Zinc in PDB 5zg0: Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1, PDB code: 5zg0 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 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	113.682, 162.582, 47.383, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1 (pdb code 5zg0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1, PDB code: 5zg0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:25.8 occ:1.00 OE2 C:GLU699 1.8 25.1 1.0 OE1 A:GLU452 2.0 24.0 1.0 NE2 A:HIS456 2.1 26.7 1.0 O C:HOH1298 2.2 22.5 1.0 CD C:GLU699 2.6 27.1 1.0 OE1 C:GLU699 2.7 29.0 1.0 CD A:GLU452 2.9 25.6 1.0 CD2 A:HIS456 3.0 27.6 1.0 CE1 A:HIS456 3.1 28.2 1.0 OE2 A:GLU452 3.3 26.2 1.0 CD2 A:LEU774 3.9 25.1 1.0 CG C:GLU699 4.1 27.4 1.0 ND1 A:HIS456 4.2 27.2 1.0 CG A:HIS456 4.2 26.5 1.0 CG A:GLU452 4.3 23.6 1.0 N C:SER701 4.3 24.5 1.0 O A:HOH1145 4.6 48.7 1.0 O C:ALA698 4.7 25.6 1.0 CB A:GLU452 4.7 22.3 1.0 CB C:GLU699 4.7 27.3 1.0 CD2 A:LEU779 4.7 34.0 1.0 CA C:PRO700 4.9 27.2 1.0 CA C:SER701 4.9 24.3 1.0 CA C:GLU699 4.9 27.1 1.0 C C:PRO700 4.9 25.6 1.0 CB C:SER701 5.0 24.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:58.5 occ:1.00 NE2 B:HIS456 2.3 41.1 1.0 OE1 B:GLU452 2.5 42.6 1.0 CE1 B:HIS456 3.2 43.8 1.0 NZ B:LYS455 3.3 49.8 1.0 CD2 B:HIS456 3.3 42.0 1.0 OE1 B:GLN777 3.5 54.9 1.0 CD B:GLU452 3.6 41.2 1.0 CD2 B:LEU774 3.7 32.5 1.0 CE B:LYS455 3.7 45.5 1.0 CD2 B:LEU779 3.7 43.8 1.0 OE2 B:GLU452 4.0 45.6 1.0 CD B:GLN777 4.3 52.0 1.0 ND1 B:HIS456 4.4 41.7 1.0 CG B:HIS456 4.4 40.2 1.0 NE2 B:GLN777 4.5 59.1 1.0 CG B:GLU452 4.7 37.1 1.0 CB B:GLU452 5.0 34.0 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:73.3 occ:1.00 ND1 B:HIS456 2.4 41.7 1.0 O B:HOH1241 2.7 43.1 1.0 CG B:HIS456 3.3 40.2 1.0 CE1 B:HIS456 3.4 43.8 1.0 CB B:HIS456 3.5 38.9 1.0 CA B:HIS456 4.0 39.5 1.0 O B:HIS456 4.0 42.2 1.0 CD B:LYS773 4.2 39.8 1.0 CG B:LYS773 4.5 37.1 1.0 C B:HIS456 4.5 40.3 1.0 CD2 B:HIS456 4.5 42.0 1.0 NE2 B:HIS456 4.5 41.1 1.0 CE B:LYS773 4.6 42.2 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:26.6 occ:1.00 NE2 C:HIS456 1.9 24.5 1.0 OE1 C:GLU452 2.0 23.5 1.0 CE1 C:HIS456 2.9 26.8 1.0 CD2 C:HIS456 2.9 23.5 1.0 CD C:GLU452 3.0 24.2 1.0 OE2 C:GLU452 3.3 27.2 1.0 CD2 C:LEU774 3.7 21.2 0.5 NZ C:LYS455 3.9 24.0 1.0 CE C:LYS455 3.9 23.8 1.0 CD1 C:LEU774 3.9 20.7 0.5 O C:HOH1258 4.0 38.7 1.0 ND1 C:HIS456 4.0 27.5 1.0 CG C:HIS456 4.1 24.5 1.0 CG C:GLU452 4.3 22.4 1.0 CG C:LEU774 4.7 21.4 0.5 CB C:GLU452 4.7 21.2 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn902 b:27.2 occ:1.00 OE2 D:GLU440 2.0 29.3 1.0 NE2 D:HIS433 2.0 26.7 1.0 OXT D:ACT906 2.3 44.4 1.0 O D:ACT906 2.6 44.4 1.0 CD D:GLU440 2.8 30.5 1.0 C D:ACT906 2.8 44.2 1.0 OE1 D:GLU440 3.0 29.7 1.0 CE1 D:HIS433 3.0 27.2 1.0 CD2 D:HIS433 3.1 27.3 1.0 NZ D:LYS430 3.9 28.1 1.0 ND1 D:HIS433 4.1 27.6 1.0 CD D:LYS430 4.1 27.3 1.0 CG D:GLU440 4.2 31.3 1.0 CG D:HIS433 4.2 27.4 1.0 O D:GLU440 4.3 26.4 1.0 CH3 D:ACT906 4.3 54.2 1.0 CE D:LYS430 4.7 28.1 1.0 O D:HOH1011 4.8 39.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 GLUA2O Lbd in Complex with Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn903 b:26.7 occ:1.00 NE2 D:HIS456 1.9 24.0 1.0 OE1 D:GLU452 2.0 24.7 1.0 O D:HOH1201 2.3 17.1 1.0 CE1 D:HIS456 2.9 26.7 1.0 CD2 D:HIS456 2.9 24.2 1.0 CD D:GLU452 3.0 25.0 1.0 OE2 D:GLU452 3.3 27.3 1.0 CD1 D:LEU774 3.8 26.7 1.0 NZ D:LYS455 3.9 24.4 1.0 CE D:LYS455 3.9 23.2 1.0 ND1 D:HIS456 4.0 28.3 1.0 O D:HOH1143 4.0 40.6 1.0 CG D:HIS456 4.1 24.8 1.0 CG D:GLU452 4.3 22.9 1.0 CB D:GLU452 4.7 21.1 1.0 CG D:LEU774 4.8 26.0 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 GLUA2O Lbd in Complex with Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn904 b:84.2 occ:1.00 OD2 D:ASP689 2.2 40.2 1.0 CG D:ASP689 3.2 37.0 1.0 OD1 D:ASP689 3.5 41.9 1.0 O D:HOH1090 4.0 29.3 1.0 CB D:ASP689 4.5 31.6 1.0 OG1 D:THR693 4.5 30.6 1.0 O D:ASP689 5.0 29.0 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 GLUA2O Lbd in Complex with Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:25.2 occ:1.00 OE2 D:GLU699 1.8 24.3 1.0 OE1 E:GLU452 2.0 22.8 1.0 NE2 E:HIS456 2.0 26.5 1.0 O D:HOH1195 2.1 22.0 1.0 CD D:GLU699 2.6 27.4 1.0 OE1 D:GLU699 2.7 29.5 1.0 CD E:GLU452 2.9 25.3 1.0 CD2 E:HIS456 3.0 26.6 1.0 CE1 E:HIS456 3.1 27.8 1.0 OE2 E:GLU452 3.3 24.4 1.0 CD2 E:LEU774 3.9 26.0 1.0 O D:HOH1157 4.0 44.8 1.0 CG D:GLU699 4.1 27.1 1.0 ND1 E:HIS456 4.1 26.2 1.0 CG E:HIS456 4.1 25.1 1.0 CG E:GLU452 4.3 22.9 1.0 N D:SER701 4.4 23.6 1.0 CB E:GLU452 4.7 22.8 1.0 O D:ALA698 4.7 25.5 1.0 CB D:GLU699 4.7 26.1 1.0 CD E:LYS455 4.8 42.4 1.0 CA D:PRO700 5.0 25.6 1.0 CA D:SER701 5.0 23.1 1.0 CB D:SER701 5.0 24.1 1.0 CA D:GLU699 5.0 25.7 1.0 C D:PRO700 5.0 24.9 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


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 GLUA2O Lbd in Complex with Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1004 b:31.1 occ:1.00 O E:HOH1210 1.8 36.6 1.0 NE2 E:HIS433 2.0 30.6 1.0 CE1 E:HIS433 3.0 30.6 1.0 CD2 E:HIS433 3.1 30.8 1.0 OE2 E:GLU434 4.0 51.5 1.0 ND1 E:HIS433 4.1 30.6 1.0 CG E:HIS433 4.2 30.5 1.0 OE1 E:GLU434 4.2 53.1 1.0 CD E:GLU434 4.3 50.6 1.0 CB E:MET429 4.8 29.5 1.0 CG E:MET429 4.9 30.6 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Compound-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn902 b:55.1 occ:1.00 NE2 F:HIS456 2.4 41.7 1.0 OE1 F:GLU452 2.4 44.3 1.0 CD2 F:HIS456 3.3 40.9 1.0 CE1 F:HIS456 3.3 43.8 1.0 CD F:GLU452 3.5 40.7 1.0 CD2 F:LEU774 3.7 32.2 1.0 NZ F:LYS455 3.8 50.5 1.0 OE1 F:GLN777 3.8 61.8 1.0 OE2 F:GLU452 3.9 44.9 1.0 ND1 F:HIS456 4.5 43.1 1.0 CG F:HIS456 4.5 41.5 1.0 CG F:GLU452 4.7 37.6 1.0 CD F:LYS455 4.8 45.8 1.0 CE F:LYS455 4.9 47.9 1.0 CD F:GLN777 4.9 59.2 1.0 CB F:GLU452 4.9 33.5 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