Atomistry » Sodium » PDB 2woi-2x2v » 2wp5
Atomistry »
  Sodium »
    PDB 2woi-2x2v »
      2wp5 »

Sodium in PDB 2wp5: Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)

Enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)

All present enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414):
1.8.1.12;

Protein crystallography data

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414), PDB code: 2wp5 was solved by M.S.Alphey, S.Patterson, A.H.Fairlamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.711 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.940, 63.300, 169.410, 90.00, 98.09, 90.00
R / Rfree (%) 16.42 / 21.93

Other elements in 2wp5:

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) (pdb code 2wp5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414), PDB code: 2wp5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 1 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1490

b:16.1
occ:1.00
O A:THR457 2.6 10.9 1.0
O A:CYS469 2.7 12.5 1.0
O A:TYR455 3.2 13.8 1.0
C A:THR457 3.7 11.1 1.0
C A:CYS469 3.9 12.7 1.0
CA A:ILE458 3.9 9.8 1.0
N A:GLY459 3.9 10.3 1.0
CB A:CYS469 4.1 11.9 1.0
N A:ILE458 4.3 10.5 1.0
C A:TYR455 4.3 13.1 1.0
C A:ILE458 4.3 10.3 1.0
OG A:SER470 4.6 17.7 1.0
CA A:CYS469 4.7 12.6 1.0
CD1 A:TYR455 4.8 8.7 0.3
N A:SER470 4.9 13.3 1.0
CA A:GLY459 4.9 9.1 1.0
N A:THR457 4.9 12.1 1.0
CA A:THR457 4.9 11.8 1.0
CA A:TYR455 4.9 13.2 0.3
CA A:TYR455 4.9 13.3 0.3
C A:ASN456 5.0 13.0 1.0
CE1 A:TYR455 5.0 6.6 0.3
CA A:SER470 5.0 15.2 1.0
CA A:TYR455 5.0 12.6 0.3

Sodium binding site 2 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 2 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1489

b:11.9
occ:1.00
O B:THR457 2.4 9.4 1.0
O B:TYR455 2.6 12.3 1.0
O B:CYS469 3.1 16.5 1.0
C B:TYR455 3.4 12.0 1.0
C B:THR457 3.5 9.6 1.0
C B:ASN456 4.0 10.8 1.0
C B:CYS469 4.0 16.3 1.0
N B:THR457 4.1 10.6 1.0
CB B:CYS469 4.1 15.2 1.0
CA B:TYR455 4.1 12.6 1.0
N B:ASN456 4.2 11.4 1.0
N B:ILE458 4.3 9.0 1.0
CA B:ILE458 4.3 7.0 1.0
O B:ASN456 4.3 9.7 1.0
CA B:ASN456 4.4 11.0 1.0
CA B:THR457 4.4 9.7 1.0
O B:PHE454 4.5 9.8 1.0
CA B:CYS469 4.6 15.8 1.0
N B:GLY459 4.6 7.3 1.0
NH2 B:ARG472 4.8 33.1 1.0
CB B:TYR455 4.8 13.1 1.0
C B:ILE458 4.9 7.2 1.0

Sodium binding site 3 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 3 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1490

b:21.0
occ:1.00
O B:PHE114 2.5 30.1 1.0
O B:LEU120 2.6 30.0 1.0
O B:THR117 3.0 34.0 1.0
OD1 B:ASP121 3.4 35.7 1.0
C B:PHE114 3.4 30.4 1.0
C B:LEU120 3.6 30.6 1.0
O B:ASN115 4.1 31.8 1.0
C B:THR117 4.2 34.2 1.0
N B:ASN115 4.2 30.4 1.0
CA B:ASN115 4.3 30.9 1.0
C B:ASN115 4.3 31.5 1.0
CA B:PHE114 4.3 30.1 1.0
CA B:ASP121 4.4 31.5 1.0
N B:ASP121 4.4 31.0 1.0
N B:LEU120 4.4 32.2 1.0
CG B:ASP121 4.5 33.1 1.0
CA B:LEU120 4.5 31.1 1.0
N B:THR117 4.7 32.4 1.0
CB B:PHE114 4.7 29.9 1.0
CB B:LEU120 4.8 30.7 1.0
CA B:THR117 4.9 33.2 1.0

Sodium binding site 4 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 4 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1489

b:25.9
occ:1.00
O C:TYR455 2.6 16.4 1.0
O C:THR457 2.8 13.2 1.0
O C:CYS469 2.9 15.7 1.0
C C:THR457 3.7 13.2 1.0
C C:TYR455 3.8 15.7 1.0
CA C:ILE458 4.1 10.2 1.0
C C:CYS469 4.1 15.5 1.0
N C:ILE458 4.3 12.0 1.0
N C:GLY459 4.4 8.8 1.0
CA C:TYR455 4.5 16.1 0.5
CA C:TYR455 4.5 16.1 0.5
C C:ASN456 4.6 15.2 1.0
CB C:CYS469 4.6 15.8 1.0
N C:THR457 4.6 14.3 1.0
C C:ILE458 4.7 9.8 1.0
N C:ASN456 4.8 15.3 1.0
CA C:THR457 4.8 13.7 1.0
O C:ASN456 4.9 15.3 1.0
CA C:CYS469 4.9 15.3 1.0
CA C:ASN456 4.9 15.6 1.0
O C:PHE454 4.9 16.1 1.0

Sodium binding site 5 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 5 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1489

b:30.6
occ:1.00
O D:THR457 2.6 15.2 1.0
O D:TYR455 2.6 15.4 1.0
O D:CYS469 2.7 21.2 1.0
C D:THR457 3.7 14.8 1.0
C D:TYR455 3.8 15.1 1.0
C D:CYS469 3.8 19.9 1.0
CB D:CYS469 3.9 19.1 1.0
CA D:ILE458 4.0 15.0 1.0
N D:GLY459 4.0 14.0 1.0
N D:ILE458 4.3 15.0 1.0
CA D:CYS469 4.5 19.5 1.0
C D:ILE458 4.5 14.5 1.0
CA D:TYR455 4.5 15.4 0.6
CA D:TYR455 4.5 14.8 0.4
N D:THR457 4.6 15.6 1.0
CD1 D:TYR455 4.6 12.3 0.4
C D:ASN456 4.6 15.4 1.0
CA D:THR457 4.8 15.3 1.0
N D:ASN456 4.8 15.2 1.0
O D:PHE454 4.8 15.2 1.0
N D:SER470 4.8 19.8 1.0
CE1 D:TYR455 4.8 11.0 0.4
O D:ASN456 4.9 15.4 1.0
CA D:ASN456 5.0 15.6 1.0
CG D:TYR455 5.0 12.7 0.4
CG1 D:ILE458 5.0 15.2 1.0

Sodium binding site 6 out of 6 in 2wp5

Go back to Sodium Binding Sites List in 2wp5
Sodium binding site 6 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1490

b:46.4
occ:1.00
O D:LEU120 2.4 15.3 1.0
O D:THR117 2.5 16.4 1.0
O D:PHE114 2.8 12.0 1.0
OD1 D:ASP121 3.0 16.8 1.0
C D:LEU120 3.4 14.9 1.0
C D:THR117 3.6 15.9 1.0
N D:LEU120 3.9 16.7 1.0
C D:PHE114 4.0 11.8 1.0
O D:ASN115 4.2 13.3 1.0
CG D:ASP121 4.2 14.6 1.0
CA D:LEU120 4.2 15.2 1.0
CA D:GLU118 4.3 17.0 1.0
N D:ASP121 4.3 13.8 1.0
N D:GLU118 4.3 16.1 1.0
N D:THR117 4.4 14.5 1.0
N D:GLY119 4.4 16.8 1.0
CA D:ASP121 4.5 12.4 1.0
CA D:THR117 4.5 15.1 1.0
C D:ASN115 4.5 13.3 1.0
C D:GLU118 4.6 16.7 1.0
CA D:ASN115 4.7 13.1 1.0
CB D:LEU120 4.7 15.0 1.0
N D:ASN115 4.8 12.4 1.0
CB D:ASP121 4.8 12.8 1.0
CA D:PHE114 4.9 11.0 1.0
C D:GLY119 5.0 17.5 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: Tue Dec 15 05:58:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy