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Calcium in PDB 7ebt: Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form

Protein crystallography data

The structure of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form, PDB code: 7ebt was solved by K.Inaba, K.Koiwai, M.Senda, T.Senda, R.Niwa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 1.51
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.877, 151.877, 147.301, 90, 90, 90
R / Rfree (%) 18.6 / 20.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form (pdb code 7ebt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form, PDB code: 7ebt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7ebt

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Calcium binding site 1 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:26.5
occ:0.50
 O A:HOH541 2.5 40.7 1.0
OD1 A:ASP47 2.6 20.5 1.0
OE1 B:GLU40 2.6 25.0 1.0
O B:HOH499 3.0 34.2 1.0
CG A:ASP47 3.6 20.8 1.0
CA D:CA304 3.7 18.4 0.5
CD B:GLU40 3.8 20.5 1.0
OD2 A:ASP47 4.1 22.7 1.0
CG A:GLU46 4.2 23.1 1.0
OE2 B:GLU40 4.3 19.2 1.0
O A:HOH520 4.4 33.7 1.0
CB A:GLU46 4.4 16.3 1.0
N A:ASP47 4.4 15.7 1.0
CA A:ASP47 4.6 17.1 1.0
CB A:ASP47 4.7 15.1 1.0
C A:GLU46 4.9 15.8 1.0
CG B:GLU40 5.0 28.8 1.0
OE2 D:GLU46 5.0 31.9 1.0

Calcium binding site 2 out of 9 in 7ebt

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Calcium binding site 2 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:14.5
occ:0.50
 OD2 B:ASP47 2.2 28.6 1.0
OE1 C:GLU40 2.4 26.7 1.0
O C:HOH432 2.4 30.0 1.0
O A:HOH402 2.4 28.2 1.0
OE1 A:GLU40 2.4 27.6 1.0
OE2 A:GLU40 2.5 26.7 1.0
O B:HOH446 2.5 32.2 1.0
O C:HOH521 2.5 30.4 1.0
CD A:GLU40 2.8 26.1 1.0
CG B:ASP47 3.2 25.6 1.0
CD C:GLU40 3.5 25.9 1.0
OD1 B:ASP47 3.6 28.7 1.0
NH2 A:ARG37 3.7 45.7 1.0
CA B:CA302 3.8 17.1 0.5
CZ A:ARG37 3.9 42.8 1.0
CB C:GLU40 4.1 23.3 1.0
CG C:GLU40 4.1 26.5 1.0
NE A:ARG37 4.2 27.9 1.0
NH1 A:ARG37 4.3 28.2 1.0
CG A:GLU40 4.3 23.0 1.0
OE2 C:GLU42 4.4 23.7 1.0
O B:HOH512 4.4 25.8 1.0
OE2 C:GLU40 4.5 26.7 1.0
O B:HOH542 4.5 35.6 1.0
CB B:ASP47 4.5 21.2 1.0
O C:GLU40 4.6 24.4 1.0
CA C:GLU40 4.9 21.4 1.0

Calcium binding site 3 out of 9 in 7ebt

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Calcium binding site 3 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:38.4
occ:0.50
 O C:HOH492 2.4 38.4 1.0
OE2 A:GLU32 2.5 27.6 1.0
O A:HOH523 2.6 38.0 1.0
CD A:GLU32 3.3 27.0 1.0
O A:HOH481 3.3 33.4 1.0
OE1 A:GLU32 3.4 26.9 1.0
NZ A:LYS3 4.1 38.4 1.0
CA D:CA303 4.1 15.4 0.5
O C:HOH419 4.4 24.6 1.0
CG D:GLU40 4.4 23.1 0.5
CG D:GLU40 4.4 23.1 0.5
CG A:GLU32 4.7 26.7 1.0
O D:HOH535 4.7 47.9 1.0
O D:PHE39 4.8 23.5 1.0
CA D:GLU40 4.8 17.6 0.5
CA D:GLU40 4.8 17.6 0.5
O A:ASP29 4.9 35.3 1.0
CE A:LYS3 4.9 35.8 1.0
CB D:GLU40 5.0 20.8 0.5
CB D:GLU40 5.0 20.8 0.5
CD D:GLU40 5.0 32.1 0.5
CD D:GLU40 5.0 32.1 0.5

Calcium binding site 4 out of 9 in 7ebt

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Calcium binding site 4 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:17.1
occ:0.50
 OE2 A:GLU40 2.3 26.7 1.0
OD1 B:ASP47 2.3 28.7 1.0
O B:HOH423 2.4 30.8 1.0
O A:HOH553 2.4 35.5 1.0
OE1 C:GLU40 2.4 26.7 1.0
OE2 C:GLU40 2.5 26.7 1.0
OE1 B:GLU46 2.5 27.4 1.0
CD C:GLU40 2.8 25.9 1.0
CG B:ASP47 3.3 25.6 1.0
CD A:GLU40 3.5 26.1 1.0
CD B:GLU46 3.5 24.3 1.0
OD2 B:ASP47 3.7 28.6 1.0
CA A:CA303 3.8 14.5 0.5
OE2 B:GLU46 3.8 28.9 1.0
O B:HOH539 4.2 38.1 1.0
CG A:GLU40 4.2 23.0 1.0
CG C:GLU40 4.3 26.5 1.0
OE1 A:GLU40 4.4 27.6 1.0
O C:HOH521 4.6 30.4 1.0
CB B:ASP47 4.6 21.2 1.0
O C:HOH408 4.7 39.3 1.0
CA B:ASP47 4.8 21.5 1.0
O A:HOH571 4.8 26.1 1.0
CG B:GLU46 4.9 20.4 1.0
N B:ASP47 4.9 16.9 1.0

Calcium binding site 5 out of 9 in 7ebt

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Calcium binding site 5 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:40.8
occ:0.50
 O B:HOH496 2.4 47.7 1.0
O B:HOH562 2.5 46.5 1.0
O B:HOH448 2.5 48.4 1.0
O B:SER124 2.8 53.0 1.0
C B:SER124 3.8 51.1 1.0
CA B:SER124 4.2 46.5 1.0
O B:ARG123 4.8 48.9 1.0
CB B:SER124 4.9 50.8 1.0
N B:ILE125 5.0 48.0 1.0

Calcium binding site 6 out of 9 in 7ebt

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Calcium binding site 6 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:16.6
occ:0.50
 OE2 D:GLU42 2.3 21.6 1.0
O C:HOH486 2.4 32.6 1.0
O D:HOH476 2.4 31.4 1.0
OD2 C:ASP47 2.4 27.3 1.0
OD1 C:ASP47 2.6 25.0 1.0
OE1 D:GLU40 2.7 27.6 1.0
O C:HOH564 2.7 27.0 1.0
CG C:ASP47 2.8 26.7 1.0
OE2 D:GLU40 3.2 50.1 1.0
CD D:GLU40 3.2 32.1 0.5
CD D:GLU40 3.2 32.1 0.5
CD D:GLU42 3.3 25.2 1.0
O D:HOH412 3.7 30.8 1.0
OE1 D:GLU42 3.7 19.4 1.0
NH2 D:ARG37 4.3 31.6 1.0
O C:HOH401 4.3 41.5 1.0
CB C:ASP47 4.4 22.8 1.0
O A:HOH581 4.5 42.8 1.0
CG D:GLU40 4.5 23.1 0.5
CG D:GLU40 4.5 23.1 0.5
CG D:GLU42 4.6 18.9 1.0
CA D:CA303 4.6 15.4 0.5
OE2 C:GLU46 4.7 34.7 1.0
CB D:GLU40 4.8 20.8 0.5
CB D:GLU40 4.8 20.8 0.5
NE D:ARG37 4.8 32.9 1.0
O C:HOH545 4.8 23.4 1.0
O D:HOH574 4.9 41.5 1.0

Calcium binding site 7 out of 9 in 7ebt

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Calcium binding site 7 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:15.4
occ:0.50
 O A:HOH401 2.4 33.0 1.0
OE2 C:GLU46 2.4 34.7 1.0
O C:HOH492 2.4 38.4 1.0
OE1 D:GLU40 2.4 27.6 1.0
O C:HOH419 2.4 24.6 1.0
OE1 A:GLU32 2.4 26.9 1.0
O D:HOH412 2.8 30.8 1.0
CD D:GLU40 3.2 32.1 0.5
CD D:GLU40 3.2 32.1 0.5
CD C:GLU46 3.4 40.3 1.0
CD A:GLU32 3.7 27.0 1.0
OE1 C:GLU46 3.7 31.4 1.0
CG D:GLU40 3.8 23.1 0.5
CG D:GLU40 3.8 23.1 0.5
O C:HOH564 3.9 27.0 1.0
CB D:GLU40 4.0 20.8 0.5
CB D:GLU40 4.0 20.8 0.5
OE2 D:GLU40 4.1 50.1 1.0
CA A:CA304 4.1 38.4 0.5
OE2 A:GLU32 4.3 27.6 1.0
O A:LEU33 4.3 29.7 1.0
O A:HOH481 4.5 33.4 1.0
O A:HOH521 4.5 25.6 1.0
N A:LEU33 4.5 18.1 1.0
CA D:CA302 4.6 16.6 0.5
CG C:GLU46 4.7 30.2 1.0
CG A:GLU32 4.8 26.7 1.0
CB A:GLU32 4.8 21.2 1.0
OE2 D:GLU42 4.8 21.6 1.0
CA D:GLU40 4.9 17.6 0.5
CA D:GLU40 4.9 17.6 0.5
CA A:GLU32 5.0 18.6 1.0

Calcium binding site 8 out of 9 in 7ebt

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Calcium binding site 8 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:18.4
occ:0.50
 O D:HOH554 2.3 37.1 1.0
O B:HOH499 2.4 34.2 1.0
OE2 D:GLU46 2.4 31.9 1.0
O A:HOH541 2.5 40.7 1.0
OD2 A:ASP47 2.5 22.7 1.0
OD1 D:ASP47 2.5 27.5 1.0
OD1 A:ASP47 2.7 20.5 1.0
OE1 D:GLU46 2.8 33.4 1.0
CG A:ASP47 2.9 20.8 1.0
CD D:GLU46 3.0 32.0 1.0
CG D:ASP47 3.7 25.7 1.0
O B:HOH480 3.7 27.9 1.0
CA A:CA302 3.7 26.5 0.5
CA D:CA305 4.0 13.3 0.5
O D:HOH489 4.3 27.4 1.0
CB A:ASP47 4.3 15.1 1.0
O A:HOH520 4.4 33.7 1.0
CA D:ASP47 4.4 20.5 1.0
OD2 D:ASP47 4.5 24.5 1.0
CG D:GLU46 4.5 27.8 1.0
OE1 B:GLU40 4.5 25.0 1.0
CG D:LYS50 4.5 29.4 1.0
CB D:ASP47 4.6 20.5 1.0
N D:ASP47 4.8 19.2 1.0
O D:HOH450 5.0 28.9 1.0

Calcium binding site 9 out of 9 in 7ebt

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Calcium binding site 9 out of 9 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:13.3
occ:0.50
 OD2 D:ASP47 2.3 24.5 1.0
OD2 A:ASP47 2.4 22.7 1.0
O D:HOH489 2.4 27.4 1.0
O D:HOH492 2.4 30.5 1.0
O B:HOH430 2.5 23.4 1.0
O B:HOH480 2.5 27.9 1.0
O D:HOH575 2.7 28.5 1.0
OD1 D:ASP47 2.8 27.5 1.0
CG D:ASP47 2.9 25.7 1.0
CG A:ASP47 3.5 20.8 1.0
O B:HOH418 3.9 25.6 1.0
CB A:ASP47 4.0 15.1 1.0
CA D:CA304 4.0 18.4 0.5
OE1 D:GLU46 4.2 33.4 1.0
O B:HOH499 4.2 34.2 1.0
O A:HOH555 4.2 19.1 1.0
OE2 B:GLU40 4.3 19.2 1.0
CB D:ASP47 4.4 20.5 1.0
O D:HOH544 4.5 22.4 1.0
OD1 A:ASP47 4.6 20.5 1.0
NH2 B:ARG37 4.6 38.9 1.0
CD B:GLU40 4.6 20.5 1.0
O A:HOH573 4.9 19.4 1.0

Reference:

K.Inaba, K.Ebihara, M.Senda, R.Yoshino, C.Sakuma, K.Koiwai, D.Takaya, C.Watanabe, A.Watanabe, Y.Kawashima, K.Fukuzawa, R.Imamura, H.Kojima, T.Okabe, N.Uemura, S.Kasai, H.Kanuka, T.Nishimura, K.Watanabe, H.Inoue, Y.Fujikawa, T.Honma, T.Hirokawa, T.Senda, R.Niwa. Molecular Action of Larvicidal Flavonoids on Ecdysteroidogenic Glutathione S-Transferase Noppera-Bo in Aedes Aegypti. Bmc Biol. V. 20 43 2022.
ISSN: ESSN 1741-7007
PubMed: 35172816
DOI: 10.1186/S12915-022-01233-2
Page generated: Fri Jul 19 00:21:27 2024

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