Magnesium in PDB 6mjk: Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine

The structure of Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine, PDB code: 6mjk was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.20 / 1.45
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	74.230, 74.230, 74.230, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 17

The binding sites of Magnesium atom in the Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine (pdb code 6mjk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine, PDB code: 6mjk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:16.5 occ:0.48 O32 A:PPV204 2.0 20.4 0.6 O A:HOH388 2.0 24.4 1.0 O11 A:PPV204 2.2 35.3 0.6 O A:HOH341 2.3 16.7 0.3 P2 A:PPV204 3.2 23.7 0.6 P1 A:PPV204 3.3 25.9 0.6 OPP A:PPV204 3.5 20.2 0.6 O22 A:PPV204 3.7 33.1 0.6 O21 A:PPV204 3.8 35.3 0.6 O A:HOH341 3.9 17.8 0.7 O12 A:PPV204 4.4 30.9 0.6 O5' A:DUR203 4.6 49.4 0.6 O31 A:PPV204 4.6 19.5 0.6 C5' A:DUR203 4.6 20.2 0.6 C5' A:DUR203 4.7 22.2 0.4 OD2 A:ASP83 4.8 14.4 1.0 O5' A:DUR203 4.9 18.9 0.4

Magnesium binding site 2 out of 2 in the Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:27.4 occ:0.34 O A:HOH309 2.2 27.9 1.0 O A:HOH386 3.2 26.6 0.5 OD2 A:ASP76 3.8 24.4 1.0 O A:HOH439 3.9 22.7 0.3 O A:HOH408 4.0 22.5 1.0 O A:HOH386 4.1 15.2 0.5 O A:HOH336 4.5 20.4 1.0 O A:VAL77 4.5 13.6 1.0 CG A:ASP76 4.6 18.8 1.0 OD1 A:ASP76 4.6 18.1 1.0

S.L.Delker, J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of Dutp Pyrophosphatase Protein, From Naegleria Fowleri in Complex with Deoxyuridine To Be Published.