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Zinc in PDB 5ybf: Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1

Protein crystallography data

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1, PDB code: 5ybf 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 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.596, 162.074, 47.103, 90.00, 89.99, 90.00
R / Rfree (%) 18.4 / 20.8

Other elements in 5ybf:

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 (pdb code 5ybf). 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 HBT1, PDB code: 5ybf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5ybf

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Zinc binding site 1 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:18.5
occ:1.00
 OE2 C:GLU699 1.7 20.5 1.0
OE1 A:GLU452 2.0 16.9 1.0
NE2 A:HIS456 2.0 18.8 1.0
O C:HOH2332 2.1 19.6 1.0
CD C:GLU699 2.5 22.7 1.0
OE1 C:GLU699 2.7 22.8 1.0
CD A:GLU452 2.9 18.2 1.0
CD2 A:HIS456 3.0 18.6 1.0
CE1 A:HIS456 3.0 20.6 1.0
OE2 A:GLU452 3.3 18.6 1.0
CD2 A:LEU774 3.9 18.5 1.0
CG C:GLU699 4.0 22.2 1.0
ND1 A:HIS456 4.1 19.8 1.0
CG A:HIS456 4.1 18.4 1.0
N C:SER701 4.3 18.4 1.0
CG A:GLU452 4.3 15.9 1.0
O C:ALA698 4.6 18.8 1.0
CB C:GLU699 4.6 22.0 1.0
CB A:GLU452 4.7 14.6 1.0
CD2 A:LEU779 4.8 25.8 1.0
CA C:GLU699 4.8 20.8 1.0
CA C:SER701 4.9 17.6 1.0
CB C:SER701 4.9 17.9 1.0
C C:PRO700 4.9 19.6 1.0
CA C:PRO700 4.9 20.8 1.0

Zinc binding site 2 out of 10 in 5ybf

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Zinc binding site 2 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:25.0
occ:1.00
 O B:HOH1018 1.7 29.5 1.0
OD2 B:ASP475 1.9 19.0 1.0
CG B:ASP475 2.7 23.3 1.0
OD1 B:ASP475 2.9 25.7 1.0
CB B:ASP475 4.2 20.8 1.0
OD2 B:ASP477 4.3 39.5 1.0
CB B:ASP477 4.6 33.7 1.0
O B:HOH1038 4.7 32.9 1.0
CG2 B:THR478 4.8 30.9 1.0
CG B:ASP477 5.0 37.9 1.0

Zinc binding site 3 out of 10 in 5ybf

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Zinc binding site 3 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:42.9
occ:1.00
 NE2 B:HIS456 2.2 34.1 1.0
OE1 B:GLU452 2.3 32.3 1.0
NZ B:LYS455 3.1 50.7 1.0
CD2 B:HIS456 3.2 31.8 1.0
CE1 B:HIS456 3.3 36.1 1.0
CD B:GLU452 3.4 31.9 1.0
CE B:LYS455 3.5 44.3 1.0
CD2 B:LEU774 3.8 21.9 1.0
OE1 B:GLN777 3.8 41.1 1.0
OE2 B:GLU452 3.8 39.3 1.0
CD2 B:LEU779 3.9 34.0 1.0
CG B:HIS456 4.3 29.8 1.0
ND1 B:HIS456 4.4 33.5 1.0
CG B:GLU452 4.6 27.4 1.0
CD B:GLN777 4.6 39.0 1.0
NE2 B:GLN777 4.7 42.3 1.0
CB B:GLU452 4.8 23.3 1.0
CD B:LYS455 4.9 41.0 1.0

Zinc binding site 4 out of 10 in 5ybf

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Zinc binding site 4 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:21.8
occ:1.00
 NE2 C:HIS433 2.0 23.6 1.0
OE2 C:GLU440 2.0 25.9 1.0
O C:HOH2339 2.2 29.6 1.0
CD C:GLU440 2.8 26.4 1.0
OE1 C:GLU440 2.9 26.2 1.0
CD2 C:HIS433 2.9 24.3 1.0
CE1 C:HIS433 3.0 23.6 1.0
NZ C:LYS430 3.9 23.1 1.0
CD C:LYS430 4.1 21.2 1.0
ND1 C:HIS433 4.1 23.3 1.0
CG C:HIS433 4.1 23.6 1.0
CG C:GLU440 4.2 26.9 1.0
O C:GLU440 4.3 22.6 1.0
CD1 C:LEU436 4.5 37.9 1.0
CE C:LYS430 4.7 21.4 1.0

Zinc binding site 5 out of 10 in 5ybf

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Zinc binding site 5 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn803

b:20.5
occ:1.00
 NE2 C:HIS456 1.9 19.4 1.0
OE1 C:GLU452 1.9 20.2 1.0
O C:HOH2102 2.1 22.7 1.0
CD C:GLU452 2.9 21.4 1.0
CE1 C:HIS456 2.9 20.5 1.0
CD2 C:HIS456 2.9 19.2 1.0
OE2 C:GLU452 3.2 23.6 1.0
CD2 C:LEU774 3.5 18.3 1.0
OE1 C:GLN777 3.6 34.8 1.0
CE C:LYS455 3.9 23.1 1.0
NZ C:LYS455 3.9 23.1 1.0
O C:HOH2159 4.0 39.8 1.0
ND1 C:HIS456 4.0 21.6 1.0
CG C:HIS456 4.0 19.1 1.0
CG C:GLU452 4.3 18.3 1.0
CD C:GLN777 4.4 30.8 1.0
NE2 C:GLN777 4.4 33.3 1.0
CB C:GLU452 4.6 15.8 1.0
O C:HOH2293 4.9 35.3 1.0

Zinc binding site 6 out of 10 in 5ybf

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Zinc binding site 6 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn902

b:22.6
occ:1.00
 OE2 D:GLU440 2.0 26.9 1.0
NE2 D:HIS433 2.0 23.9 1.0
O D:HOH1243 2.2 29.9 1.0
CD D:GLU440 2.8 26.8 1.0
OE1 D:GLU440 2.9 26.7 1.0
CD2 D:HIS433 3.0 24.6 1.0
CE1 D:HIS433 3.1 24.2 1.0
NZ D:LYS430 3.9 23.3 1.0
CD D:LYS430 4.0 21.8 1.0
CG D:HIS433 4.1 24.1 1.0
ND1 D:HIS433 4.1 24.1 1.0
CG D:GLU440 4.2 26.8 1.0
O D:GLU440 4.3 22.9 1.0
CD1 D:LEU436 4.5 39.2 1.0
CE D:LYS430 4.7 21.9 1.0

Zinc binding site 7 out of 10 in 5ybf

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Zinc binding site 7 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn903

b:20.1
occ:1.00
 NE2 D:HIS456 1.9 18.9 1.0
OE1 D:GLU452 2.0 19.6 1.0
O D:HOH1234 2.2 21.6 1.0
CD D:GLU452 2.9 20.3 1.0
CE1 D:HIS456 2.9 19.9 1.0
CD2 D:HIS456 2.9 18.0 1.0
OE2 D:GLU452 3.2 22.3 1.0
CD2 D:LEU774 3.6 16.9 1.0
CE D:LYS455 3.9 21.4 1.0
NZ D:LYS455 3.9 22.1 1.0
O D:HOH1078 3.9 39.3 1.0
ND1 D:HIS456 4.0 21.6 1.0
O D:HOH1275 4.1 37.0 1.0
CG D:HIS456 4.1 18.9 1.0
OE1 D:GLN777 4.2 34.9 1.0
CG D:GLU452 4.3 18.6 1.0
CB D:GLU452 4.6 15.6 1.0
O D:HOH1166 4.9 36.6 1.0

Zinc binding site 8 out of 10 in 5ybf

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Zinc binding site 8 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn905

b:18.3
occ:1.00
 OE2 D:GLU699 1.7 21.1 1.0
OE1 E:GLU452 2.0 16.6 1.0
NE2 E:HIS456 2.0 18.7 1.0
O D:HOH1238 2.0 18.9 1.0
CD D:GLU699 2.5 22.4 1.0
OE1 D:GLU699 2.7 22.5 1.0
CD E:GLU452 2.9 17.6 1.0
CD2 E:HIS456 3.0 18.2 1.0
CE1 E:HIS456 3.0 20.4 1.0
OE2 E:GLU452 3.3 18.4 1.0
O D:HOH1207 3.9 32.9 1.0
CD2 E:LEU774 3.9 18.4 1.0
CG D:GLU699 4.0 22.0 1.0
ND1 E:HIS456 4.1 19.4 1.0
CG E:HIS456 4.1 18.1 1.0
N D:SER701 4.3 18.8 1.0
CG E:GLU452 4.3 15.6 1.0
O D:ALA698 4.6 18.5 1.0
CB D:GLU699 4.7 21.4 1.0
CB E:GLU452 4.7 14.2 1.0
CD2 E:LEU779 4.8 24.5 1.0
CA D:SER701 4.8 17.6 1.0
CA D:GLU699 4.8 20.2 1.0
CB D:SER701 4.9 18.2 1.0
CA D:PRO700 4.9 20.4 1.0
C D:PRO700 4.9 19.3 1.0

Zinc binding site 9 out of 10 in 5ybf

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Zinc binding site 9 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn902

b:24.7
occ:1.00
 O F:HOH1013 1.6 27.2 1.0
OD2 F:ASP475 1.9 19.0 1.0
CG F:ASP475 2.7 23.4 1.0
OD1 F:ASP475 2.8 25.4 1.0
CB F:ASP475 4.2 21.1 1.0
OD2 F:ASP477 4.3 40.9 1.0
CB F:ASP477 4.7 34.4 1.0
O F:HOH1031 4.7 32.4 1.0
CG2 F:THR478 4.8 29.0 1.0
CG F:ASP477 5.0 38.6 1.0

Zinc binding site 10 out of 10 in 5ybf

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Zinc binding site 10 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 HBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn903

b:41.0
occ:1.00
 NE2 F:HIS456 2.2 31.6 1.0
OE1 F:GLU452 2.2 30.2 1.0
CD2 F:HIS456 3.1 29.6 1.0
CE1 F:HIS456 3.2 34.2 1.0
CD F:GLU452 3.3 31.1 1.0
NZ F:LYS455 3.6 49.4 1.0
OE2 F:GLU452 3.7 37.8 1.0
CD2 F:LEU774 3.8 21.7 1.0
OE1 F:GLN777 3.8 40.3 1.0
CG F:HIS456 4.3 28.0 1.0
ND1 F:HIS456 4.3 33.1 1.0
CD F:LYS455 4.4 39.8 1.0
NE2 F:GLN777 4.6 39.5 1.0
CG F:GLU452 4.6 25.5 1.0
CE F:LYS455 4.6 46.3 1.0
CD F:GLN777 4.6 37.3 1.0
CB F:GLU452 4.8 21.9 1.0

Reference:

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
Page generated: Mon Oct 28 15:28:15 2024

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