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Sodium in PDB 2wpe: Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)

Enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)

All present enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359):
1.8.1.12;

Protein crystallography data

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359), PDB code: 2wpe 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) 45.979 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.640, 63.290, 169.160, 90.00, 98.20, 90.00
R / Rfree (%) 16.8 / 23

Other elements in 2wpe:

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359) also contains other interesting chemical elements:

Chlorine (Cl) 22 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359) (pdb code 2wpe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359), PDB code: 2wpe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2wpe

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Sodium binding site 1 out of 4 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)


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 (DDD00073359) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1489

b:26.3
occ:1.00
 O A:THR457 2.2 23.6 1.0
O A:TYR455 2.4 25.3 1.0
O A:CYS469 2.4 23.9 1.0
O A:HOH2338 2.7 26.5 1.0
C A:THR457 3.3 23.1 1.0
C A:TYR455 3.5 26.5 1.0
C A:CYS469 3.5 25.2 1.0
CB A:CYS469 3.9 22.6 1.0
N A:THR457 4.0 24.8 1.0
C A:ASN456 4.0 27.4 1.0
CA A:ILE458 4.1 23.2 1.0
N A:ILE458 4.1 22.4 1.0
O A:PHE454 4.1 21.8 1.0
CA A:CYS469 4.2 24.2 1.0
CA A:TYR455 4.3 25.9 1.0
N A:GLY459 4.3 24.8 1.0
CA A:THR457 4.3 22.8 1.0
N A:ASN456 4.4 25.8 1.0
O A:ASN456 4.4 29.0 1.0
CA A:ASN456 4.5 26.9 1.0
C A:ILE458 4.6 24.3 1.0
N A:SER470 4.6 25.9 1.0
CD1 A:TYR455 4.8 30.5 1.0
CG A:TYR455 4.9 27.2 1.0
CA A:SER470 4.9 28.6 1.0
O B:HOH2188 5.0 31.5 1.0

Sodium binding site 2 out of 4 in 2wpe

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Sodium binding site 2 out of 4 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)


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 (DDD00073359) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1489

b:37.2
occ:1.00
 O A:HOH2271 2.4 48.4 1.0
O B:THR457 2.4 19.1 1.0
O B:CYS469 2.5 24.9 1.0
O B:TYR455 2.6 22.8 1.0
O B:HOH2245 2.6 28.5 1.0
C B:TYR455 3.5 23.3 1.0
C B:THR457 3.6 18.8 1.0
C B:CYS469 3.6 24.2 1.0
CB B:CYS469 3.8 21.5 1.0
N B:THR457 4.1 19.6 1.0
CA B:TYR455 4.2 22.3 1.0
CA B:CYS469 4.2 22.4 1.0
O B:PHE454 4.3 22.2 1.0
C B:ASN456 4.4 21.1 1.0
O A:HOH2269 4.4 36.9 1.0
N B:ILE458 4.4 19.3 1.0
CA B:ILE458 4.4 19.4 1.0
N B:GLY459 4.5 18.7 1.0
N B:ASN456 4.5 23.0 1.0
O A:HOH2013 4.5 44.3 1.0
CA B:THR457 4.5 18.0 1.0
O A:HOH2272 4.5 51.1 1.0
CA B:ASN456 4.6 22.7 1.0
N B:SER470 4.7 24.8 1.0
CD2 B:TYR455 4.8 33.5 1.0
C B:ILE458 4.8 19.3 1.0
CG B:TYR455 4.9 29.1 1.0
O B:ASN456 5.0 22.6 1.0
CA B:SER470 5.0 26.7 1.0

Sodium binding site 3 out of 4 in 2wpe

Go back to Sodium Binding Sites List in 2wpe
Sodium binding site 3 out of 4 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)


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 (DDD00073359) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1487

b:26.9
occ:1.00
 O C:HOH2240 2.2 29.0 1.0
O C:CYS469 2.4 23.9 1.0
O C:THR457 2.4 19.1 1.0
O C:TYR455 2.6 20.7 1.0
C C:CYS469 3.5 23.7 1.0
C C:THR457 3.5 19.2 1.0
C C:TYR455 3.5 21.7 1.0
CB C:CYS469 3.7 21.9 1.0
O C:HOH2247 4.1 45.0 1.0
CA C:CYS469 4.2 22.3 1.0
CA C:ILE458 4.2 19.2 1.0
N C:THR457 4.2 20.7 1.0
N C:GLY459 4.3 20.9 1.0
O C:PHE454 4.3 21.2 1.0
N C:ILE458 4.3 19.3 1.0
CA C:TYR455 4.3 21.4 1.0
C C:ASN456 4.3 22.8 1.0
O D:HOH2097 4.4 32.1 1.0
N C:ASN456 4.4 22.3 1.0
CA C:THR457 4.6 18.8 1.0
CA C:ASN456 4.6 24.4 1.0
N C:SER470 4.6 23.4 1.0
C C:ILE458 4.6 19.4 1.0
O D:HOH2240 4.6 30.8 1.0
CD2 C:TYR455 4.7 29.3 1.0
O C:ASN456 4.7 23.1 1.0
CA C:SER470 4.8 25.1 1.0
O C:HOH2238 4.9 38.8 1.0
CE2 C:TYR455 4.9 27.5 1.0

Sodium binding site 4 out of 4 in 2wpe

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Sodium binding site 4 out of 4 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073359)


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 (DDD00073359) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1487

b:33.5
occ:1.00
 O D:THR457 2.3 26.1 1.0
O D:CYS469 2.3 30.9 1.0
O D:HOH2299 2.4 48.1 1.0
O D:TYR455 2.4 30.5 1.0
O D:HOH2305 2.6 28.1 1.0
C D:THR457 3.5 27.1 1.0
C D:TYR455 3.5 30.4 1.0
C D:CYS469 3.5 29.9 1.0
CB D:CYS469 3.9 27.1 1.0
N D:THR457 4.1 28.2 1.0
O D:PHE454 4.2 27.2 1.0
CA D:TYR455 4.2 31.1 1.0
CA D:CYS469 4.2 27.9 1.0
C D:ASN456 4.2 29.4 1.0
CA D:ILE458 4.2 25.6 1.0
N D:ILE458 4.3 26.8 1.0
N D:GLY459 4.3 24.4 1.0
N D:ASN456 4.4 29.9 1.0
CA D:THR457 4.4 27.6 1.0
O D:ASN456 4.5 29.5 1.0
N D:SER470 4.6 30.2 1.0
CA D:ASN456 4.6 31.0 1.0
C D:ILE458 4.7 26.2 1.0
CA D:SER470 4.8 32.5 1.0
CD2 D:TYR455 4.9 40.4 1.0
O C:HOH2193 4.9 34.2 1.0
CG D:TYR455 4.9 36.7 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 04:51:37 2024

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