Fluorine 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:

Zinc (Zn) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2, PDB code: 5zg2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F901

b:12.3
occ:1.00
FAF A:ZK1901 0.0 12.3 1.0
CAZ A:ZK1901 1.3 11.5 1.0
FAG A:ZK1901 2.1 12.1 1.0
FAH A:ZK1901 2.1 12.3 1.0
CAS A:ZK1901 2.3 10.2 1.0
CAJ A:ZK1901 2.7 10.4 1.0
OH A:TYR753 3.1 11.5 1.0
OH A:TYR426 3.3 11.8 0.5
CZ A:TYR426 3.4 10.8 0.5
CE2 A:TYR426 3.4 9.7 0.5
CE2 A:TYR426 3.5 10.6 0.5
CB A:PRO499 3.6 9.9 1.0
CG A:PRO499 3.7 10.0 1.0
CZ A:TYR753 3.7 10.2 1.0
CAR A:ZK1901 3.7 10.7 1.0
CAV A:ZK1901 4.1 9.4 1.0
CZ A:TYR426 4.1 9.8 0.5
OH A:TYR426 4.1 12.1 0.5
OG1 A:THR728 4.1 14.4 1.0
CE1 A:TYR426 4.2 9.4 0.5
OH A:TYR471 4.2 14.3 1.0
NAX A:ZK1901 4.2 12.1 1.0
CE2 A:TYR753 4.2 10.6 1.0
CD2 A:TYR426 4.3 9.6 0.5
CD2 A:TYR426 4.3 9.7 0.5
CE1 A:TYR753 4.3 9.9 1.0
CG A:GLU423 4.4 15.9 1.0
O A:PRO499 4.6 9.0 1.0
CAI A:ZK1901 4.8 9.7 1.0
NAP A:ZK1901 4.9 9.7 1.0
CAN A:ZK1901 4.9 14.7 1.0
CD1 A:TYR426 4.9 9.4 0.5
CA A:PRO499 5.0 9.4 1.0
CAW A:ZK1901 5.0 9.1 1.0
CG A:TYR426 5.0 9.4 0.5
CZ A:TYR471 5.0 11.0 1.0

Fluorine binding site 2 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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:F901

b:12.1
occ:1.00
FAG A:ZK1901 0.0 12.1 1.0
CAZ A:ZK1901 1.3 11.5 1.0
FAF A:ZK1901 2.1 12.3 1.0
FAH A:ZK1901 2.2 12.3 1.0
CAS A:ZK1901 2.3 10.2 1.0
NAX A:ZK1901 3.0 12.1 1.0
CAR A:ZK1901 3.0 10.7 1.0
OH A:TYR753 3.3 11.5 1.0
CAJ A:ZK1901 3.4 10.4 1.0
CB A:MET729 3.7 10.6 1.0
OG1 A:THR728 3.7 14.4 1.0
CB A:GLU726 3.8 12.4 1.0
OH A:TYR426 3.8 11.8 0.5
CAM A:ZK1901 3.9 15.4 1.0
CG A:GLU726 3.9 13.2 1.0
CAN A:ZK1901 4.1 14.7 1.0
N A:MET729 4.2 9.0 1.0
CAK A:ZK1901 4.3 17.8 1.0
CAI A:ZK1901 4.3 9.7 1.0
CD A:GLU726 4.4 13.6 1.0
CZ A:TYR753 4.5 10.2 1.0
CA A:MET729 4.5 9.2 1.0
CZ A:TYR426 4.5 10.8 0.5
CAV A:ZK1901 4.6 9.4 1.0
CAL A:ZK1901 4.6 17.2 1.0
CE A:MET729 4.6 16.2 1.0
CE2 A:TYR426 4.6 9.7 0.5
CG A:MET729 4.7 10.8 1.0
OE2 A:GLU726 4.7 11.9 1.0
O A:HOH1065 4.9 16.5 1.0
CAW A:ZK1901 4.9 9.1 1.0
OE1 A:GLU726 5.0 15.5 1.0
CE2 A:TYR426 5.0 10.6 0.5
OAQ A:ZK1901 5.0 18.7 1.0

Fluorine binding site 3 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F 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
A:F901

b:12.3
occ:1.00
FAH A:ZK1901 0.0 12.3 1.0
CAZ A:ZK1901 1.3 11.5 1.0
FAF A:ZK1901 2.1 12.3 1.0
FAG A:ZK1901 2.2 12.1 1.0
CAS A:ZK1901 2.3 10.2 1.0
NAX A:ZK1901 2.9 12.1 1.0
CAR A:ZK1901 3.0 10.7 1.0
CAN A:ZK1901 3.1 14.7 1.0
CG A:GLU423 3.2 15.9 1.0
CD A:GLU423 3.4 17.8 1.0
CAJ A:ZK1901 3.5 10.4 1.0
CE A:MET729 3.6 16.2 1.0
CAL A:ZK1901 3.7 17.2 1.0
OE2 A:GLU423 3.7 18.6 1.0
CE2 A:TYR426 3.7 9.7 0.5
OH A:TYR471 3.9 14.3 1.0
OE1 A:GLU423 4.0 17.4 1.0
OH A:TYR426 4.2 11.8 0.5
CAM A:ZK1901 4.3 15.4 1.0
CZ A:TYR426 4.3 10.8 0.5
CAI A:ZK1901 4.3 9.7 1.0
CB A:MET729 4.5 10.6 1.0
CE2 A:TYR426 4.5 10.6 0.5
CAK A:ZK1901 4.6 17.8 1.0
CD2 A:TYR426 4.6 9.7 0.5
CB A:GLU423 4.6 13.3 1.0
CAV A:ZK1901 4.6 9.4 1.0
O A:HOH1065 4.7 16.5 1.0
OAQ A:ZK1901 4.7 18.7 1.0
CG A:MET729 4.8 10.8 1.0
CZ A:TYR471 4.9 11.0 1.0
OH A:TYR753 4.9 11.5 1.0
SD A:MET729 4.9 13.3 1.0
CD2 A:TYR426 5.0 9.6 0.5
CG A:PRO499 5.0 10.0 1.0

Fluorine binding site 4 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F 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:F901

b:13.0
occ:1.00
FAF B:ZK1901 0.0 13.0 1.0
CAZ B:ZK1901 1.3 10.9 1.0
FAH B:ZK1901 2.1 13.0 1.0
FAG B:ZK1901 2.1 12.8 1.0
CAS B:ZK1901 2.3 10.1 1.0
CAJ B:ZK1901 2.7 9.5 1.0
O B:HOH1110 3.2 18.7 1.0
OH B:TYR753 3.3 12.7 1.0
CB B:PRO499 3.6 9.7 1.0
CE2 B:TYR426 3.6 13.0 1.0
CG B:PRO499 3.7 10.0 1.0
CAR B:ZK1901 3.7 10.6 1.0
CZ B:TYR753 3.9 10.8 1.0
OH B:TYR471 4.0 12.9 1.0
CAV B:ZK1901 4.1 9.1 1.0
OH B:TYR426 4.1 15.1 1.0
CG B:GLU423 4.1 13.4 1.0
CZ B:TYR426 4.1 11.7 1.0
NAX B:ZK1901 4.2 11.6 1.0
CD2 B:TYR426 4.4 11.4 1.0
CE2 B:TYR753 4.4 11.1 1.0
CE1 B:TYR753 4.5 10.3 1.0
O B:PRO499 4.5 9.1 1.0
OG1 B:THR728 4.5 14.6 1.0
CD B:GLU423 4.7 15.0 1.0
OE2 B:GLU423 4.7 15.1 1.0
CAI B:ZK1901 4.8 9.4 1.0
CZ B:TYR471 4.8 11.4 1.0
NAP B:ZK1901 4.9 9.2 1.0
CAN B:ZK1901 4.9 13.9 1.0
CAW B:ZK1901 5.0 9.3 1.0
CA B:PRO499 5.0 8.9 1.0

Fluorine binding site 5 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F 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:F901

b:12.8
occ:1.00
FAG B:ZK1901 0.0 12.8 1.0
CAZ B:ZK1901 1.3 10.9 1.0
FAF B:ZK1901 2.1 13.0 1.0
FAH B:ZK1901 2.1 13.0 1.0
CAS B:ZK1901 2.3 10.1 1.0
NAX B:ZK1901 3.0 11.6 1.0
CAR B:ZK1901 3.0 10.6 1.0
O B:HOH1110 3.0 18.7 1.0
OH B:TYR753 3.4 12.7 1.0
CAJ B:ZK1901 3.4 9.5 1.0
CB B:MET729 3.8 10.4 1.0
CB B:GLU726 3.8 12.7 1.0
CAM B:ZK1901 3.9 14.4 1.0
CG B:GLU726 3.9 13.9 1.0
OG1 B:THR728 4.0 14.6 1.0
CAN B:ZK1901 4.1 13.9 1.0
CAI B:ZK1901 4.3 9.4 1.0
CAK B:ZK1901 4.3 15.1 1.0
CD B:GLU726 4.3 13.7 1.0
CAL B:ZK1901 4.5 15.8 1.0
N B:MET729 4.5 10.4 1.0
CE B:MET729 4.5 13.4 1.0
CZ B:TYR753 4.5 10.8 1.0
CAV B:ZK1901 4.6 9.1 1.0
CG B:MET729 4.7 10.9 1.0
CA B:MET729 4.7 9.8 1.0
OE1 B:GLU726 4.7 12.5 1.0
OE2 B:GLU726 4.8 15.1 1.0
CAW B:ZK1901 4.9 9.3 1.0
OAQ B:ZK1901 5.0 16.3 1.0

Fluorine binding site 6 out of 6 in 5zg2

Go back to Fluorine Binding Sites List in 5zg2
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F binding site number 6 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:F901

b:13.0
occ:1.00
FAH B:ZK1901 0.0 13.0 1.0
CAZ B:ZK1901 1.3 10.9 1.0
FAF B:ZK1901 2.1 13.0 1.0
FAG B:ZK1901 2.1 12.8 1.0
CAS B:ZK1901 2.4 10.1 1.0
NAX B:ZK1901 2.9 11.6 1.0
CAR B:ZK1901 3.0 10.6 1.0
CAN B:ZK1901 3.1 13.9 1.0
CD B:GLU423 3.2 15.0 1.0
CG B:GLU423 3.2 13.4 1.0
OE2 B:GLU423 3.4 15.1 1.0
CAJ B:ZK1901 3.5 9.5 1.0
CE B:MET729 3.5 13.4 1.0
CAL B:ZK1901 3.6 15.8 1.0
OE1 B:GLU423 3.7 16.2 1.0
O B:HOH1110 3.8 18.7 1.0
OH B:TYR471 3.9 12.9 1.0
CAM B:ZK1901 4.2 14.4 1.0
CAI B:ZK1901 4.3 9.4 1.0
CB B:MET729 4.6 10.4 1.0
CAK B:ZK1901 4.6 15.1 1.0
CE2 B:TYR426 4.6 13.0 1.0
CB B:GLU423 4.7 12.7 1.0
OAQ B:ZK1901 4.7 16.3 1.0
CAV B:ZK1901 4.7 9.1 1.0
CG B:MET729 4.8 10.9 1.0
O B:HOH1118 4.9 15.0 1.0
CZ B:TYR471 4.9 11.4 1.0
SD B:MET729 4.9 12.3 1.0
OH B:TYR753 5.0 12.7 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: Sun Dec 13 12:43:42 2020

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