Zinc in PDB 7f3o: Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653

Protein crystallography data

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653, PDB code: 7f3o 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 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 114.313, 163.508, 47.558, 90, 89.99, 90
R / Rfree (%) 19.4 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653 (pdb code 7f3o). 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 Tak- 653, PDB code: 7f3o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7f3o

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Zinc binding site 1 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:41.4
occ:1.00
NE2 B:HIS456 2.1 30.1 1.0
OE1 B:GLU452 2.2 34.1 1.0
O B:HOH1050 2.3 45.6 1.0
CD2 B:HIS456 3.1 29.8 1.0
CE1 B:HIS456 3.1 36.8 1.0
CD B:GLU452 3.3 33.1 1.0
OE1 B:GLN777 3.6 45.5 1.0
CD2 B:LEU774 3.7 26.0 1.0
OE2 B:GLU452 3.8 45.9 1.0
NZ B:LYS455 3.8 51.4 1.0
CE B:LYS455 3.8 44.7 1.0
CD2 B:LEU779 4.1 36.4 1.0
ND1 B:HIS456 4.2 33.7 1.0
CG B:HIS456 4.3 29.4 1.0
NE2 B:GLN777 4.4 47.2 1.0
CD B:GLN777 4.4 41.6 1.0
CG B:GLU452 4.5 28.6 1.0
CB B:GLU452 4.8 23.5 1.0

Zinc binding site 2 out of 10 in 7f3o

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Zinc binding site 2 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:19.6
occ:1.00
OE2 C:GLU699 1.4 23.9 1.0
OE1 A:GLU452 2.0 18.0 1.0
NE2 A:HIS456 2.0 19.1 1.0
O C:HOH1128 2.3 17.9 1.0
CD C:GLU699 2.4 29.0 1.0
OE1 C:GLU699 2.7 26.6 1.0
CD A:GLU452 2.9 19.9 1.0
CD2 A:HIS456 3.0 19.6 1.0
CE1 A:HIS456 3.1 22.1 1.0
OE2 A:GLU452 3.3 19.7 1.0
CG C:GLU699 3.9 27.8 1.0
CD2 A:LEU774 4.0 21.8 1.0
O C:HOH1033 4.1 33.7 1.0
CG A:HIS456 4.1 19.7 1.0
ND1 A:HIS456 4.2 20.0 1.0
CG A:GLU452 4.3 17.6 1.0
N C:SER701 4.3 18.0 1.0
O A:HOH1079 4.5 39.8 1.0
CB C:GLU699 4.7 25.4 1.0
CD2 A:LEU779 4.7 30.9 1.0
O C:ALA698 4.7 20.5 1.0
CB A:GLU452 4.7 16.2 1.0
CA C:GLU699 4.9 22.9 1.0
CA C:SER701 4.9 17.0 1.0
C C:PRO700 4.9 18.7 1.0
CA C:PRO700 4.9 20.7 1.0
CB C:SER701 4.9 17.3 1.0

Zinc binding site 3 out of 10 in 7f3o

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Zinc binding site 3 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn803

b:20.3
occ:1.00
NE2 C:HIS456 1.9 19.2 1.0
OE1 C:GLU452 2.1 20.7 1.0
O C:HOH1124 2.2 15.1 1.0
CE1 C:HIS456 2.9 19.4 1.0
CD2 C:HIS456 3.0 18.1 1.0
CD C:GLU452 3.0 19.4 1.0
OE2 C:GLU452 3.3 23.9 1.0
CD2 C:LEU774 3.6 20.6 1.0
CE C:LYS455 3.9 22.4 1.0
NZ C:LYS455 4.0 23.7 1.0
ND1 C:HIS456 4.0 24.0 1.0
O C:HOH1049 4.1 32.3 1.0
CG C:HIS456 4.1 18.8 1.0
OE1 C:GLN777 4.1 36.2 1.0
CG C:GLU452 4.4 19.2 1.0
CB C:GLU452 4.8 16.3 1.0

Zinc binding site 4 out of 10 in 7f3o

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Zinc binding site 4 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:21.8
occ:1.00
OE2 D:GLU440 1.9 25.1 1.0
NE2 D:HIS433 2.0 25.6 1.0
OXT D:ACT805 2.0 36.8 1.0
O D:ACT805 2.6 45.4 1.0
C D:ACT805 2.6 28.6 1.0
CD D:GLU440 2.7 24.1 1.0
CE1 D:HIS433 3.0 24.5 1.0
OE1 D:GLU440 3.0 25.8 1.0
CD2 D:HIS433 3.0 26.1 1.0
NZ D:LYS430 3.9 24.5 1.0
CD D:LYS430 4.1 20.9 1.0
CH3 D:ACT805 4.1 51.6 1.0
ND1 D:HIS433 4.1 24.4 1.0
CG D:HIS433 4.2 23.8 1.0
CG D:GLU440 4.2 25.6 1.0
O D:GLU440 4.3 23.8 1.0
CE D:LYS430 4.7 23.6 1.0

Zinc binding site 5 out of 10 in 7f3o

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Zinc binding site 5 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn803

b:20.6
occ:1.00
NE2 D:HIS456 1.9 20.3 1.0
OE1 D:GLU452 2.1 20.1 1.0
O D:HOH1108 2.2 15.8 1.0
CE1 D:HIS456 2.9 19.2 1.0
CD D:GLU452 3.0 18.6 1.0
CD2 D:HIS456 3.0 18.3 1.0
OE2 D:GLU452 3.3 24.6 1.0
CD2 D:LEU774 3.6 21.3 1.0
O D:HOH1070 3.9 35.2 1.0
NZ D:LYS455 4.0 23.7 1.0
CE D:LYS455 4.0 21.9 1.0
ND1 D:HIS456 4.1 22.8 1.0
OE1 D:GLN777 4.1 37.0 1.0
CG D:HIS456 4.1 18.4 1.0
CG D:GLU452 4.4 18.1 1.0
CB D:GLU452 4.7 15.8 1.0

Zinc binding site 6 out of 10 in 7f3o

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Zinc binding site 6 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn807

b:19.7
occ:1.00
OE2 D:GLU699 1.3 21.9 1.0
OE1 E:GLU452 2.0 18.1 1.0
NE2 E:HIS456 2.0 20.1 1.0
O D:HOH1114 2.2 17.6 1.0
CD D:GLU699 2.4 29.4 1.0
OE1 D:GLU699 2.7 26.6 1.0
CD2 E:HIS456 2.9 19.9 1.0
CD E:GLU452 3.0 19.9 1.0
CE1 E:HIS456 3.1 22.4 1.0
OE2 E:GLU452 3.3 20.2 1.0
CG D:GLU699 3.8 27.8 1.0
CD2 E:LEU774 4.0 21.8 1.0
CG E:HIS456 4.1 20.0 1.0
ND1 E:HIS456 4.1 20.0 1.0
O D:HOH1040 4.2 33.5 1.0
CG E:GLU452 4.3 17.7 1.0
N D:SER701 4.3 18.4 1.0
CB D:GLU699 4.6 25.8 1.0
CB E:GLU452 4.7 16.5 1.0
O D:ALA698 4.7 20.4 1.0
CD2 E:LEU779 4.7 34.8 1.0
CA D:GLU699 4.9 22.7 1.0
CA D:SER701 4.9 17.3 1.0
CA D:PRO700 4.9 21.4 1.0
C D:PRO700 4.9 19.5 1.0
CB D:SER701 5.0 17.5 1.0

Zinc binding site 7 out of 10 in 7f3o

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Zinc binding site 7 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn802

b:25.9
occ:1.00
NE2 E:HIS433 2.0 26.1 1.0
CE1 E:HIS433 3.0 26.2 1.0
CD2 E:HIS433 3.1 25.8 1.0
OE2 E:GLU434 4.0 48.1 1.0
ND1 E:HIS433 4.1 24.7 1.0
CG E:HIS433 4.2 26.4 1.0
CB E:MET429 4.8 23.2 1.0
CG E:MET429 4.9 26.1 1.0
CD E:GLU434 5.0 44.8 1.0

Zinc binding site 8 out of 10 in 7f3o

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Zinc binding site 8 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn802

b:42.6
occ:1.00
NE2 F:HIS456 2.1 30.6 1.0
OE1 F:GLU452 2.3 35.0 1.0
O F:HOH1049 2.4 41.5 1.0
CD2 F:HIS456 3.1 29.8 1.0
CE1 F:HIS456 3.2 34.3 1.0
CD F:GLU452 3.3 34.9 1.0
OE2 F:GLU452 3.6 43.4 1.0
OE1 F:GLN777 3.6 42.3 1.0
CD2 F:LEU774 3.8 26.5 1.0
NZ F:LYS455 4.0 48.8 1.0
ND1 F:HIS456 4.3 33.6 1.0
CG F:HIS456 4.3 30.3 1.0
NE2 F:GLN777 4.4 45.9 1.0
CD F:GLN777 4.4 40.8 1.0
CG F:GLU452 4.6 29.3 1.0
CD F:LYS455 4.8 36.7 1.0
CB F:GLU452 4.9 24.1 1.0

Zinc binding site 9 out of 10 in 7f3o

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Zinc binding site 9 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn803

b:26.2
occ:1.00
OD2 F:ASP475 1.9 19.6 1.0
CG F:ASP475 2.7 24.2 1.0
OD1 F:ASP475 2.9 25.1 1.0
CB F:ASP475 4.1 21.5 1.0
OD2 F:ASP477 4.3 40.9 1.0
O F:HOH920 4.6 34.8 1.0
CB F:ASP477 4.7 34.3 1.0
CG2 F:THR478 4.7 31.0 1.0

Zinc binding site 10 out of 10 in 7f3o

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Zinc binding site 10 out of 10 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and Tak- 653


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 Tak- 653 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn804

b:22.0
occ:1.00
O F:ACT805 2.0 36.1 1.0
NE2 F:HIS433 2.1 25.4 1.0
C F:ACT805 2.7 33.0 1.0
OXT F:ACT805 2.8 44.5 1.0
CD2 F:HIS433 3.0 26.3 1.0
CE1 F:HIS433 3.1 25.9 1.0
CG F:GLU434 3.7 48.8 1.0
CD F:GLU434 4.1 52.8 1.0
OE2 F:GLU434 4.1 52.8 1.0
CG F:HIS433 4.2 25.6 1.0
CH3 F:ACT805 4.2 46.3 1.0
ND1 F:HIS433 4.2 25.2 1.0
SD F:MET429 4.6 27.8 1.0
OE1 F:GLU434 5.0 49.8 1.0

Reference:

A.Suzuki, A.Kunugi, Y.Tajima, N.Suzuki, M.Suzuki, M.Toyofuku, H.Kuno, S.Sogabe, Y.Kosugi, Y.Awasaki, T.Kaku, H.Kimura. Strictly Regulated Agonist-Dependent Activation of Ampa-R Is the Key Characteristic of Tak-653 For Robust Synaptic Responses and Cognitive Improvement. Sci Rep V. 11 14532 2021.
ISSN: ESSN 2045-2322
PubMed: 34267258
DOI: 10.1038/S41598-021-93888-0
Page generated: Sun Aug 22 09:42:52 2021

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