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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

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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

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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

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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

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