Zinc in PDB 5ybg: Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395, PDB code: 5ybg 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 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	113.724, 161.913, 46.964, 90.00, 89.97, 90.00
R / Rfree (%)	20.2 / 23.3

The binding sites of Zinc atom in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395 (pdb code 5ybg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395, PDB code: 5ybg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:29.1 occ:1.00 OXT A:ACT904 1.7 32.2 1.0 NE2 A:HIS433 2.1 27.2 1.0 O A:HOH1004 2.1 30.2 1.0 C A:ACT904 2.8 41.2 1.0 CE1 A:HIS433 3.0 27.4 1.0 CD2 A:HIS433 3.0 26.8 1.0 O A:ACT904 3.2 40.0 1.0 CH3 A:ACT904 4.1 40.2 1.0 ND1 A:HIS433 4.1 27.5 1.0 CG A:HIS433 4.2 26.7 1.0 OE1 A:GLU434 4.4 55.1 1.0 CB A:MET429 4.7 27.6 1.0 CG A:MET429 4.9 28.0 1.0 O A:HOH1076 4.9 34.1 1.0 CG A:GLU434 5.0 44.6 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:18.5 occ:1.00 OE2 C:GLU699 1.7 19.6 1.0 OE1 A:GLU452 2.0 18.5 1.0 NE2 A:HIS456 2.1 19.5 1.0 O C:HOH2321 2.2 14.1 1.0 CD C:GLU699 2.6 21.2 1.0 OE1 C:GLU699 2.8 24.4 1.0 CD A:GLU452 2.9 17.2 1.0 CD2 A:HIS456 3.0 21.2 1.0 CE1 A:HIS456 3.0 21.8 1.0 OE2 A:GLU452 3.2 17.5 1.0 CD2 A:LEU774 3.9 19.3 1.0 CG C:GLU699 4.1 20.5 1.0 ND1 A:HIS456 4.1 21.7 1.0 CG A:HIS456 4.1 21.0 1.0 O C:HOH2297 4.2 29.5 1.0 N C:SER701 4.2 16.1 1.0 CG A:GLU452 4.3 16.8 1.0 CB A:GLU452 4.6 16.2 1.0 CB C:GLU699 4.7 19.8 1.0 O C:ALA698 4.7 17.3 1.0 CA C:PRO700 4.8 18.0 1.0 CD2 A:LEU779 4.8 24.6 1.0 CA C:GLU699 4.8 18.9 1.0 C C:PRO700 4.9 16.1 1.0 CA C:SER701 4.9 15.1 1.0 CD A:LYS455 4.9 37.3 1.0 CB C:SER701 5.0 16.2 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:46.7 occ:1.00 O B:HOH1002 1.7 33.3 1.0 NE2 B:HIS456 2.1 40.2 1.0 OE1 B:GLU452 2.2 38.9 1.0 O B:HOH1172 2.3 39.3 1.0 CD2 B:HIS456 3.0 37.1 1.0 CD B:GLU452 3.1 35.8 1.0 CE1 B:HIS456 3.2 41.8 1.0 OE2 B:GLU452 3.4 43.2 1.0 OE1 B:GLN777 3.7 44.8 1.0 CD2 B:LEU774 3.7 28.8 1.0 CE B:LYS455 3.9 44.9 1.0 CG B:HIS456 4.2 37.7 1.0 ND1 B:HIS456 4.2 39.3 1.0 CD1 B:LEU779 4.4 44.8 1.0 CG B:GLU452 4.4 31.9 1.0 NE2 B:GLN777 4.5 44.5 1.0 CD B:GLN777 4.5 43.6 1.0 NZ B:LYS455 4.5 45.8 1.0 CB B:GLU452 4.8 29.1 1.0 O B:GLU452 5.0 30.7 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn803 b:21.4 occ:1.00 OE2 C:GLU440 2.0 28.2 1.0 NE2 C:HIS433 2.0 20.8 1.0 O C:HOH2326 2.2 28.2 1.0 CD C:GLU440 2.8 26.6 1.0 CE1 C:HIS433 3.0 21.6 1.0 OE1 C:GLU440 3.0 26.6 1.0 CD2 C:HIS433 3.0 23.1 1.0 NZ C:LYS430 4.0 23.3 1.0 ND1 C:HIS433 4.1 22.0 1.0 CD C:LYS430 4.1 22.1 1.0 CG C:HIS433 4.2 21.7 1.0 CG C:GLU440 4.2 27.9 1.0 O C:GLU440 4.3 22.1 1.0 CE C:LYS430 4.8 22.2 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn804 b:21.6 occ:1.00 NE2 C:HIS456 1.8 19.1 1.0 OE1 C:GLU452 2.0 18.8 1.0 O C:HOH2320 2.3 15.5 1.0 CE1 C:HIS456 2.8 23.1 1.0 CD2 C:HIS456 2.8 19.1 1.0 CD C:GLU452 2.9 20.8 1.0 OE2 C:GLU452 3.2 24.2 1.0 CD2 C:LEU774 3.6 22.1 1.0 NZ C:LYS455 3.9 23.7 1.0 CE C:LYS455 3.9 24.1 1.0 ND1 C:HIS456 3.9 22.7 1.0 CG C:HIS456 4.0 19.9 1.0 O C:HOH2249 4.0 30.4 1.0 OE1 C:GLN777 4.3 35.6 1.0 CG C:GLU452 4.3 17.5 1.0 CB C:GLU452 4.7 16.4 1.0 CG C:LEU779 4.9 20.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn902 b:21.4 occ:1.00 OE2 D:GLU440 2.0 25.8 1.0 NE2 D:HIS433 2.0 20.8 1.0 CD D:GLU440 2.8 25.4 1.0 CE1 D:HIS433 2.9 21.9 1.0 OE1 D:GLU440 3.0 26.1 1.0 CD2 D:HIS433 3.0 23.0 1.0 NZ D:LYS430 4.0 21.8 1.0 ND1 D:HIS433 4.1 21.2 1.0 CG D:HIS433 4.1 21.7 1.0 CD D:LYS430 4.1 21.6 1.0 CG D:GLU440 4.2 27.6 1.0 O D:GLU440 4.3 23.1 1.0 CE D:LYS430 4.7 20.5 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn903 b:21.9 occ:1.00 NE2 D:HIS456 1.8 19.0 1.0 OE1 D:GLU452 2.0 19.3 1.0 O D:HOH1221 2.3 16.6 1.0 CE1 D:HIS456 2.8 21.7 1.0 CD2 D:HIS456 2.8 19.1 1.0 CD D:GLU452 2.9 21.4 1.0 OE2 D:GLU452 3.2 24.0 1.0 CD2 D:LEU774 3.5 23.3 1.0 CE D:LYS455 3.9 24.1 1.0 NZ D:LYS455 3.9 24.0 1.0 O D:HOH1123 3.9 32.2 1.0 ND1 D:HIS456 3.9 23.5 1.0 CG D:HIS456 3.9 19.6 1.0 CG D:GLU452 4.3 17.5 1.0 OE1 D:GLN777 4.3 33.2 1.0 CB D:GLU452 4.6 16.5 1.0 CG D:LEU779 4.9 21.0 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn905 b:18.9 occ:1.00 OE2 D:GLU699 1.7 20.6 1.0 OE1 E:GLU452 1.9 19.4 1.0 NE2 E:HIS456 2.0 19.9 1.0 O D:HOH1226 2.2 14.6 1.0 CD D:GLU699 2.6 21.7 1.0 OE1 D:GLU699 2.8 25.3 1.0 CD E:GLU452 2.9 18.0 1.0 CD2 E:HIS456 2.9 21.7 1.0 CE1 E:HIS456 3.1 23.1 1.0 OE2 E:GLU452 3.2 17.8 1.0 CD2 E:LEU774 3.9 18.8 1.0 CG D:GLU699 4.1 21.4 1.0 CG E:HIS456 4.1 21.8 1.0 ND1 E:HIS456 4.1 22.3 1.0 N D:SER701 4.2 16.0 1.0 O D:HOH1210 4.2 30.6 1.0 CG E:GLU452 4.3 16.8 1.0 CB E:GLU452 4.6 16.5 1.0 CB D:GLU699 4.7 20.1 1.0 O D:ALA698 4.7 17.3 1.0 CD2 E:LEU779 4.7 26.9 1.0 CA D:PRO700 4.8 18.0 1.0 CA D:GLU699 4.9 19.0 1.0 C D:PRO700 4.9 16.1 1.0 CA D:SER701 4.9 15.1 1.0 CB D:SER701 5.0 16.7 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn903 b:28.9 occ:1.00 OXT E:ACT904 1.9 35.1 1.0 NE2 E:HIS433 2.0 28.0 1.0 C E:ACT904 2.9 44.9 1.0 CD2 E:HIS433 3.0 27.9 1.0 CE1 E:HIS433 3.0 28.8 1.0 O E:ACT904 3.3 43.5 1.0 ND1 E:HIS433 4.1 28.4 1.0 CG E:HIS433 4.2 27.2 1.0 CH3 E:ACT904 4.2 40.5 1.0 CB E:MET429 4.7 27.7 1.0 OE1 E:GLU434 4.7 53.3 1.0 CG E:MET429 4.9 27.3 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and LY451395


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 LY451395 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn902 b:46.2 occ:1.00 O F:HOH1007 1.7 33.0 1.0 NE2 F:HIS456 2.2 40.7 1.0 OE1 F:GLU452 2.2 37.8 1.0 NZ F:LYS455 2.7 49.3 1.0 CD2 F:HIS456 3.0 38.2 1.0 CD F:GLU452 3.1 36.3 1.0 CE1 F:HIS456 3.3 41.5 1.0 OE2 F:GLU452 3.4 41.8 1.0 CD2 F:LEU774 3.7 27.5 1.0 OE1 F:GLN777 3.8 46.9 1.0 CE F:LYS455 3.9 50.2 1.0 CG F:HIS456 4.2 38.4 1.0 ND1 F:HIS456 4.3 39.8 1.0 CD F:LYS455 4.4 46.4 1.0 CG F:GLU452 4.5 31.8 1.0 CD F:GLN777 4.6 46.2 1.0 NE2 F:GLN777 4.6 49.9 1.0 CB F:GLU452 4.8 28.6 1.0

A.Kunugi, Y.Tajima, H.Kuno, S.Sogabe, H.Kimura. HBT1, A Novel Ampa Receptor Potentiator with Lower Agonistic Effect, Avoided Bell-Shaped Response in in Vitro Bdnf Production. J. Pharmacol. Exp. Ther. V. 364 377 2018.
ISSN: ESSN 1521-0103
PubMed: 29298820
DOI: 10.1124/JPET.117.245050