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

Protein crystallography data

The structure of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and Glutathione-Bound Form, PDB code: 7ebw 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) 47.85 / 1.94
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.314, 151.314, 146.147, 90, 90, 90
R / Rfree (%) 17.2 / 21.9

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 7ebw

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Calcium binding site 1 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:53.0
occ:1.00
 O D:HOH401 2.4 49.7 1.0
OE2 A:GLU32 2.5 37.4 1.0
O A:HOH507 2.6 44.1 1.0
OE1 D:GLU40 2.7 52.0 1.0
O A:HOH421 2.8 56.0 1.0
O A:HOH402 2.9 54.3 1.0
OE2 D:GLU40 2.9 61.4 1.0
OE1 A:GLU32 3.1 35.9 1.0
CD A:GLU32 3.1 35.2 1.0
CD D:GLU40 3.1 50.3 1.0
CA C:CA305 3.9 40.4 1.0
O C:HOH412 4.4 34.6 1.0
CG A:GLU32 4.6 30.7 1.0
CG D:GLU40 4.6 37.9 1.0
OE2 C:GLU46 4.8 41.4 1.0
O A:ASP29 4.9 43.0 1.0
O D:PHE39 4.9 33.2 1.0
CA D:GLU40 4.9 32.5 1.0

Calcium binding site 2 out of 8 in 7ebw

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Calcium binding site 2 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:53.3
occ:1.00
 O A:HOH533 2.5 42.1 1.0
OD1 A:ASP47 2.6 25.4 1.0
OE1 B:GLU40 2.7 31.8 1.0
O B:HOH411 2.9 44.1 1.0
CD A:GLU46 3.4 40.6 1.0
CG A:ASP47 3.6 30.8 1.0
CA D:CA304 3.8 38.9 1.0
CD B:GLU40 3.8 36.0 1.0
O B:HOH534 4.1 45.0 1.0
O A:HOH512 4.2 35.7 1.0
OD2 A:ASP47 4.2 28.8 1.0
N A:ASP47 4.2 26.7 1.0
CG A:GLU46 4.3 34.4 1.0
CB A:GLU46 4.3 28.4 1.0
OE2 B:GLU40 4.3 24.8 1.0
CA A:ASP47 4.4 25.6 1.0
CB A:ASP47 4.6 23.9 1.0
C A:GLU46 4.6 25.7 1.0

Calcium binding site 3 out of 8 in 7ebw

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Calcium binding site 3 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:47.1
occ:1.00
 OD2 B:ASP47 2.4 43.6 1.0
OE1 C:GLU40 2.5 42.8 1.0
OE2 A:GLU40 3.1 39.9 1.0
CG B:ASP47 3.2 40.2 1.0
OD1 B:ASP47 3.3 34.5 1.0
CD A:GLU40 3.4 48.4 1.0
CD C:GLU40 3.6 47.7 1.0
CA C:CA304 3.7 49.9 1.0
NH1 A:ARG37 3.8 52.8 1.0
NH2 A:ARG37 3.9 48.5 1.0
OE1 A:GLU40 3.9 40.6 1.0
CG A:GLU40 3.9 49.1 1.0
CZ A:ARG37 3.9 54.6 1.0
OE2 C:GLU42 4.1 38.7 1.0
CB C:GLU40 4.1 37.4 1.0
CG C:GLU40 4.2 44.2 1.0
NE A:ARG37 4.6 46.0 1.0
OE2 C:GLU40 4.7 42.8 1.0
CB B:ASP47 4.7 35.5 1.0
O C:GLU40 4.7 33.3 1.0
O A:HOH542 4.7 46.1 1.0
NH2 C:ARG37 4.7 48.4 1.0
O A:HOH522 4.8 48.9 1.0
NH1 C:ARG37 4.9 51.2 1.0
CD C:GLU42 5.0 35.8 1.0
CA C:GLU40 5.0 35.5 1.0

Calcium binding site 4 out of 8 in 7ebw

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Calcium binding site 4 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:60.5
occ:1.00
 OE2 D:GLU42 2.3 36.5 1.0
OD1 C:ASP47 2.5 39.9 1.0
O D:HOH443 2.6 41.7 1.0
OD2 C:ASP47 2.7 41.3 1.0
O D:HOH453 2.7 43.9 1.0
CG C:ASP47 2.9 36.9 1.0
O C:HOH545 3.0 41.4 1.0
CD D:GLU42 3.3 38.1 1.0
OE1 D:GLU42 3.8 31.9 1.0
CG D:GLU40 4.4 37.9 1.0
CB C:ASP47 4.4 35.4 1.0
CG D:GLU42 4.6 35.8 1.0
CA C:CA305 4.6 40.4 1.0
O A:HOH410 4.6 34.9 1.0
OE2 C:GLU46 4.6 41.4 1.0
CD D:ARG37 4.6 46.7 1.0
O C:HOH510 4.7 34.5 1.0
CB D:GLU40 4.8 36.4 1.0
OE2 D:GLU40 4.9 61.4 1.0

Calcium binding site 5 out of 8 in 7ebw

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Calcium binding site 5 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:49.9
occ:1.00
 OE2 A:GLU40 2.2 39.9 1.0
OE1 C:GLU40 2.4 42.8 1.0
OE1 B:GLU46 2.4 37.0 1.0
OD1 B:ASP47 2.5 34.5 1.0
OE2 C:GLU40 2.9 42.8 1.0
CD C:GLU40 2.9 47.7 1.0
O A:HOH445 3.3 42.5 1.0
CD A:GLU40 3.4 48.4 1.0
CD B:GLU46 3.5 33.0 1.0
CG B:ASP47 3.5 40.2 1.0
CA B:CA303 3.7 47.1 1.0
OE2 B:GLU46 4.0 35.5 1.0
OD2 B:ASP47 4.1 43.6 1.0
OE1 A:GLU40 4.2 40.6 1.0
CG C:GLU40 4.4 44.2 1.0
CG A:GLU40 4.5 49.1 1.0
O A:HOH534 4.5 38.9 1.0
CA B:ASP47 4.7 27.6 1.0
N B:ASP47 4.7 23.1 1.0
CB B:ASP47 4.7 35.5 1.0
CG B:GLU46 4.7 27.6 1.0
O A:HOH542 4.7 46.1 1.0
O C:HOH532 4.8 45.7 1.0
CB B:GLU46 4.9 27.9 1.0

Calcium binding site 6 out of 8 in 7ebw

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Calcium binding site 6 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:40.4
occ:1.00
 O A:HOH410 2.3 34.9 1.0
OE2 C:GLU46 2.3 41.4 1.0
OE1 A:GLU32 2.5 35.9 1.0
O C:HOH412 2.5 34.6 1.0
OE2 D:GLU40 2.6 61.4 1.0
O D:HOH401 2.7 49.7 1.0
CD C:GLU46 3.3 46.8 1.0
CD D:GLU40 3.4 50.3 1.0
OE1 C:GLU46 3.6 38.1 1.0
CD A:GLU32 3.7 35.2 1.0
CA A:CA303 3.9 53.0 1.0
CG D:GLU40 3.9 37.9 1.0
O C:HOH545 4.0 41.4 1.0
OE1 D:GLU40 4.2 52.0 1.0
CB D:GLU40 4.3 36.4 1.0
O A:LEU33 4.4 34.0 1.0
OE2 A:GLU32 4.4 37.4 1.0
O A:HOH529 4.4 36.0 1.0
CG C:GLU46 4.5 42.9 1.0
N A:LEU33 4.6 27.0 1.0
CA C:CA303 4.6 60.5 1.0
CB A:GLU32 4.7 28.6 1.0
CG A:GLU32 4.8 30.7 1.0
CA A:GLU32 4.9 28.5 1.0
O D:GLU40 4.9 31.3 1.0
CA D:GLU40 5.0 32.5 1.0

Calcium binding site 7 out of 8 in 7ebw

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Calcium binding site 7 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:31.6
occ:1.00
 OD2 A:ASP47 2.3 28.8 1.0
OD2 D:ASP47 2.4 38.0 1.0
O A:HOH526 2.5 35.4 1.0
O B:HOH405 2.5 28.1 1.0
O B:HOH427 2.5 34.0 1.0
O A:HOH552 2.6 42.5 1.0
O D:HOH508 2.6 40.8 1.0
OD1 D:ASP47 2.8 33.6 1.0
CG D:ASP47 2.9 33.9 1.0
CG A:ASP47 3.4 30.8 1.0
CB A:ASP47 3.8 23.9 1.0
O B:HOH402 3.9 29.6 1.0
CA D:CA304 4.0 38.9 1.0
OE2 B:GLU40 4.1 24.8 1.0
O A:HOH548 4.1 28.9 1.0
NH2 B:ARG37 4.2 43.2 1.0
OE1 D:GLU46 4.3 42.2 1.0
CB D:ASP47 4.4 28.5 1.0
OD1 A:ASP47 4.5 25.4 1.0
O B:HOH503 4.5 43.7 1.0
CD B:GLU40 4.5 36.0 1.0
O B:HOH411 4.5 44.1 1.0
O D:HOH525 4.5 35.9 1.0
O A:HOH560 4.9 25.3 1.0
CG B:GLU40 4.9 35.5 1.0

Calcium binding site 8 out of 8 in 7ebw

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Calcium binding site 8 out of 8 in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Desmethylglycitein and 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 Desmethylglycitein and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:38.9
occ:1.00
 OD2 A:ASP47 2.5 28.8 1.0
O A:HOH533 2.5 42.1 1.0
OD1 D:ASP47 2.5 33.6 1.0
O B:HOH411 2.6 44.1 1.0
OD1 A:ASP47 2.7 25.4 1.0
OE2 D:GLU46 2.8 42.0 1.0
CG A:ASP47 2.9 30.8 1.0
OE1 D:GLU46 3.0 42.2 1.0
CD D:GLU46 3.3 41.3 1.0
O B:HOH427 3.4 34.0 1.0
CG D:ASP47 3.8 33.9 1.0
CA A:CA304 3.8 53.3 1.0
CA D:CA303 4.0 31.6 1.0
CB A:ASP47 4.4 23.9 1.0
OE1 B:GLU40 4.4 31.8 1.0
CA D:ASP47 4.4 30.2 1.0
O A:HOH512 4.5 35.7 1.0
OD2 D:ASP47 4.6 38.0 1.0
O A:HOH526 4.7 35.4 1.0
CB D:ASP47 4.7 28.5 1.0
CG D:GLU46 4.8 33.3 1.0
N D:ASP47 4.8 29.5 1.0
O D:HOH408 4.9 39.3 1.0
CD B:GLU40 4.9 36.0 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 00:22:00 2024

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