Calcium in PDB 2yay: The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp

All present enzymatic activity of The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp:
3.6.1.23;

The structure of The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp, PDB code: 2yay was solved by G.R.Hemsworth, O.V.Moroz, M.J.Fogg, B.Scott, C.Bosch-Navarrete, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.42 / 1.86
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	86.830, 86.830, 145.280, 90.00, 90.00, 120.00
R / Rfree (%)	21.436 / 24.852

The binding sites of Calcium atom in the The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp (pdb code 2yay). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp, PDB code: 2yay:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1266 b:23.6 occ:1.00 O2A A:DUP1265 2.2 23.7 1.0 OE2 A:GLU48 2.3 23.9 1.0 OE2 A:GLU51 2.4 31.6 1.0 O A:HOH2011 2.4 17.3 1.0 O1G A:DUP1265 2.4 38.3 1.0 O1B A:DUP1265 2.5 22.0 1.0 OE1 A:GLU51 2.8 30.1 1.0 CD A:GLU51 3.0 33.4 1.0 CD A:GLU48 3.1 22.1 1.0 OE1 A:GLU48 3.1 24.6 1.0 PA A:DUP1265 3.5 25.0 1.0 PB A:DUP1265 3.5 28.2 1.0 CA A:CA1267 3.6 23.8 1.0 N3A A:DUP1265 3.6 22.5 1.0 PG A:DUP1265 3.8 80.3 1.0 O A:HOH2010 4.0 18.7 1.0 O3B A:DUP1265 4.1 53.1 1.0 C5' A:DUP1265 4.4 21.3 1.0 CG A:GLU51 4.4 25.0 1.0 CG A:GLU48 4.5 38.0 1.0 O5' A:DUP1265 4.5 22.5 1.0 O2G A:DUP1265 4.5 37.0 1.0 O1A A:DUP1265 4.6 23.6 1.0 O3G A:DUP1265 4.8 74.4 1.0 O2B A:DUP1265 4.8 32.1 1.0 O A:HOH2009 4.9 29.2 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Leishmania Major Dutpase in Complex with Substrate Analogue Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1267 b:23.8 occ:1.00 O1B A:DUP1265 2.1 22.0 1.0 OE1 A:GLU76 2.2 30.0 1.0 OE1 A:GLU48 2.3 24.6 1.0 OD2 A:ASP79 2.3 22.6 1.0 O A:HOH2026 2.3 21.9 1.0 OE1 A:GLU51 2.4 30.1 1.0 CD A:GLU76 3.3 28.1 1.0 PB A:DUP1265 3.4 28.2 1.0 CG A:ASP79 3.4 30.6 1.0 CD A:GLU48 3.5 22.1 1.0 CD A:GLU51 3.5 33.4 1.0 CA A:CA1266 3.6 23.6 1.0 OE2 A:GLU76 3.8 31.2 1.0 O2B A:DUP1265 3.9 32.1 1.0 O3B A:DUP1265 4.0 53.1 1.0 CB A:ASP79 4.0 27.6 1.0 OE2 A:GLU48 4.0 23.9 1.0 OE2 A:GLU51 4.2 31.6 1.0 O1G A:DUP1265 4.2 38.3 1.0 O A:HOH2025 4.2 12.0 1.0 OD1 A:ASP79 4.4 28.5 1.0 CB A:GLU51 4.4 23.0 1.0 CG A:GLU51 4.6 25.0 1.0 CA A:GLU76 4.6 26.4 1.0 PG A:DUP1265 4.6 80.3 1.0 CG A:GLU76 4.6 22.0 1.0 O A:HOH2022 4.7 26.6 1.0 NZ A:LYS179 4.7 24.7 1.0 CG A:GLU48 4.7 38.0 1.0 N3A A:DUP1265 4.8 22.5 1.0 CB A:GLU76 4.9 22.9 1.0 O3G A:DUP1265 4.9 74.4 1.0 O2A A:DUP1265 4.9 23.7 1.0 CG2 A:ILE75 5.0 28.3 1.0

G.R.Hemsworth, O.V.Moroz, M.J.Fogg, B.Scott, C.Bosch-Navarrete, D.Gonzalez-Pacanowska, K.S.Wilson. The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine. J.Biol.Chem. V. 286 16470 2011.
ISSN: ISSN 0021-9258
PubMed: 21454646
DOI: 10.1074/JBC.M111.224873