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Calcium in PDB 1r4f: Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine

Enzymatic activity of Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine

All present enzymatic activity of Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine:
3.2.2.1;

Protein crystallography data

The structure of Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine, PDB code: 1r4f was solved by W.Versees, S.Loverix, A.Vandemeulebroucke, P.Geerlings, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.996, 74.865, 81.369, 90.00, 102.29, 90.00
R / Rfree (%) 20.5 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine (pdb code 1r4f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine, PDB code: 1r4f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1r4f

Go back to Calcium Binding Sites List in 1r4f
Calcium binding site 1 out of 2 in the Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:24.9
occ:1.00
 O A:HOH329 2.4 21.6 1.0
O A:THR137 2.4 21.4 1.0
OD2 A:ASP10 2.4 24.7 1.0
OD1 A:ASP15 2.5 24.1 1.0
OD2 A:ASP15 2.6 24.9 1.0
OD2 A:ASP261 2.6 20.9 1.0
O A:HOH331 2.7 23.6 1.0
CG A:ASP15 2.9 21.7 1.0
O A:HOH330 3.1 45.3 1.0
CG A:ASP10 3.4 25.0 1.0
C A:THR137 3.6 21.6 1.0
OD1 A:ASP10 3.6 26.1 1.0
CG A:ASP261 3.6 22.5 1.0
OD1 A:ASP261 3.9 21.8 1.0
CA A:GLY138 4.3 23.5 1.0
N A:GLY138 4.4 22.9 1.0
CB A:ASP15 4.4 21.7 1.0
CB A:THR137 4.4 22.8 1.0
OD1 A:ASN186 4.4 27.3 1.0
OD1 A:ASP14 4.5 36.0 1.0
CB A:ASN12 4.5 34.6 1.0
O A:HOH333 4.5 44.0 1.0
CA A:THR137 4.6 22.5 1.0
OG1 A:THR137 4.6 24.1 1.0
ND2 A:ASN186 4.6 28.2 1.0
N A:ASP10 4.7 26.1 1.0
CB A:ASP10 4.7 26.3 1.0
OD2 A:ASP14 4.8 32.8 1.0
CB A:ASP261 4.9 24.0 1.0
CG A:ASP14 5.0 33.5 1.0
CA A:ASP15 5.0 23.1 1.0
CG A:ASN186 5.0 28.9 1.0
N A:ASP15 5.0 24.5 1.0

Calcium binding site 2 out of 2 in 1r4f

Go back to Calcium Binding Sites List in 1r4f
Calcium binding site 2 out of 2 in the Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma Vivax: TRP260ALA Mutant in Complex with 3- Deaza-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca329

b:24.8
occ:1.00
 O B:THR137 2.3 25.4 1.0
OD2 B:ASP15 2.4 22.2 1.0
OD2 B:ASP10 2.4 26.9 1.0
O3' B:AD3330 2.5 43.7 1.0
OD2 B:ASP261 2.5 26.5 1.0
O2' B:AD3330 2.5 45.4 1.0
O B:HOH331 2.6 18.3 1.0
OD1 B:ASP15 2.7 19.6 1.0
CG B:ASP15 2.9 22.9 1.0
CG B:ASP10 3.3 24.6 1.0
C2' B:AD3330 3.5 49.7 1.0
C B:THR137 3.5 23.8 1.0
CG B:ASP261 3.5 25.5 1.0
C3' B:AD3330 3.5 47.9 1.0
OD1 B:ASP10 3.6 26.8 1.0
OD1 B:ASP261 3.8 26.4 1.0
CA B:GLY138 4.2 22.9 1.0
N B:GLY138 4.3 24.6 1.0
C1' B:AD3330 4.3 53.1 1.0
CB B:ASP15 4.4 21.4 1.0
CB B:THR137 4.4 24.8 1.0
OD1 B:ASN186 4.5 21.7 1.0
OG1 B:THR137 4.5 28.2 1.0
OD1 B:ASP14 4.5 31.3 1.0
CA B:THR137 4.5 24.9 1.0
C4' B:AD3330 4.6 48.2 1.0
N B:ASP10 4.6 25.6 1.0
CB B:ASN12 4.6 36.0 1.0
CB B:ASP10 4.7 24.8 1.0
ND2 B:ASN186 4.7 22.2 1.0
O4' B:AD3330 4.8 49.5 1.0
CB B:ASP261 4.9 25.6 1.0
CA B:ASP15 5.0 23.0 1.0

Reference:

W.Versees, S.Loverix, A.Vandemeulebroucke, P.Geerlings, J.Steyaert. Leaving Group Activation By Aromatic Stacking: An Alternative to General Acid Catalysis. J.Mol.Biol. V. 338 1 2004.
ISSN: ISSN 0022-2836
PubMed: 15050818
DOI: 10.1016/J.JMB.2004.02.049
Page generated: Thu Jul 11 22:02:58 2024

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