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

Protein crystallography data

The structure of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Luteolin- and Glutathione-Bound Form, PDB code: 7ebv 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) 36.69 / 1.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.703, 151.703, 146.75, 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 Luteolin- and Glutathione-Bound Form (pdb code 7ebv). 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 Luteolin- and Glutathione-Bound Form, PDB code: 7ebv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:19.0
occ:0.56
 OD2 B:ASP47 2.2 31.0 1.0
O C:HOH422 2.3 36.6 1.0
OE1 A:GLU40 2.4 31.4 1.0
OE1 C:GLU40 2.5 29.6 1.0
O B:HOH405 2.5 35.0 1.0
O C:HOH509 2.5 34.3 1.0
O A:HOH413 2.5 33.6 1.0
OE2 A:GLU40 2.6 29.9 1.0
CD A:GLU40 2.8 30.2 1.0
CG B:ASP47 3.1 27.3 1.0
OD1 B:ASP47 3.4 29.1 1.0
CD C:GLU40 3.5 29.1 1.0
CA B:CA303 3.9 24.1 0.6
NH2 A:ARG37 4.0 40.9 1.0
CG C:GLU40 4.0 26.9 1.0
CZ A:ARG37 4.0 40.4 1.0
NH1 A:ARG37 4.1 32.6 1.0
CB C:GLU40 4.1 23.9 1.0
OE2 C:GLU42 4.2 27.7 1.0
CG A:GLU40 4.3 30.2 1.0
O B:HOH503 4.4 26.8 1.0
CB B:ASP47 4.5 22.2 1.0
OE2 C:GLU40 4.5 30.5 1.0
O B:HOH565 4.6 37.0 1.0
O B:HOH551 4.6 38.4 1.0
O C:GLU40 4.6 24.2 1.0
NE A:ARG37 4.6 36.5 1.0
CA C:GLU40 4.9 22.8 1.0

Calcium binding site 2 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:68.5
occ:1.00
 CA C:CA303 2.9 22.8 0.7
OE1 A:GLU32 3.1 28.2 1.0
OE2 A:GLU32 3.2 32.1 1.0
CG D:GLU40 3.5 22.2 1.0
CD A:GLU32 3.6 26.1 1.0
OE1 D:GLU40 3.7 29.0 1.0
O C:HOH420 3.7 27.1 1.0
O A:HOH497 3.7 32.6 1.0
OE2 C:GLU46 3.8 37.4 1.0
CD D:GLU40 3.9 24.9 1.0
O C:HOH521 4.2 36.8 1.0
CB D:GLU40 4.2 21.6 1.0
CD C:GLU46 4.5 40.0 1.0
CA D:GLU40 4.6 18.1 1.0
CE2 D:PHE39 4.8 34.5 1.0
OE1 C:GLU46 4.9 36.8 1.0
CD2 D:PHE39 4.9 34.3 1.0

Calcium binding site 3 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:24.7
occ:0.60
 O B:HOH519 2.4 38.8 1.0
O A:HOH541 2.4 39.1 1.0
OD2 A:ASP47 2.5 24.2 1.0
OD1 D:ASP47 2.5 28.1 1.0
OD1 A:ASP47 2.7 23.4 1.0
CG A:ASP47 2.9 22.1 1.0
CA A:CA306 3.5 26.1 0.6
O A:HOH503 3.6 31.1 1.0
CG D:ASP47 3.7 25.7 1.0
CA D:CA303 4.0 20.9 0.7
O A:HOH511 4.2 36.9 1.0
O A:HOH506 4.3 31.7 1.0
CB A:ASP47 4.3 16.8 1.0
CA D:ASP47 4.4 21.4 1.0
OD2 D:ASP47 4.5 28.3 1.0
CG D:GLU46 4.6 31.4 1.0
OE1 B:GLU40 4.6 28.2 1.0
CB D:ASP47 4.6 24.7 1.0
N D:ASP47 4.8 18.7 1.0
O D:HOH432 5.0 29.8 1.0

Calcium binding site 4 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:26.1
occ:0.57
 OE1 A:GLU46 2.2 39.3 1.0
O A:HOH541 2.4 39.1 1.0
O A:HOH554 2.5 41.2 1.0
OD1 A:ASP47 2.5 23.4 1.0
OE1 B:GLU40 2.7 28.2 1.0
O B:HOH519 2.7 38.8 1.0
CD A:GLU46 3.4 35.3 1.0
CG A:ASP47 3.4 22.1 1.0
CA A:CA305 3.5 24.7 0.6
CD B:GLU40 3.8 30.4 1.0
OD2 A:ASP47 3.9 24.2 1.0
OE2 A:GLU46 4.0 40.2 1.0
CE2 B:PHE39 4.1 38.1 1.0
OE2 B:GLU40 4.3 22.1 1.0
O A:HOH511 4.4 36.9 1.0
CD2 B:PHE39 4.5 34.5 1.0
CG A:GLU46 4.5 25.3 1.0
N A:ASP47 4.5 16.6 1.0
CB A:ASP47 4.6 16.8 1.0
CA A:ASP47 4.6 17.4 1.0
CB A:GLU46 4.7 18.6 1.0
O A:HOH503 5.0 31.1 1.0

Calcium binding site 5 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:24.1
occ:0.61
 OE2 A:GLU40 2.2 29.9 1.0
OD1 B:ASP47 2.3 29.1 1.0
O B:HOH421 2.4 35.1 1.0
OE1 C:GLU40 2.4 29.6 1.0
OE2 C:GLU40 2.5 30.5 1.0
OE1 B:GLU46 2.5 26.1 1.0
O A:HOH552 2.5 41.8 1.0
CD C:GLU40 2.7 29.1 1.0
CD A:GLU40 3.4 30.2 1.0
CG B:ASP47 3.4 27.3 1.0
CD B:GLU46 3.5 24.3 1.0
O B:HOH513 3.7 39.7 1.0
OE2 B:GLU46 3.8 27.3 1.0
CA A:CA303 3.9 19.0 0.6
OD2 B:ASP47 3.9 31.0 1.0
CG A:GLU40 4.1 30.2 1.0
CG C:GLU40 4.2 26.9 1.0
OE1 A:GLU40 4.3 31.4 1.0
O C:HOH509 4.5 34.3 1.0
CB B:ASP47 4.7 22.2 1.0
O A:HOH562 4.7 26.6 1.0
CA B:ASP47 4.7 23.8 1.0
CG B:GLU46 4.9 20.3 1.0
N B:ASP47 4.9 17.1 1.0
CE2 A:PHE39 4.9 31.1 1.0
O B:HOH405 5.0 35.0 1.0

Calcium binding site 6 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:22.8
occ:0.72
 OE2 C:GLU46 2.3 37.4 1.0
OE1 D:GLU40 2.3 29.0 1.0
O A:HOH401 2.4 36.2 1.0
OE1 A:GLU32 2.4 28.2 1.0
O C:HOH420 2.4 27.1 1.0
CA A:CA304 2.9 68.5 1.0
O D:HOH511 2.9 33.7 1.0
CD C:GLU46 3.3 40.0 1.0
CD D:GLU40 3.4 24.9 1.0
CD A:GLU32 3.6 26.1 1.0
OE1 C:GLU46 3.6 36.8 1.0
CG D:GLU40 3.8 22.2 1.0
O C:HOH556 3.9 29.5 1.0
CB D:GLU40 4.0 21.6 1.0
OE2 A:GLU32 4.2 32.1 1.0
O C:HOH521 4.3 36.8 1.0
O A:LEU33 4.3 29.4 1.0
O A:HOH497 4.4 32.6 1.0
OE2 D:GLU40 4.5 26.2 1.0
O A:HOH521 4.5 26.2 1.0
N A:LEU33 4.6 21.0 1.0
CA D:CA304 4.6 21.7 0.7
CG C:GLU46 4.6 28.0 1.0
CG A:GLU32 4.8 27.0 1.0
OE2 D:GLU42 4.8 22.6 1.0
CB A:GLU32 4.9 21.8 1.0
CA D:GLU40 5.0 18.1 1.0

Calcium binding site 7 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:20.9
occ:0.73
 OD2 D:ASP47 2.3 28.3 1.0
OD2 A:ASP47 2.4 24.2 1.0
O B:HOH433 2.4 22.8 1.0
O D:HOH474 2.4 31.1 1.0
O A:HOH503 2.5 31.1 1.0
O A:HOH506 2.5 31.7 1.0
OD1 D:ASP47 2.7 28.1 1.0
O A:HOH505 2.8 30.9 1.0
CG D:ASP47 2.8 25.7 1.0
CG A:ASP47 3.5 22.1 1.0
O B:HOH422 3.9 28.2 1.0
CB A:ASP47 4.0 16.8 1.0
CA A:CA305 4.0 24.7 0.6
OE2 B:GLU40 4.2 22.1 1.0
O A:HOH543 4.2 20.6 1.0
O B:HOH519 4.3 38.8 1.0
CB D:ASP47 4.3 24.7 1.0
NH2 B:ARG37 4.5 34.8 1.0
O D:HOH547 4.5 24.7 1.0
OD1 A:ASP47 4.6 23.4 1.0
CD B:GLU40 4.6 30.4 1.0
O A:HOH568 4.9 21.9 1.0

Calcium binding site 8 out of 8 in 7ebv

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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 Luteolin- 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 Luteolin- and Glutathione-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:21.7
occ:0.66
 OE2 D:GLU42 2.2 22.6 1.0
O D:HOH482 2.4 35.4 1.0
O D:HOH463 2.4 29.8 1.0
OD2 C:ASP47 2.4 31.4 1.0
OE2 D:GLU40 2.5 26.2 1.0
OD1 C:ASP47 2.6 29.4 1.0
O C:HOH556 2.6 29.5 1.0
OE1 D:GLU40 2.7 29.0 1.0
CG C:ASP47 2.8 25.3 1.0
CD D:GLU40 2.9 24.9 1.0
CD D:GLU42 3.3 25.5 1.0
OE1 D:GLU42 3.7 21.4 1.0
O D:HOH511 3.9 33.7 1.0
NH2 D:ARG37 4.1 34.7 1.0
CB C:ASP47 4.4 24.3 1.0
CG D:GLU40 4.4 22.2 1.0
O C:HOH521 4.4 36.8 1.0
NE D:ARG37 4.5 33.6 1.0
OE2 C:GLU46 4.5 37.4 1.0
CG D:GLU42 4.5 20.7 1.0
CA C:CA303 4.6 22.8 0.7
O C:HOH543 4.8 25.6 1.0
CZ D:ARG37 4.8 34.4 1.0
CB D:GLU40 4.8 21.6 1.0
O A:HOH401 4.9 36.2 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 00:21:35 2024

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