51.2 1.0 HE2 B:HIS80 4.9 76.3 1.0 HD2 B:HIS80 5.0 61.8 1.0

J.Kumari, R.Vinnakota, J.Kumar. Structural and Functional Insights Into GLUK3-Kainate Receptor Desensitization and Recovery. Sci Rep V. 9 10254 2019.
ISSN: ESSN 2045-2322
PubMed: 31311973
DOI: 10.1038/S41598-019-46770-Z