Zinc in PDB 5o4f: Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution, PDB code: 5o4f was solved by S.Moellerud, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.49 / 2.10
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.392, 56.205, 87.462, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.5

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Zinc atom in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution (pdb code 5o4f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution, PDB code: 5o4f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:31.7 occ:1.00 OE1 A:GLU96 1.9 40.6 1.0 OD1 B:ASP240 1.9 38.0 1.0 ND1 A:HIS93 2.0 35.2 1.0 ND1 B:HIS243 2.0 41.2 1.0 CG B:ASP240 2.6 30.8 1.0 OD2 B:ASP240 2.6 31.5 1.0 CE1 A:HIS93 2.7 32.5 1.0 CD A:GLU96 2.9 34.6 1.0 CG B:HIS243 3.0 37.9 1.0 CE1 B:HIS243 3.0 40.6 1.0 CG A:HIS93 3.2 33.6 1.0 OE2 A:GLU96 3.3 33.4 1.0 CB B:HIS243 3.3 33.6 1.0 CB A:HIS93 3.7 34.0 1.0 CA A:HIS93 3.9 32.1 1.0 NE2 A:HIS93 3.9 31.6 1.0 CB B:ASP240 4.1 30.1 1.0 NE2 B:HIS243 4.1 42.3 1.0 CD2 B:HIS243 4.1 39.5 1.0 O A:HOH440 4.1 44.2 1.0 CD2 A:HIS93 4.1 31.6 1.0 CG A:GLU96 4.2 32.4 1.0 CB A:GLU96 4.5 30.4 1.0 N A:HIS93 4.7 29.9 1.0 CA B:ASP240 4.7 28.3 1.0 O B:ASP240 4.8 32.6 1.0 CA B:HIS243 4.8 33.0 1.0 O A:HIS93 4.9 39.1 1.0 C A:HIS93 4.9 34.4 1.0

Zinc binding site 2 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn307 b:89.1 occ:0.50 O B:HOH413 1.9 54.5 1.0 ND1 B:HIS80 2.5 73.1 1.0 CG B:HIS80 2.9 69.0 1.0 CB B:HIS80 3.1 62.6 1.0 CE1 B:HIS80 3.4 74.5 1.0 CD2 B:HIS80 4.0 71.8 1.0 NE2 B:HIS80 4.1 73.8 1.0 CA B:HIS80 4.6 57.1 1.0

Zinc binding site 3 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:95.0 occ:1.00 OE1 B:GLU42 2.1 42.3 1.0 NZ B:LYS241 2.3 65.3 1.0 CD B:GLU42 2.9 46.1 1.0 OE2 B:GLU42 3.0 51.4 1.0 CE B:LYS241 3.2 59.6 1.0 CD B:LYS241 3.4 51.0 1.0 OE1 B:GLU239 4.2 64.2 1.0 CG B:GLU42 4.3 39.3 1.0 CD2 B:LEU236 4.4 30.8 1.0 CB B:GLU42 4.8 33.7 1.0 CG B:LYS241 4.8 42.9 1.0

Zinc binding site 4 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:32.7 occ:1.00 OE2 A:GLU194 1.9 45.6 1.0 NZ A:LYS246 2.0 46.2 1.0 CD A:GLU194 2.6 35.8 1.0 OE1 A:GLU194 2.7 37.3 1.0 CE A:LYS246 3.1 43.8 1.0 CG A:GLU194 4.0 36.5 1.0 CD A:LYS246 4.4 39.9 1.0 NE2 A:GLN198 4.6 47.9 1.0 O A:HOH405 4.7 40.3 1.0

Zinc binding site 5 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:97.2 occ:1.00 ND1 A:HIS80 2.2 90.3 1.0 CG A:HIS80 2.5 86.2 1.0 CB A:HIS80 2.6 77.3 1.0 ZN A:ZN305 2.9 96.5 1.0 CE1 A:HIS80 3.2 92.8 1.0 CD2 A:HIS80 3.6 90.6 1.0 NE2 A:HIS80 3.9 93.1 1.0 CA A:HIS80 3.9 68.4 1.0 O A:HIS80 4.4 66.7 1.0 O A:ACT308 4.5 65.6 1.0 C A:HIS80 4.7 65.7 1.0 N A:HIS80 5.0 63.3 1.0

Zinc binding site 6 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:96.5 occ:1.00 ZN A:ZN304 2.9 97.2 1.0 OXT A:ACT308 3.0 65.3 1.0 O A:HIS80 3.1 66.7 1.0 O A:ACT308 3.1 65.6 1.0 CB A:HIS80 3.5 77.3 1.0 C A:ACT308 3.5 64.7 1.0 C A:HIS80 4.1 65.7 1.0 CA A:HIS80 4.3 68.4 1.0 CG A:HIS80 4.5 86.2 1.0 ND1 A:HIS80 4.7 90.3 1.0 NH2 A:ARG4 4.9 82.9 1.0

S.Mllerud, A.Pinto, L.Marconi, K.Frydenvang, T.S.Thorsen, S.Laulumaa, R.Venskutonyte, S.Winther, A.M.C.Moral, L.Tamborini, P.Conti, D.S.Pickering, J.S.Kastrup. Structure and Affinity of Two Bicyclic Glutamate Analogues at Ampa and Kainate Receptors. Acs Chem Neurosci V. 8 2056 2017.
ISSN: ESSN 1948-7193
PubMed: 28691798
DOI: 10.1021/ACSCHEMNEURO.7B00201