Zinc in PDB 5zg2: Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2

The structure of Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2, PDB code: 5zg2 was solved by S.Sogabe, S.Igaki, A.Hirokawa, Y.Zama, W.Lane, G.Snell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.384, 56.565, 90.779, 90.00, 91.74, 90.00
R / Rfree (%)	16.9 / 19

The structure of Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2 (pdb code 5zg2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2, PDB code: 5zg2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 GLUA2O Lbd in Complex with ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:18.1 occ:1.00 NE2 A:HIS456 2.0 15.7 1.0 OE1 A:GLU452 2.3 22.7 1.0 O A:HOH1001 2.5 11.5 1.0 CE1 A:HIS456 3.0 19.6 1.0 CD2 A:HIS456 3.0 14.9 1.0 CD A:GLU452 3.2 20.9 1.0 OE1 A:GLN777 3.5 24.2 1.0 OE2 A:GLU452 3.5 27.6 1.0 CD2 A:LEU774 3.7 17.3 1.0 ND1 A:HIS456 4.1 21.7 1.0 CG A:HIS456 4.1 15.7 1.0 NE2 A:GLN777 4.2 24.3 1.0 CD A:GLN777 4.3 20.5 1.0 CG A:GLU452 4.5 19.9 1.0 NZ A:LYS455 4.5 27.8 1.0 O A:HOH1013 4.5 32.8 1.0 CB A:GLU452 4.8 14.2 1.0 CD A:LYS455 4.8 19.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 GLUA2O Lbd in Complex with ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:34.4 occ:1.00 NE2 A:HIS433 2.1 17.1 1.0 O A:HOH1035 2.2 33.2 1.0 O A:HOH1238 2.2 43.7 1.0 O A:HOH1218 2.4 34.1 1.0 CE1 A:HIS433 3.0 19.1 1.0 CD2 A:HIS433 3.1 17.4 1.0 O A:HOH1272 3.3 40.9 1.0 OE1 A:GLU434 4.1 40.8 1.0 ND1 A:HIS433 4.1 17.8 1.0 CG A:HIS433 4.2 16.2 1.0 O A:HOH1139 4.5 22.5 1.0 CG A:GLU434 4.6 25.7 1.0 CD A:GLU434 4.8 33.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 GLUA2O Lbd in Complex with ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:17.1 occ:1.00 OE1 B:GLU437 1.9 20.2 1.0 CD B:GLU437 2.6 21.8 1.0 OE2 B:GLU437 2.7 21.4 1.0 CG B:GLU437 4.1 19.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 GLUA2O Lbd in Complex with ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:20.2 occ:1.00 O B:HOH1206 1.7 27.3 1.0 OXT B:ACT907 2.0 27.0 1.0 NE2 B:HIS433 2.1 14.6 1.0 C B:ACT907 2.9 32.5 1.0 CE1 B:HIS433 3.0 14.7 1.0 CD2 B:HIS433 3.1 14.7 1.0 O B:ACT907 3.1 33.7 1.0 ND1 B:HIS433 4.2 16.6 1.0 CG B:HIS433 4.2 14.7 1.0 CH3 B:ACT907 4.3 32.7 1.0 O B:HOH1055 4.6 20.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 GLUA2O Lbd in Complex with ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:27.0 occ:1.00 OD2 B:ASP475 1.9 19.7 1.0 O B:ACT905 2.0 22.2 1.0 CG B:ASP475 2.7 19.8 1.0 OD1 B:ASP475 2.7 19.2 1.0 C B:ACT905 2.8 20.9 1.0 OXT B:ACT905 3.0 21.3 1.0 O B:HOH1257 3.4 32.5 1.0 OD2 B:ASP477 3.8 30.9 1.0 O B:HOH1234 4.1 25.0 1.0 CB B:ASP475 4.1 17.0 1.0 CB B:ASP477 4.1 24.5 1.0 CH3 B:ACT905 4.3 20.4 1.0 CG B:ASP477 4.5 27.8 1.0 N B:ASP477 4.8 19.9 1.0 CG2 B:THR478 4.9 18.7 1.0

A.Kunugi, M.Tanaka, A.Suzuki, Y.Tajima, N.Suzuki, M.Suzuki, S.Nakamura, H.Kuno, A.Yokota, S.Sogabe, Y.Kosugi, Y.Awasaki, T.Kaku, H.Kimura. Tak-137, An Ampa-R Potentiator with Little Agonistic Effect, Has A Wide Therapeutic Window. Neuropsychopharmacology V. 44 961 2019.
ISSN: ISSN 1740-634X
PubMed: 30209408
DOI: 10.1038/S41386-018-0213-7