Magnesium in PDB 2yaz: The Crystal Structure of Leishmania Major Dutpase in Complex Dump

All present enzymatic activity of The Crystal Structure of Leishmania Major Dutpase in Complex Dump:
3.6.1.23;

The structure of The Crystal Structure of Leishmania Major Dutpase in Complex Dump, PDB code: 2yaz 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)	103.10 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.110, 109.110, 309.311, 90.00, 90.00, 120.00
R / Rfree (%)	20.268 / 22.532

The binding sites of Magnesium atom in the The Crystal Structure of Leishmania Major Dutpase in Complex Dump (pdb code 2yaz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of Leishmania Major Dutpase in Complex Dump, PDB code: 2yaz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Crystal Structure of Leishmania Major Dutpase in Complex Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Leishmania Major Dutpase in Complex Dump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1267 b:76.8 occ:1.00 OD2 A:ASP79 2.4 45.5 1.0 OE2 A:GLU76 2.6 54.3 1.0 OE1 A:GLU48 2.6 56.8 1.0 OE1 A:GLU76 2.8 55.0 1.0 CD A:GLU76 3.0 52.7 1.0 CG A:ASP79 3.5 45.1 1.0 CD A:GLU48 3.8 55.0 1.0 OP1 A:UMP1265 4.0 64.2 1.0 OD1 A:ASP79 4.3 36.2 1.0 CB A:ASP79 4.4 35.9 1.0 OE2 A:GLU48 4.4 86.0 1.0 CG A:GLU76 4.4 34.9 1.0 NZ A:LYS198 4.5 57.3 1.0 NZ A:LYS179 4.5 32.9 1.0 CG2 A:ILE75 4.6 28.6 1.0 CA A:GLU76 4.8 30.9 1.0 OP3 A:UMP1265 4.8 73.4 1.0

Magnesium binding site 2 out of 3 in the The Crystal Structure of Leishmania Major Dutpase in Complex Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Leishmania Major Dutpase in Complex Dump within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1266 b:71.7 occ:1.00 OD2 D:ASP79 2.1 51.9 1.0 OE2 D:GLU76 3.1 45.5 1.0 CG D:ASP79 3.2 48.9 1.0 OP1 D:UMP1265 3.6 77.9 1.0 CD D:GLU76 3.7 48.8 1.0 OE1 D:GLU48 3.7 64.3 1.0 NZ D:LYS179 3.7 45.6 1.0 OD1 D:ASP79 3.8 43.6 1.0 CG2 D:ILE75 3.8 40.2 1.0 OE1 D:GLU76 4.0 52.0 1.0 ND2 D:ASN206 4.2 41.7 1.0 CB D:ASP79 4.4 43.8 1.0 CG D:GLU76 4.7 35.1 1.0 O D:ILE75 4.7 41.9 1.0 CD D:GLU48 4.8 58.4 1.0 P D:UMP1265 4.8 65.7 1.0 OP3 D:UMP1265 4.8 66.0 1.0 CG D:ASN206 4.9 57.9 1.0 C D:ILE75 4.9 40.2 1.0 CA D:GLU76 4.9 37.4 1.0 OD1 D:ASN206 4.9 53.1 1.0 CB D:ILE75 4.9 42.2 1.0 N D:GLU76 5.0 39.6 1.0

Magnesium binding site 3 out of 3 in the The Crystal Structure of Leishmania Major Dutpase in Complex Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Leishmania Major Dutpase in Complex Dump within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1267 b:59.6 occ:1.00 OP3 E:UMP1266 2.6 61.6 1.0 OE1 E:GLU48 2.7 46.4 1.0 OE2 E:GLU76 3.0 60.3 1.0 OD2 E:ASP79 3.0 61.8 1.0 CD E:GLU48 3.4 65.3 1.0 OE2 E:GLU48 3.4 79.3 1.0 CD E:GLU76 3.7 58.0 1.0 OE1 E:GLU76 3.7 67.4 1.0 P E:UMP1266 3.8 69.6 1.0 CG E:ASP79 3.9 55.4 1.0 OP1 E:UMP1266 4.0 74.5 1.0 C5' E:UMP1266 4.3 51.4 1.0 CB E:ASP79 4.5 42.3 1.0 O5' E:UMP1266 4.6 65.7 1.0 OD1 E:ASP79 4.6 40.5 1.0 CG E:GLU48 4.8 50.1 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