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Calcium in PDB 3epx: Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol

Enzymatic activity of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol

All present enzymatic activity of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)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)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol, PDB code: 3epx 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) 23.33 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.422, 74.198, 73.553, 90.00, 98.36, 90.00
R / Rfree (%) 16 / 21

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)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol (pdb code 3epx). 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)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol, PDB code: 3epx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3epx

Go back to Calcium Binding Sites List in 3epx
Calcium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)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)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:13.9
occ:1.00
 O A:THR137 2.3 15.0 1.0
OD1 A:ASP10 2.4 13.8 1.0
O2' A:IMQ1002 2.4 15.4 1.0
OD2 A:ASP261 2.4 15.5 1.0
O3' A:IMQ1002 2.5 13.3 1.0
OD1 A:ASP15 2.5 11.4 1.0
OD2 A:ASP15 2.5 13.1 1.0
O A:HOH1027 2.6 15.9 1.0
CG A:ASP15 2.8 13.5 1.0
C A:THR137 3.4 14.7 1.0
CG A:ASP261 3.4 16.0 1.0
C2' A:IMQ1002 3.5 16.8 1.0
CG A:ASP10 3.5 14.6 1.0
C3' A:IMQ1002 3.5 17.8 1.0
OD1 A:ASP261 3.7 15.0 1.0
OD2 A:ASP10 4.0 15.9 1.0
N A:GLY138 4.2 14.3 1.0
OD1 A:ASP14 4.2 20.7 1.0
CA A:GLY138 4.2 14.7 1.0
CB A:ASP15 4.3 13.2 1.0
CB A:THR137 4.4 14.9 1.0
C4' A:IMQ1002 4.4 17.6 1.0
ND2 A:ASN186 4.4 13.2 1.0
CA A:THR137 4.5 14.6 1.0
N4' A:IMQ1002 4.5 19.8 1.0
C1' A:IMQ1002 4.5 18.7 1.0
OD1 A:ASN186 4.5 14.8 1.0
N A:ASP10 4.5 14.7 1.0
OG1 A:THR137 4.5 16.1 1.0
CB A:ASP10 4.8 14.8 1.0
CB A:ASP261 4.8 14.4 1.0
CB A:ASN12 4.8 14.5 1.0
N A:ASP15 4.9 14.4 1.0
CA A:ASP15 4.9 13.7 1.0
CG A:ASN186 4.9 14.3 1.0
CG A:ASP14 4.9 17.5 1.0
OD2 A:ASP14 5.0 17.8 1.0
CA A:ASP10 5.0 14.6 1.0
N A:ASN12 5.0 14.6 1.0

Calcium binding site 2 out of 2 in 3epx

Go back to Calcium Binding Sites List in 3epx
Calcium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase in Complex with the Inhibitor (2R,3R,4S)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)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)-2-(Hydroxymethyl)-1-(Quinolin-8- Ylmethyl)Pyrrolidin-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:15.5
occ:1.00
 OD1 B:ASP10 2.3 16.6 1.0
O B:THR137 2.4 16.4 1.0
O B:HOH1214 2.4 17.7 1.0
O2' B:IMQ1003 2.5 19.4 1.0
OD2 B:ASP261 2.5 16.3 1.0
OD2 B:ASP15 2.5 15.2 1.0
OD1 B:ASP15 2.6 14.7 1.0
O3' B:IMQ1003 2.6 17.7 1.0
CG B:ASP15 2.9 14.9 1.0
CG B:ASP10 3.5 16.1 1.0
CG B:ASP261 3.5 17.7 1.0
C B:THR137 3.5 16.9 1.0
C2' B:IMQ1003 3.5 19.2 1.0
C3' B:IMQ1003 3.6 18.0 1.0
OD1 B:ASP261 3.8 15.6 1.0
OD2 B:ASP10 3.9 17.1 1.0
N B:GLY138 4.2 17.5 1.0
OD1 B:ASP14 4.2 25.5 1.0
CA B:GLY138 4.2 17.3 1.0
CB B:ASP15 4.3 14.8 1.0
CB B:THR137 4.4 16.9 1.0
C4' B:IMQ1003 4.4 18.9 1.0
ND2 B:ASN186 4.5 18.2 1.0
OG1 B:THR137 4.5 17.6 1.0
CA B:THR137 4.5 17.1 1.0
OD1 B:ASN186 4.5 18.5 1.0
N4' B:IMQ1003 4.5 20.3 1.0
C1' B:IMQ1003 4.5 20.6 1.0
N B:ASP10 4.6 16.4 1.0
CB B:ASN12 4.7 15.9 1.0
CB B:ASP10 4.8 16.5 1.0
CB B:ASP261 4.8 16.2 1.0
N B:ASP15 4.9 15.2 1.0
OD2 B:ASP14 4.9 24.1 1.0
CA B:ASP15 4.9 15.2 1.0
CG B:ASP14 4.9 20.8 1.0
CG B:ASN186 4.9 18.5 1.0
CA B:ASP10 5.0 15.8 1.0
N B:ASN12 5.0 16.2 1.0
C B:ASP10 5.0 16.1 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 11:58:31 2025

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