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Sodium in PDB 2wov: Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.

Enzymatic activity of Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.

All present enzymatic activity of Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.:
1.8.1.12;

Protein crystallography data

The structure of Trypanosoma Brucei Trypanothione Reductase with Bound Nadp., PDB code: 2wov 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) 19.85 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.870, 63.450, 169.350, 90.00, 97.85, 90.00
R / Rfree (%) 17.9 / 25.1

Sodium Binding Sites:

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

Sodium binding site 1 out of 7 in 2wov

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Sodium binding site 1 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1489

b:40.0
occ:1.00
 O A:HOH2110 2.4 19.4 1.0
O A:THR457 2.5 25.4 1.0
O A:TYR455 2.5 29.5 1.0
O A:CYS469 2.6 27.6 1.0
C A:THR457 3.6 25.9 1.0
C A:TYR455 3.6 29.0 1.0
C A:CYS469 3.7 28.3 1.0
CA A:ILE458 4.2 24.0 1.0
CB A:CYS469 4.3 26.4 1.0
O B:HOH2070 4.3 29.0 1.0
CA A:TYR455 4.3 28.6 1.0
N A:ILE458 4.3 24.7 1.0
O A:PHE454 4.4 27.6 1.0
N A:GLY459 4.4 24.4 1.0
C A:ASN456 4.4 28.4 1.0
N A:THR457 4.4 27.3 1.0
CA A:CYS469 4.5 27.3 1.0
N A:ASN456 4.6 29.1 1.0
CA A:THR457 4.6 26.4 1.0
O A:ASN456 4.7 28.6 1.0
N A:SER470 4.7 30.2 1.0
C A:ILE458 4.7 24.4 1.0
CA A:ASN456 4.8 28.8 1.0
CD1 A:TYR455 4.8 31.5 1.0
CA A:SER470 4.9 32.2 1.0
CG A:TYR455 4.9 29.0 1.0

Sodium binding site 2 out of 7 in 2wov

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Sodium binding site 2 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1488

b:32.5
occ:1.00
 O B:CYS469 2.4 27.6 1.0
O B:TYR455 2.4 30.6 1.0
O B:THR457 2.5 25.3 1.0
C B:TYR455 3.6 30.2 1.0
C B:CYS469 3.6 27.4 1.0
C B:THR457 3.7 25.4 1.0
CB B:CYS469 4.1 25.2 1.0
N B:GLY459 4.2 21.2 1.0
CA B:ILE458 4.2 23.1 1.0
CA B:TYR455 4.4 30.4 1.0
CA B:CYS469 4.4 25.8 1.0
N B:ILE458 4.5 24.1 1.0
O B:PHE454 4.5 27.5 1.0
N B:ASN456 4.5 30.1 1.0
N B:THR457 4.6 26.5 1.0
OG B:SER470 4.6 31.9 1.0
C B:ASN456 4.6 28.2 1.0
N B:SER470 4.6 28.8 1.0
C B:ILE458 4.7 22.3 1.0
CA B:ASN456 4.7 29.4 1.0
CA B:THR457 4.8 26.2 1.0
CD2 B:TYR455 4.8 34.7 1.0
CA B:SER470 4.8 30.0 1.0

Sodium binding site 3 out of 7 in 2wov

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Sodium binding site 3 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1489

b:41.4
occ:1.00
 O B:PHE114 2.4 48.6 1.0
O B:LEU120 2.8 41.6 1.0
O B:THR117 2.8 51.6 1.0
C B:PHE114 3.6 48.9 1.0
OD2 B:ASP121 3.7 49.0 1.0
C B:LEU120 3.9 42.5 1.0
C B:THR117 4.0 50.8 1.0
CA B:ASN115 4.3 50.6 1.0
N B:ASN115 4.3 49.5 1.0
C B:ASN115 4.5 51.0 1.0
CG B:ASP121 4.5 45.2 1.0
N B:THR117 4.5 50.2 1.0
CA B:PHE114 4.6 48.3 1.0
N B:LEU120 4.6 44.8 1.0
O B:HOH2023 4.7 36.6 1.0
CA B:LEU120 4.7 43.6 1.0
O B:ASN115 4.8 51.5 1.0
CA B:THR117 4.8 50.4 1.0
N B:ASP121 4.9 42.1 1.0
CA B:ASP121 4.9 42.0 1.0
N B:ASP116 4.9 51.0 1.0
CA B:GLU118 5.0 50.9 1.0
CB B:LEU120 5.0 44.2 1.0
OD1 B:ASP121 5.0 45.9 1.0

Sodium binding site 4 out of 7 in 2wov

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Sodium binding site 4 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1489

b:34.5
occ:1.00
 O C:TYR455 2.4 28.9 1.0
O C:THR457 2.5 25.4 1.0
O C:HOH2112 2.5 20.3 1.0
O C:CYS469 2.6 26.1 1.0
C C:THR457 3.6 25.3 1.0
C C:TYR455 3.6 29.1 1.0
C C:CYS469 3.8 26.6 1.0
CA C:ILE458 4.2 24.5 1.0
CB C:CYS469 4.2 25.2 1.0
C C:ASN456 4.2 28.0 1.0
N C:ILE458 4.3 24.6 1.0
O C:ASN456 4.3 28.1 1.0
CA C:TYR455 4.4 29.4 1.0
N C:GLY459 4.4 23.9 1.0
N C:THR457 4.4 26.5 1.0
O C:PHE454 4.5 25.6 1.0
CA C:CYS469 4.5 25.4 1.0
N C:ASN456 4.5 29.1 1.0
CA C:THR457 4.6 25.8 1.0
CA C:ASN456 4.7 28.5 1.0
CD1 C:TYR455 4.7 36.8 1.0
C C:ILE458 4.8 24.5 1.0
N C:SER470 4.9 27.9 1.0
CE1 C:TYR455 4.9 37.9 1.0
CG C:TYR455 5.0 33.0 1.0

Sodium binding site 5 out of 7 in 2wov

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Sodium binding site 5 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1490

b:23.4
occ:1.00
 O C:PHE114 2.2 28.7 1.0
O C:THR117 2.4 29.7 1.0
O C:HOH2032 2.6 21.6 1.0
O C:LEU120 2.6 23.0 1.0
OD1 C:ASP121 3.3 28.7 1.0
C C:PHE114 3.4 28.1 1.0
C C:THR117 3.4 29.7 1.0
C C:LEU120 3.6 22.5 1.0
N C:THR117 4.2 29.9 1.0
N C:LEU120 4.2 23.3 1.0
CA C:PHE114 4.2 27.4 1.0
CA C:THR117 4.3 29.4 1.0
N C:GLU118 4.3 29.7 1.0
N C:ASN115 4.3 28.9 1.0
O C:ASN115 4.4 29.2 1.0
C C:ASN115 4.4 29.7 1.0
CA C:LEU120 4.4 22.4 1.0
CA C:ASN115 4.5 30.0 1.0
CG C:ASP121 4.6 26.1 1.0
CA C:GLU118 4.6 29.4 1.0
N C:ASP121 4.6 21.8 1.0
CA C:ASP121 4.6 22.0 1.0
CB C:PHE114 4.7 27.4 1.0
N C:GLY119 4.8 26.6 1.0
CB C:THR117 4.8 28.9 1.0
CB C:LEU120 4.8 22.0 1.0
N C:ASP116 4.8 29.8 1.0
C C:GLU118 4.9 28.4 1.0

Sodium binding site 6 out of 7 in 2wov

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Sodium binding site 6 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1489

b:35.6
occ:1.00
 O D:CYS469 2.4 24.9 1.0
O D:TYR455 2.8 22.9 1.0
O D:THR457 2.8 21.3 1.0
C D:CYS469 3.7 25.1 1.0
C D:TYR455 3.9 23.4 1.0
C D:THR457 3.9 21.1 1.0
N D:GLY459 4.2 19.0 1.0
CB D:CYS469 4.2 25.1 1.0
CA D:ILE458 4.3 19.3 1.0
N D:ILE458 4.5 20.6 1.0
CA D:CYS469 4.5 24.5 1.0
N D:SER470 4.6 25.8 1.0
C D:ILE458 4.7 19.0 1.0
C D:ASN456 4.7 21.7 1.0
CA D:SER470 4.7 26.5 1.0
CA D:TYR455 4.7 24.4 1.0
O D:PHE454 4.8 23.7 1.0
N D:THR457 4.8 21.1 1.0
N D:ASN456 4.8 22.8 1.0
OG D:SER470 4.8 28.2 1.0
CA D:ASN456 4.9 22.6 1.0
CD1 D:TYR455 5.0 26.5 1.0
O D:ASN456 5.0 21.4 1.0

Sodium binding site 7 out of 7 in 2wov

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Sodium binding site 7 out of 7 in the Trypanosoma Brucei Trypanothione Reductase with Bound Nadp.


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 with Bound Nadp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1490

b:58.5
occ:1.00
 O D:THR117 2.3 46.5 1.0
O D:LEU120 2.7 34.8 1.0
O D:PHE114 3.0 43.0 1.0
OD2 D:ASP121 3.2 35.5 1.0
C D:THR117 3.5 46.3 1.0
C D:LEU120 3.5 36.0 1.0
N D:LEU120 3.8 38.6 1.0
CG D:ASP121 3.9 37.7 1.0
CA D:GLU118 4.1 45.9 1.0
N D:GLY119 4.1 43.8 1.0
CA D:LEU120 4.1 37.2 1.0
N D:GLU118 4.2 45.8 1.0
C D:PHE114 4.2 42.9 1.0
OD1 D:ASP121 4.3 39.5 1.0
C D:GLU118 4.3 45.0 1.0
N D:ASP121 4.3 35.4 1.0
CA D:ASP121 4.5 36.0 1.0
CA D:THR117 4.6 46.6 1.0
N D:THR117 4.6 47.3 1.0
CB D:LEU120 4.6 36.6 1.0
CB D:ASP121 4.8 36.4 1.0
C D:GLY119 4.9 40.2 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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