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Calcium 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:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3epw

Go back to Calcium Binding Sites List in 3epw
Calcium 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 Calcium with other atoms in the Ca 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:Ca1001

b:9.9
occ:1.00
 O A:THR137 2.3 10.2 1.0
O2' A:JMQ1002 2.4 9.6 1.0
OD1 A:ASP10 2.4 10.9 1.0
OD2 A:ASP261 2.4 10.4 1.0
OD2 A:ASP15 2.4 10.4 1.0
O3' A:JMQ1002 2.5 9.9 1.0
O A:HOH1017 2.5 10.4 1.0
OD1 A:ASP15 2.6 9.4 1.0
CG A:ASP15 2.8 9.9 1.0
CG A:ASP261 3.4 10.8 1.0
C A:THR137 3.4 10.7 1.0
C2' A:JMQ1002 3.4 9.9 1.0
C3' A:JMQ1002 3.5 11.1 1.0
CG A:ASP10 3.5 10.2 1.0
OD1 A:ASP261 3.7 10.7 1.0
OD2 A:ASP10 4.0 10.2 1.0
OD1 A:ASP14 4.1 11.8 1.0
N A:GLY138 4.1 11.2 1.0
CA A:GLY138 4.2 11.3 1.0
CB A:ASP15 4.3 10.3 1.0
CB A:THR137 4.3 11.9 1.0
N4' A:JMQ1002 4.3 11.0 1.0
C4' A:JMQ1002 4.3 10.3 1.0
C1' A:JMQ1002 4.4 11.7 1.0
ND2 A:ASN186 4.4 11.1 1.0
CA A:THR137 4.4 11.6 1.0
OG1 A:THR137 4.4 12.9 1.0
OD1 A:ASN186 4.5 11.0 1.0
N A:ASP10 4.5 10.3 1.0
CB A:ASN12 4.7 11.6 1.0
CB A:ASP10 4.7 11.1 1.0
CB A:ASP261 4.7 10.3 1.0
N A:ASP15 4.8 10.1 1.0
CG A:ASP14 4.8 10.8 1.0
OD2 A:ASP14 4.8 11.0 1.0
CA A:ASP15 4.9 10.3 1.0
CG A:ASN186 4.9 10.6 1.0
N A:ASN12 4.9 10.3 1.0
CA A:ASP10 4.9 10.7 1.0
C A:ASP10 5.0 10.8 1.0

Calcium binding site 2 out of 2 in 3epw

Go back to Calcium Binding Sites List in 3epw
Calcium 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 Calcium with other atoms in the Ca 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:Ca1002

b:9.5
occ:1.00
 O B:THR137 2.3 9.8 1.0
O2' B:JMQ1003 2.4 9.4 1.0
OD1 B:ASP10 2.4 10.1 1.0
OD2 B:ASP261 2.4 10.3 1.0
OD2 B:ASP15 2.4 9.9 1.0
O3' B:JMQ1003 2.5 10.2 1.0
OD1 B:ASP15 2.5 9.4 1.0
O B:HOH1320 2.5 10.1 1.0
CG B:ASP15 2.8 10.0 1.0
CG B:ASP261 3.4 10.5 1.0
C B:THR137 3.4 10.1 1.0
C2' B:JMQ1003 3.4 9.9 1.0
C3' B:JMQ1003 3.5 10.5 1.0
CG B:ASP10 3.5 9.9 1.0
OD1 B:ASP261 3.7 11.0 1.0
OD2 B:ASP10 4.0 10.2 1.0
N B:GLY138 4.1 11.0 1.0
CA B:GLY138 4.2 10.9 1.0
OD1 B:ASP14 4.2 11.3 1.0
CB B:ASP15 4.3 9.9 1.0
CB B:THR137 4.3 11.3 1.0
N4' B:JMQ1003 4.3 11.4 1.0
C4' B:JMQ1003 4.4 10.7 1.0
C1' B:JMQ1003 4.4 11.3 1.0
OG1 B:THR137 4.4 11.6 1.0
CA B:THR137 4.4 10.7 1.0
ND2 B:ASN186 4.5 10.4 1.0
OD1 B:ASN186 4.5 11.3 1.0
N B:ASP10 4.5 9.2 1.0
CB B:ASN12 4.7 10.1 1.0
CB B:ASP261 4.7 9.8 1.0
CB B:ASP10 4.7 10.1 1.0
N B:ASP15 4.8 9.7 1.0
OD2 B:ASP14 4.9 11.2 1.0
CA B:ASP15 4.9 10.0 1.0
CG B:ASP14 4.9 11.0 1.0
N B:ASN12 4.9 9.9 1.0
CG B:ASN186 4.9 10.9 1.0
CA B:ASP10 4.9 9.5 1.0
C B:ASP10 4.9 10.0 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: Tue Jul 8 11:58:20 2025

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