Atomistry » Calcium » PDB 7e4z-7est » 7ebt
Atomistry »
  Calcium »
    PDB 7e4z-7est »
      7ebt »

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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Go back to Calcium Binding Sites List in 7ebt
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy