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Sodium in PDB 2wpc: Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)

Enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)

All present enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357):
1.8.1.12;

Protein crystallography data

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357), PDB code: 2wpc 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) 46.881 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.250, 63.430, 169.370, 90.00, 98.58, 90.00
R / Rfree (%) 16.52 / 23.2

Other elements in 2wpc:

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357) also contains other interesting chemical elements:

Chlorine (Cl) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357) (pdb code 2wpc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357), PDB code: 2wpc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2wpc

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Sodium binding site 1 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1491

b:19.5
occ:1.00
 O A:THR457 2.2 15.2 1.0
O A:HOH3334 2.3 29.7 1.0
O A:CYS469 2.4 18.8 1.0
O A:TYR455 2.4 20.5 1.0
O A:HOH3339 2.5 28.6 1.0
O B:HOH3243 2.6 30.2 1.0
C A:THR457 3.3 15.3 1.0
C A:CYS469 3.5 19.1 1.0
C A:TYR455 3.6 20.8 1.0
CB A:CYS469 3.9 18.2 1.0
CA A:ILE458 4.0 13.7 1.0
N A:ILE458 4.1 13.3 1.0
O A:HOH3335 4.2 35.0 1.0
N A:GLY459 4.2 13.4 1.0
N A:THR457 4.2 18.2 1.0
CA A:CYS469 4.2 19.2 1.0
C A:ASN456 4.2 20.6 1.0
O A:PHE454 4.3 17.6 1.0
CA A:THR457 4.4 15.8 1.0
CA A:TYR455 4.4 20.5 1.0
C A:ILE458 4.4 13.6 1.0
O B:HOH3244 4.5 32.1 1.0
N A:ASN456 4.5 20.5 1.0
O A:ASN456 4.5 21.0 1.0
O B:HOH3242 4.6 27.3 1.0
N A:SER470 4.6 20.3 1.0
CA A:ASN456 4.7 20.8 1.0
CA A:SER470 4.9 22.3 1.0

Sodium binding site 2 out of 8 in 2wpc

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Sodium binding site 2 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1492

b:28.0
occ:1.00
 OD1 A:ASP121 2.6 12.2 1.0
O A:THR117 2.7 17.0 1.0
O A:LEU120 2.8 12.7 1.0
O A:PHE114 3.0 27.3 1.0
C A:LEU120 3.4 13.9 1.0
CG A:ASP121 3.8 16.3 1.0
C A:THR117 3.8 20.1 1.0
N A:LEU120 3.9 14.7 1.0
CA A:ASP121 4.1 13.8 1.0
N A:ASP121 4.1 13.2 1.0
C A:PHE114 4.1 26.2 1.0
CA A:LEU120 4.2 13.7 1.0
O A:ASN115 4.3 28.6 1.0
N A:THR117 4.4 22.7 1.0
O A:HOH3098 4.5 13.4 1.0
O A:HOH3097 4.5 23.4 1.0
CB A:ASP121 4.5 14.2 1.0
CA A:THR117 4.6 20.2 1.0
OD2 A:ASP121 4.6 16.0 1.0
N A:GLY119 4.7 16.9 1.0
N A:GLU118 4.7 20.1 1.0
C A:ASN115 4.7 27.8 1.0
CA A:GLU118 4.7 21.1 1.0
C A:GLU118 4.9 18.8 1.0
O A:HOH3093 4.9 39.5 1.0
C A:GLY119 4.9 14.8 1.0
CA A:PHE114 5.0 24.1 1.0

Sodium binding site 3 out of 8 in 2wpc

Go back to Sodium Binding Sites List in 2wpc
Sodium binding site 3 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2004

b:31.0
occ:1.00
 O B:PHE114 2.3 26.0 1.0
O B:HOH3083 2.3 42.2 1.0
O B:HOH3093 2.3 29.5 1.0
O B:HOH3092 2.5 23.3 1.0
O B:THR117 2.6 29.7 1.0
O B:LEU120 2.6 25.3 1.0
C B:PHE114 3.5 27.1 1.0
C B:THR117 3.6 29.4 1.0
C B:LEU120 3.6 26.4 1.0
N B:THR117 3.9 29.4 1.0
O B:ASN115 4.1 29.8 1.0
N B:LEU120 4.2 26.8 1.0
CA B:THR117 4.2 29.2 1.0
C B:ASN115 4.2 29.4 1.0
CA B:LEU120 4.3 26.0 1.0
N B:ASN115 4.4 26.9 1.0
CA B:PHE114 4.4 26.4 1.0
CB B:LEU120 4.5 26.8 1.0
CA B:ASN115 4.5 29.0 1.0
OD1 B:ASP121 4.5 31.0 1.0
N B:GLU118 4.6 29.4 1.0
O B:HOH3095 4.6 30.3 1.0
N B:ASP121 4.6 26.3 1.0
CB B:THR117 4.7 28.5 1.0
O B:HOH3084 4.7 34.0 1.0
CG B:ASP121 4.7 31.1 1.0
N B:ASP116 4.7 29.8 1.0
O B:HOH3090 4.8 27.2 1.0
CA B:ASP121 4.8 26.9 1.0
CA B:GLU118 4.9 30.3 1.0
OD2 B:ASP121 4.9 37.8 1.0
C B:ASP116 4.9 30.2 1.0

Sodium binding site 4 out of 8 in 2wpc

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Sodium binding site 4 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2005

b:32.6
occ:1.00
 O B:THR457 2.4 13.4 1.0
O B:CYS469 2.4 18.7 1.0
O B:HOH3316 2.5 25.3 1.0
O B:TYR455 2.6 17.4 1.0
O A:HOH3274 3.5 38.7 1.0
C B:THR457 3.6 13.6 1.0
C B:CYS469 3.6 18.1 1.0
C B:TYR455 3.6 17.6 1.0
O B:HOH3325 3.7 41.3 1.0
CB B:CYS469 3.9 17.2 1.0
O B:HOH3308 4.1 36.4 1.0
N B:THR457 4.2 14.1 1.0
CA B:CYS469 4.3 18.2 1.0
O B:PHE454 4.3 14.6 1.0
O A:HOH3273 4.3 15.6 1.0
CA B:TYR455 4.3 16.5 1.0
CA B:ILE458 4.4 13.9 1.0
N B:ILE458 4.4 14.1 1.0
C B:ASN456 4.4 16.1 1.0
N B:GLY459 4.4 14.5 1.0
N B:ASN456 4.5 17.1 1.0
CA B:THR457 4.5 12.3 1.0
N B:SER470 4.7 18.9 1.0
CA B:ASN456 4.7 16.9 1.0
C B:ILE458 4.8 13.9 1.0
O B:HOH3310 4.8 33.3 1.0
O B:ASN456 4.9 16.2 1.0
CA B:SER470 4.9 19.5 1.0
CD2 B:TYR455 5.0 21.8 1.0

Sodium binding site 5 out of 8 in 2wpc

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Sodium binding site 5 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1492

b:44.5
occ:1.00
 O C:THR117 2.2 39.2 1.0
O C:LEU120 2.4 34.5 1.0
O C:HOH3090 2.5 29.8 1.0
O C:PHE114 2.6 37.0 1.0
OD2 C:ASP121 3.1 39.3 1.0
C C:LEU120 3.4 34.9 1.0
C C:THR117 3.5 39.6 1.0
N C:LEU120 3.8 37.0 1.0
C C:PHE114 3.8 36.9 1.0
CA C:LEU120 4.1 35.6 1.0
CG C:ASP121 4.2 35.5 1.0
N C:THR117 4.3 39.5 1.0
CA C:THR117 4.3 39.4 1.0
N C:GLY119 4.3 38.7 1.0
CB C:LEU120 4.4 35.0 1.0
N C:ASP121 4.4 34.1 1.0
O C:ASN115 4.4 38.8 1.0
N C:GLU118 4.4 38.8 1.0
CA C:GLU118 4.6 39.4 1.0
CA C:ASP121 4.6 33.0 1.0
C C:GLU118 4.6 38.9 1.0
C C:ASN115 4.6 38.6 1.0
CA C:PHE114 4.7 36.2 1.0
CA C:ASN115 4.8 37.7 1.0
N C:ASN115 4.8 37.5 1.0
O C:HOH3095 4.8 25.7 1.0
CB C:THR117 4.8 39.2 1.0
C C:GLY119 4.9 37.7 1.0

Sodium binding site 6 out of 8 in 2wpc

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Sodium binding site 6 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


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 (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1493

b:19.7
occ:1.00
 O C:HOH3314 2.1 38.5 1.0
O C:HOH3318 2.2 21.6 1.0
O C:THR457 2.3 14.3 1.0
O C:CYS469 2.4 17.6 1.0
O C:TYR455 2.5 14.4 1.0
O D:HOH3271 2.6 34.9 1.0
C C:THR457 3.5 12.9 1.0
C C:TYR455 3.5 14.2 1.0
C C:CYS469 3.6 17.6 1.0
O C:HOH3113 4.0 39.7 1.0
CB C:CYS469 4.0 15.8 1.0
N C:THR457 4.1 12.3 1.0
O C:HOH3327 4.2 28.3 1.0
O C:PHE454 4.2 13.5 1.0
O C:HOH3313 4.2 33.9 1.0
CA C:TYR455 4.3 14.8 1.0
N C:ILE458 4.3 12.2 1.0
CA C:ILE458 4.3 11.1 1.0
C C:ASN456 4.3 13.3 1.0
CA C:CYS469 4.3 15.6 1.0
N C:GLY459 4.4 12.5 1.0
CA C:THR457 4.4 12.8 1.0
N C:ASN456 4.4 14.0 1.0
CA C:ASN456 4.6 14.3 1.0
O D:HOH3270 4.6 22.2 1.0
N C:SER470 4.7 18.0 1.0
C C:ILE458 4.7 11.7 1.0
CD2 C:TYR455 4.7 26.0 1.0
O C:ASN456 4.7 12.6 1.0
CA C:SER470 4.9 19.5 1.0
CE2 C:TYR455 4.9 29.3 1.0
CG C:TYR455 4.9 22.0 1.0

Sodium binding site 7 out of 8 in 2wpc

Go back to Sodium Binding Sites List in 2wpc
Sodium binding site 7 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1492

b:29.5
occ:1.00
 O D:THR457 2.2 15.2 1.0
O D:TYR455 2.3 19.0 1.0
O D:CYS469 2.5 21.0 1.0
O D:HOH3347 2.7 21.2 1.0
C D:THR457 3.3 16.8 1.0
C D:TYR455 3.4 19.7 1.0
C D:CYS469 3.6 21.0 1.0
CB D:CYS469 3.7 18.9 1.0
N D:THR457 3.9 18.4 1.0
O D:PHE454 4.0 17.2 1.0
CA D:ILE458 4.0 16.2 1.0
N D:ILE458 4.1 16.5 1.0
O D:HOH3353 4.1 34.2 1.0
CA D:TYR455 4.1 19.7 1.0
C D:ASN456 4.1 19.8 1.0
CA D:CYS469 4.2 19.3 1.0
CA D:THR457 4.2 16.8 1.0
N D:GLY459 4.3 16.0 1.0
N D:ASN456 4.4 19.4 1.0
C D:ILE458 4.5 16.1 1.0
CA D:ASN456 4.5 20.5 1.0
O D:ASN456 4.5 20.9 1.0
N D:SER470 4.7 22.6 1.0
O C:HOH3252 4.7 37.6 1.0
C D:PHE454 5.0 18.1 1.0

Sodium binding site 8 out of 8 in 2wpc

Go back to Sodium Binding Sites List in 2wpc
Sodium binding site 8 out of 8 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00073357) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1493

b:19.2
occ:1.00
 O D:THR117 2.3 13.9 1.0
O D:HOH3107 2.4 17.3 1.0
O D:LEU120 2.4 16.4 1.0
O D:PHE114 2.4 17.2 1.0
O D:HOH3108 2.6 21.8 1.0
O D:HOH3094 2.7 20.8 1.0
C D:THR117 3.4 17.0 1.0
C D:LEU120 3.4 16.1 1.0
C D:PHE114 3.6 17.2 1.0
OD1 D:ASP121 3.8 16.7 1.0
N D:LEU120 3.9 16.4 1.0
N D:THR117 4.0 17.4 1.0
CA D:LEU120 4.1 15.5 1.0
CA D:THR117 4.2 16.2 1.0
O D:ASN115 4.3 20.7 1.0
N D:GLU118 4.3 16.9 1.0
CB D:LEU120 4.3 14.6 1.0
CA D:PHE114 4.4 15.9 1.0
CA D:GLU118 4.4 17.3 0.3
C D:ASN115 4.4 19.5 1.0
N D:ASP121 4.4 15.4 1.0
O D:HOH3102 4.4 36.0 1.0
CA D:GLU118 4.5 18.8 0.7
N D:ASN115 4.5 17.9 1.0
CA D:ASN115 4.5 18.5 1.0
N D:GLY119 4.6 18.8 1.0
CB D:THR117 4.6 16.0 1.0
CA D:ASP121 4.6 14.4 1.0
C D:GLU118 4.7 18.7 1.0
O D:HOH3109 4.7 24.4 1.0
OE2 D:GLU118 4.8 2.5 0.3
CG D:ASP121 4.9 17.8 1.0
N D:ASP116 4.9 19.4 1.0
CB D:PHE114 4.9 15.5 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: Mon Oct 7 04:51:37 2024

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