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

Protein crystallography data

The structure of Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Daidzein- and Glutathione-Bound Form, PDB code: 7ebu 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) 48.13 / 1.95
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.213, 152.213, 146.825, 90, 90, 90
R / Rfree (%) 19 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Aedes Aegypti Noppera-Bo, Glutathione S- Transferase Epsilon 8, in Daidzein- and Glutathione-Bound Form (pdb code 7ebu). 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 Daidzein- and Glutathione-Bound Form, PDB code: 7ebu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7ebu

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

b:52.1
occ:1.00
 OD1 A:ASP47 2.7 28.4 1.0
OE1 B:GLU40 2.7 28.6 1.0
O A:HOH519 2.9 39.9 1.0
CD A:GLU46 3.1 35.0 1.0
O B:HOH438 3.1 34.9 1.0
CG A:ASP47 3.7 30.8 1.0
CD B:GLU40 3.9 31.9 1.0
O B:HOH543 3.9 41.9 1.0
CG A:GLU46 4.0 37.1 1.0
CB A:GLU46 4.0 20.7 1.0
O A:HOH447 4.0 30.4 1.0
N A:ASP47 4.1 23.7 1.0
CA D:CA305 4.1 28.4 0.7
OD2 A:ASP47 4.3 20.0 1.0
OE2 B:GLU40 4.3 21.7 1.0
CA A:ASP47 4.4 19.1 1.0
C A:GLU46 4.5 21.5 1.0
CB A:ASP47 4.6 21.4 1.0
CA A:GLU46 4.9 19.9 1.0
O A:GLU46 5.0 22.6 1.0

Calcium binding site 2 out of 8 in 7ebu

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

b:27.5
occ:0.61
 OD2 B:ASP47 2.3 28.0 1.0
O C:HOH540 2.4 36.1 1.0
OE1 A:GLU40 2.4 39.5 1.0
O B:HOH462 2.5 39.7 1.0
OE1 C:GLU40 2.6 33.5 1.0
OE2 A:GLU40 2.7 35.5 1.0
CD A:GLU40 2.9 40.7 1.0
CG B:ASP47 3.3 28.7 1.0
NH2 C:ARG37 3.4 42.3 1.0
OD1 B:ASP47 3.6 27.6 1.0
CD C:GLU40 3.7 44.2 1.0
CA B:CA303 3.8 39.8 1.0
CB C:GLU40 4.1 29.0 1.0
CG C:GLU40 4.2 40.9 1.0
CZ A:ARG37 4.2 46.7 1.0
OE2 C:GLU42 4.3 32.9 1.0
NH2 A:ARG37 4.3 45.0 1.0
CG A:GLU40 4.3 36.4 1.0
NE A:ARG37 4.4 30.4 1.0
O B:HOH494 4.5 26.3 1.0
NH1 A:ARG37 4.6 36.9 1.0
CB B:ASP47 4.6 22.3 1.0
O A:HOH536 4.6 37.2 1.0
O B:HOH538 4.6 36.5 1.0
CZ C:ARG37 4.7 51.1 1.0
OE2 C:GLU40 4.8 39.9 1.0
O C:GLU40 4.8 33.5 1.0
O A:HOH539 4.9 37.5 1.0
CA C:GLU40 5.0 28.6 1.0

Calcium binding site 3 out of 8 in 7ebu

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

b:62.8
occ:1.00
 OE1 D:GLU40 2.3 32.1 0.5
OE2 A:GLU32 2.6 29.6 1.0
OE1 A:GLU32 3.0 30.0 1.0
O A:HOH422 3.1 34.5 1.0
CD A:GLU32 3.2 33.4 1.0
O A:HOH425 3.3 40.3 1.0
CD D:GLU40 3.3 31.9 0.5
OE2 D:GLU40 3.8 37.2 0.5
NZ A:LYS3 3.8 37.1 1.0
CA D:CA304 4.0 39.5 1.0
O C:HOH434 4.4 29.8 1.0
CG D:GLU40 4.4 32.9 0.6
O A:ASP29 4.5 37.1 1.0
CG D:GLU40 4.6 32.1 0.5
CG A:GLU32 4.7 29.8 1.0
CA D:GLU40 4.7 26.9 0.5
O D:PHE39 4.8 29.6 1.0
CA D:GLU40 4.8 26.9 0.6
CB D:GLU40 4.8 29.5 0.5
O D:HOH405 4.8 40.9 1.0

Calcium binding site 4 out of 8 in 7ebu

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

b:39.8
occ:1.00
 OD1 B:ASP47 2.2 27.6 1.0
OE1 B:GLU46 2.3 33.1 1.0
OE2 A:GLU40 2.4 35.5 1.0
O B:HOH408 2.4 42.5 1.0
OE1 C:GLU40 2.4 33.5 1.0
OE2 C:GLU40 2.9 39.9 1.0
CD C:GLU40 3.0 44.2 1.0
CG B:ASP47 3.2 28.7 1.0
CD B:GLU46 3.4 28.6 1.0
CD A:GLU40 3.6 40.7 1.0
OD2 B:ASP47 3.6 28.0 1.0
OE2 B:GLU46 3.7 35.6 1.0
O B:HOH480 3.8 34.4 1.0
CA A:CA304 3.8 27.5 0.6
OE1 A:GLU40 4.4 39.5 1.0
CB B:ASP47 4.5 22.3 1.0
CG C:GLU40 4.5 40.9 1.0
O C:HOH540 4.5 36.1 1.0
CG A:GLU40 4.6 36.4 1.0
CA B:ASP47 4.6 25.3 1.0
O A:HOH540 4.6 35.9 1.0
N B:ASP47 4.7 18.8 1.0
CG B:GLU46 4.7 21.6 1.0
O A:HOH539 4.9 37.5 1.0

Calcium binding site 5 out of 8 in 7ebu

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

b:32.8
occ:0.73
 OE2 D:GLU42 2.2 29.1 1.0
O D:HOH457 2.3 37.5 1.0
OD2 C:ASP47 2.5 37.2 1.0
O D:HOH459 2.6 38.6 1.0
OE1 D:GLU40 2.7 29.8 0.6
OE2 D:GLU40 2.7 31.9 0.6
OD1 C:ASP47 2.8 35.9 1.0
O C:HOH493 2.8 32.6 1.0
CG C:ASP47 3.0 32.9 1.0
CD D:GLU40 3.0 32.7 0.6
CD D:GLU42 3.3 34.4 1.0
OE1 D:GLU42 3.8 30.0 1.0
O D:HOH527 4.0 35.7 1.0
NH2 D:ARG37 4.0 34.1 1.0
OE2 C:GLU46 4.3 42.7 1.0
O C:HOH407 4.3 39.6 1.0
CG D:GLU40 4.5 32.9 0.6
CB C:ASP47 4.5 25.4 1.0
CG D:GLU42 4.5 28.2 1.0
O C:HOH473 4.6 45.4 1.0
CA D:CA304 4.7 39.5 1.0
O A:HOH401 4.8 36.4 1.0
NE D:ARG37 4.9 42.5 1.0
CG D:GLU40 4.9 32.1 0.5
O C:HOH547 4.9 32.9 1.0
CB D:GLU40 4.9 29.5 0.6
CZ D:ARG37 5.0 44.6 1.0
CB D:GLU40 5.0 29.5 0.5

Calcium binding site 6 out of 8 in 7ebu

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

b:39.5
occ:1.00
 OE2 C:GLU46 2.5 42.7 1.0
OE2 D:GLU40 2.5 31.9 0.6
O C:HOH434 2.6 29.8 1.0
OE1 A:GLU32 2.6 30.0 1.0
O A:HOH401 2.7 36.4 1.0
O D:HOH527 2.9 35.7 1.0
OE1 D:GLU40 3.4 32.1 0.5
CD C:GLU46 3.4 43.2 1.0
CD D:GLU40 3.5 32.7 0.6
OE1 C:GLU46 3.6 31.3 1.0
CG D:GLU40 3.7 32.9 0.6
CD A:GLU32 3.9 33.4 1.0
CA A:CA305 4.0 62.8 1.0
O C:HOH493 4.0 32.6 1.0
CB D:GLU40 4.2 29.5 0.5
CB D:GLU40 4.3 29.5 0.6
CD D:GLU40 4.3 31.9 0.5
CG D:GLU40 4.3 32.1 0.5
O A:LEU33 4.4 30.6 1.0
O A:HOH485 4.5 29.2 1.0
O C:HOH473 4.5 45.4 1.0
N A:LEU33 4.6 21.0 1.0
OE2 A:GLU32 4.6 29.6 1.0
OE1 D:GLU40 4.6 29.8 0.6
CA D:CA303 4.7 32.8 0.7
O A:HOH422 4.7 34.5 1.0
CG C:GLU46 4.8 36.6 1.0
CB A:GLU32 4.8 25.8 1.0
CG A:GLU32 4.9 29.8 1.0
CA A:GLU32 4.9 24.7 1.0
OE2 D:GLU42 5.0 29.1 1.0

Calcium binding site 7 out of 8 in 7ebu

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

b:28.4
occ:0.74
 O B:HOH438 2.4 34.9 1.0
O D:HOH549 2.5 31.6 1.0
OD2 A:ASP47 2.5 20.0 1.0
O A:HOH519 2.6 39.9 1.0
OD1 D:ASP47 2.6 28.5 1.0
OE2 D:GLU46 2.6 38.7 1.0
OD1 A:ASP47 2.7 28.4 1.0
OE1 D:GLU46 2.9 30.9 1.0
CG A:ASP47 2.9 30.8 1.0
CD D:GLU46 3.1 34.7 1.0
O B:HOH425 3.7 32.4 1.0
CG D:ASP47 3.8 27.1 1.0
CA D:CA306 4.0 27.7 1.0
CA A:CA303 4.1 52.1 1.0
O A:HOH447 4.2 30.4 1.0
O D:HOH500 4.4 25.8 1.0
CB A:ASP47 4.4 21.4 1.0
CA D:ASP47 4.4 27.5 1.0
OD2 D:ASP47 4.5 32.8 1.0
OE1 B:GLU40 4.5 28.6 1.0
CG D:GLU46 4.6 28.8 1.0
CB D:ASP47 4.7 26.1 1.0
CG D:LYS50 4.7 32.2 1.0
N D:ASP47 4.8 25.5 1.0

Calcium binding site 8 out of 8 in 7ebu

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

b:27.7
occ:1.00
 OD2 A:ASP47 2.3 20.0 1.0
OD2 D:ASP47 2.4 32.8 1.0
O B:HOH425 2.5 32.4 1.0
O D:HOH500 2.5 25.8 1.0
O D:HOH505 2.5 31.0 1.0
O D:HOH553 2.6 35.5 1.0
O B:HOH410 2.6 20.6 1.0
OD1 D:ASP47 2.8 28.5 1.0
CG D:ASP47 3.0 27.1 1.0
CG A:ASP47 3.4 30.8 1.0
CB A:ASP47 3.9 21.4 1.0
CA D:CA305 4.0 28.4 0.7
O B:HOH437 4.0 24.7 1.0
O A:HOH542 4.3 21.9 1.0
OE2 B:GLU40 4.3 21.7 1.0
OE1 D:GLU46 4.3 30.9 1.0
O B:HOH438 4.3 34.9 1.0
NH2 B:ARG37 4.4 31.0 1.0
CB D:ASP47 4.5 26.1 1.0
O D:HOH510 4.5 24.3 1.0
OD1 A:ASP47 4.5 28.4 1.0
CD B:GLU40 4.6 31.9 1.0
O A:HOH554 4.9 19.9 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 00:21:28 2024

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