Atomistry » Zinc » PDB 5z8l-5zhf » 5zg2
Atomistry »
  Zinc »
    PDB 5z8l-5zhf »
      5zg2 »

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

Protein crystallography data

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

Other elements in 5zg2:

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

Zinc Binding Sites:

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 5zg2

Go back to Zinc Binding Sites List in 5zg2
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 5zg2

Go back to Zinc Binding Sites List in 5zg2
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 5zg2

Go back to Zinc Binding Sites List in 5zg2
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 5zg2

Go back to Zinc Binding Sites List in 5zg2
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 5zg2

Go back to Zinc Binding Sites List in 5zg2
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

Reference:

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
Page generated: Wed Dec 16 11:26:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy