Atomistry » Sodium » PDB 2woi-2x2v » 2woi
Atomistry »
  Sodium »
    PDB 2woi-2x2v »
      2woi »

Sodium in PDB 2woi: Trypanothione Reductase From Trypanosoma Brucei

Enzymatic activity of Trypanothione Reductase From Trypanosoma Brucei

All present enzymatic activity of Trypanothione Reductase From Trypanosoma Brucei:
1.8.1.12;

Protein crystallography data

The structure of Trypanothione Reductase From Trypanosoma Brucei, PDB code: 2woi was solved by M.S.Alphey, A.H.Fairlamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.913 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.800, 63.620, 169.820, 90.00, 97.90, 90.00
R / Rfree (%) 15.95 / 20.82

Other elements in 2woi:

The structure of Trypanothione Reductase From Trypanosoma Brucei also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Trypanothione Reductase From Trypanosoma Brucei (pdb code 2woi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Trypanothione Reductase From Trypanosoma Brucei, PDB code: 2woi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2woi

Go back to Sodium Binding Sites List in 2woi
Sodium binding site 1 out of 5 in the Trypanothione Reductase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trypanothione Reductase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1491

b:31.4
occ:1.00
 O A:CYS469 2.4 24.1 1.0
O A:THR457 2.4 19.2 1.0
O A:HOH2364 2.4 37.0 1.0
O A:TYR455 2.5 22.1 1.0
O A:HOH2368 2.6 37.2 1.0
C A:THR457 3.5 19.9 1.0
C A:TYR455 3.5 22.9 1.0
C A:CYS469 3.5 24.5 1.0
CB A:CYS469 3.8 22.7 1.0
N A:THR457 4.1 21.7 1.0
CA A:TYR455 4.2 21.6 1.0
O A:PHE454 4.2 19.0 1.0
N A:ILE458 4.2 19.3 1.0
C A:ASN456 4.2 22.7 1.0
CA A:CYS469 4.2 23.6 1.0
CA A:ILE458 4.3 19.1 1.0
CA A:THR457 4.4 19.1 1.0
N A:GLY459 4.5 18.1 1.0
N A:ASN456 4.5 22.3 1.0
N A:SER470 4.6 25.1 1.0
CA A:ASN456 4.6 23.4 1.0
CD1 A:TYR455 4.7 29.8 1.0
O B:HOH2203 4.7 35.8 1.0
C A:ILE458 4.7 19.6 1.0
O A:ASN456 4.8 22.7 1.0
CA A:SER470 4.8 27.1 1.0
CG A:TYR455 4.8 26.9 1.0
CE1 A:TYR455 4.9 33.4 1.0

Sodium binding site 2 out of 5 in 2woi

Go back to Sodium Binding Sites List in 2woi
Sodium binding site 2 out of 5 in the Trypanothione Reductase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trypanothione Reductase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1491

b:46.5
occ:1.00
 O B:LEU120 2.3 42.0 1.0
O B:PHE114 2.6 47.2 1.0
O B:THR117 2.6 50.3 1.0
O B:HOH2077 2.8 46.9 1.0
C B:LEU120 3.4 41.8 1.0
C B:PHE114 3.6 47.1 1.0
C B:THR117 3.8 50.7 1.0
N B:LEU120 4.1 44.3 1.0
OD2 B:ASP121 4.2 47.9 1.0
N B:ASP121 4.3 41.9 1.0
CA B:LEU120 4.3 41.8 1.0
CA B:PHE114 4.4 46.4 1.0
CA B:ASP121 4.4 41.5 1.0
N B:THR117 4.5 50.5 1.0
N B:ASN115 4.5 47.8 1.0
CG B:ASP121 4.6 45.2 1.0
CA B:GLU118 4.6 49.8 1.0
CB B:LEU120 4.6 41.7 1.0
N B:GLU118 4.7 50.4 1.0
CA B:ASN115 4.7 49.6 1.0
CA B:THR117 4.7 50.2 1.0
CB B:PHE114 4.8 45.7 1.0
N B:GLY119 4.8 47.5 1.0
C B:ASN115 4.8 50.1 1.0
OD1 B:ASP121 5.0 45.3 1.0

Sodium binding site 3 out of 5 in 2woi

Go back to Sodium Binding Sites List in 2woi
Sodium binding site 3 out of 5 in the Trypanothione Reductase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trypanothione Reductase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1488

b:53.8
occ:1.00
 O C:LEU120 2.4 48.1 1.0
O C:HOH2062 2.4 41.7 1.0
O C:PHE114 2.5 57.3 1.0
O C:THR117 2.6 62.9 1.0
C C:PHE114 3.5 57.2 1.0
C C:LEU120 3.5 48.8 1.0
C C:THR117 3.9 63.1 1.0
OD2 C:ASP121 3.9 52.2 1.0
CG C:ASP121 4.2 49.4 1.0
CA C:PHE114 4.3 55.7 1.0
N C:LEU120 4.3 52.4 1.0
OD1 C:ASP121 4.4 48.5 1.0
N C:ASP121 4.4 47.4 1.0
CA C:ASP121 4.4 47.0 1.0
N C:ASN115 4.4 58.9 1.0
CA C:LEU120 4.4 50.3 1.0
N C:THR117 4.5 63.7 1.0
C C:ASN115 4.6 61.7 1.0
CA C:ASN115 4.7 60.7 1.0
O C:ASN115 4.7 62.7 1.0
CB C:LEU120 4.7 49.5 1.0
CB C:PHE114 4.7 54.5 1.0
CA C:THR117 4.7 63.4 1.0
N C:GLU118 4.8 62.7 1.0
CB C:ASP121 4.9 48.0 1.0
N C:ASP116 4.9 62.2 1.0
CA C:GLU118 5.0 61.8 1.0

Sodium binding site 4 out of 5 in 2woi

Go back to Sodium Binding Sites List in 2woi
Sodium binding site 4 out of 5 in the Trypanothione Reductase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Trypanothione Reductase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1488

b:36.5
occ:1.00
 O D:CYS469 2.3 31.2 1.0
O D:TYR455 2.5 27.6 1.0
O D:THR457 2.5 24.4 1.0
O D:HOH2298 2.8 27.6 1.0
C D:TYR455 3.5 28.1 1.0
C D:CYS469 3.5 30.0 1.0
C D:THR457 3.6 24.5 1.0
CB D:CYS469 4.1 27.3 1.0
N D:THR457 4.1 25.0 1.0
CA D:TYR455 4.1 27.9 1.0
O D:PHE454 4.3 24.6 1.0
CA D:CYS469 4.3 28.5 1.0
C D:ASN456 4.3 27.0 1.0
CA D:ILE458 4.4 26.5 1.0
N D:ILE458 4.4 26.2 1.0
N D:GLY459 4.4 25.7 1.0
N D:ASN456 4.5 27.1 1.0
N D:SER470 4.5 30.6 1.0
CA D:THR457 4.5 24.2 1.0
CA D:ASN456 4.6 27.9 1.0
CA D:SER470 4.7 32.5 1.0
CD2 D:TYR455 4.7 40.3 1.0
O C:HOH2188 4.7 37.4 1.0
CG D:TYR455 4.8 35.2 1.0
C D:ILE458 4.8 26.8 1.0
O D:ASN456 4.9 27.4 1.0
CE2 D:TYR455 4.9 42.5 1.0
CD1 D:TYR455 5.0 39.5 1.0

Sodium binding site 5 out of 5 in 2woi

Go back to Sodium Binding Sites List in 2woi
Sodium binding site 5 out of 5 in the Trypanothione Reductase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Trypanothione Reductase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1489

b:21.7
occ:1.00
 O D:PHE114 2.3 22.4 1.0
O D:LEU120 2.3 16.9 1.0
O D:THR117 2.4 22.6 1.0
O D:HOH2091 2.5 22.1 1.0
O D:HOH2100 2.5 28.0 1.0
O D:HOH2098 2.5 26.1 1.0
C D:THR117 3.4 25.0 1.0
C D:LEU120 3.4 17.4 1.0
C D:PHE114 3.4 22.8 1.0
OD1 D:ASP121 3.9 27.0 1.0
N D:LEU120 3.9 21.0 1.0
N D:THR117 4.0 24.4 1.0
CA D:LEU120 4.1 18.8 1.0
CA D:PHE114 4.2 22.2 1.0
CA D:THR117 4.2 24.2 1.0
O D:ASN115 4.3 26.8 1.0
N D:GLU118 4.4 25.0 1.0
N D:ASP121 4.4 16.1 1.0
C D:ASN115 4.4 25.9 1.0
N D:ASN115 4.4 22.1 1.0
CB D:LEU120 4.5 18.9 1.0
O D:HOH2101 4.5 24.3 1.0
CA D:GLU118 4.5 27.2 1.0
CA D:ASN115 4.6 25.5 1.0
CA D:ASP121 4.6 17.8 1.0
N D:GLY119 4.7 23.8 1.0
CB D:THR117 4.7 23.7 1.0
CB D:PHE114 4.8 20.8 1.0
C D:GLU118 4.8 25.8 1.0
N D:ASP116 4.9 25.5 1.0
CG D:ASP121 4.9 24.9 1.0
C D:ASP116 4.9 26.7 1.0
O D:HOH2095 5.0 26.2 1.0

Reference:

S.Patterson, M.S.Alphey, D.C.Jones, E.J.Shanks, I.P.Street, J.A.Frearson, P.G.Wyatt, I.H.Gilbert, A.H.Fairlamb. Dihydroquinazolines As A Novel Class of Trypanosoma Brucei Trypanothione Reductase Inhibitors: Discovery, Synthesis, and Characterization of Their Binding Mode By Protein Crystallography. J.Med.Chem. V. 54 6514 2011.
ISSN: ISSN 0022-2623
PubMed: 21851087
DOI: 10.1021/JM200312V
Page generated: Mon Oct 7 04:51:36 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