Atomistry » Calcium » PDB 3ecj-3eqd » 3epw
Atomistry »
  Calcium »
    PDB 3ecj-3eqd »
      3epw »

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: Sat Jul 13 09:31:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy