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Magnesium in PDB 3epw: Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol

Enzymatic activity of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol

All present enzymatic activity of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol, PDB code: 3epw was solved by W.Versees, A.Goeminne, M.Berg, A.Vandemeulebroucke, A.Haemers, K.Augustyns, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.86 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.449, 73.728, 81.147, 90.00, 75.18, 90.00
R / Rfree (%) 16.5 / 18.3

Other elements in 3epw:

The structure of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol (pdb code 3epw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol, PDB code: 3epw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3epw

Go back to Magnesium Binding Sites List in 3epw
Magnesium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:11.1
occ:1.00
 OD2 A:ASP180 2.0 11.5 1.0
O A:HOH1019 2.0 12.6 1.0
O A:HOH1004 2.1 12.0 1.0
O A:HOH1014 2.1 12.1 1.0
CG A:ASP180 3.1 11.3 1.0
CB A:ASP180 3.6 11.9 1.0
O A:HOH1100 4.2 14.8 1.0
OD1 A:ASP180 4.2 11.1 1.0
O A:HOH1047 4.2 12.8 1.0
O A:HOH1129 4.3 21.1 1.0
O A:HOH1039 4.4 14.3 1.0
O A:HOH1037 4.5 14.9 1.0
CB A:ASN290 4.6 11.6 1.0
CG2 A:THR182 4.7 12.8 1.0
OG1 A:THR182 5.0 11.9 1.0
CG A:ASN290 5.0 11.2 1.0

Magnesium binding site 2 out of 2 in 3epw

Go back to Magnesium Binding Sites List in 3epw
Magnesium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-1-[(4-Hydroxy-5H-Pyrrolo[3,2- D]Pyrimidin-7-Yl)Methyl]-2-(Hydroxymethyl)Pyrrolidin-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:17.8
occ:1.00
 O B:HOH1458 1.9 19.6 1.0
O B:HOH1437 1.9 19.8 1.0
O B:ASN59 2.0 12.8 1.0
O B:HOH1446 2.1 20.2 1.0
C B:ASN59 3.2 12.6 1.0
CA B:ASN59 3.9 12.2 1.0
CB B:ASN59 4.1 12.6 1.0
OD1 B:ASN60 4.2 15.2 1.0
N B:ASN60 4.2 13.1 1.0
OE1 B:GLU100 4.2 18.3 1.0
OE2 B:GLU100 4.3 19.3 1.0
O B:HOH1635 4.4 28.3 1.0
CA B:ASN60 4.4 13.7 1.0
CG B:ASN60 4.6 14.7 1.0
CD B:GLU100 4.6 15.6 1.0
O B:HOH1731 4.8 36.7 1.0
CG B:ASN59 4.9 12.7 1.0

Reference:

W.Versees, A.Goeminne, M.Berg, A.Vandemeulebroucke, A.Haemers, K.Augustyns, J.Steyaert. Crystal Structures of T. Vivax Nucleoside Hydrolase in Complex with New Potent and Specific Inhibitors. Biochim.Biophys.Acta V.1794 953 2009.
ISSN: ISSN 0006-3002
PubMed: 19281874
DOI: 10.1016/J.BBAPAP.2009.02.011
Page generated: Sun Aug 10 20:39:30 2025

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