Magnesium in PDB 5u2i: Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri

The structure of Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri, PDB code: 5u2i 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)	40.58 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.900, 110.380, 68.140, 90.00, 118.55, 90.00
R / Rfree (%)	14.1 / 16.9

The binding sites of Magnesium atom in the Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri (pdb code 5u2i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri, PDB code: 5u2i:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri


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 A Nucleoside Diphosphate Kinase From Naegleria Fowleri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:44.1 occ:1.00 O B:HOH399 2.4 11.8 1.0 O B:HOH331 2.4 33.8 1.0 NZ B:LYS33 2.7 9.5 1.0 O B:HOH398 2.7 50.8 1.0 OE1 B:GLU78 2.9 10.0 1.0 NH2 B:ARG5 3.1 10.1 1.0 O B:HOH384 3.2 41.5 1.0 OE2 B:GLU78 3.2 10.7 1.0 CD B:GLU78 3.4 8.2 1.0 CE B:LYS33 3.6 11.2 1.0 O1 B:EDO201 3.7 24.7 1.0 OE2 B:GLU140 3.8 23.5 1.0 OE1 B:GLU140 4.0 29.7 1.0 O B:HOH486 4.2 39.0 1.0 CD B:GLU140 4.2 21.8 1.0 CZ B:ARG5 4.3 9.2 1.0 O B:TRP141 4.4 8.9 1.0 NE B:ARG5 4.6 8.4 1.0 CG2 B:VAL35 4.8 9.4 1.0 CD B:LYS33 4.8 10.6 1.0 CG B:GLU78 4.8 7.1 1.0 N B:TRP141 4.9 7.9 1.0 O B:ASN139 4.9 9.9 1.0 O B:HOH406 4.9 14.9 1.0 C1 B:EDO201 5.0 28.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri


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 A Nucleoside Diphosphate Kinase From Naegleria Fowleri within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:27.3 occ:1.00 O D:HOH496 2.9 27.4 1.0 OD1 D:ASP55 2.9 14.9 1.0 CG D:ASP55 3.4 11.9 1.0 N D:GLY56 3.4 9.1 1.0 CA D:GLY56 3.5 11.4 1.0 C D:ASP55 3.6 8.6 1.0 O D:ASP55 3.8 10.8 1.0 OD2 D:ASP55 4.0 15.1 1.0 CB D:ASP55 4.0 11.3 1.0 O D:HOH318 4.2 18.0 1.0 CA D:ASP55 4.4 8.6 1.0 O D:HOH531 4.5 29.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg204 b:17.6 occ:0.72 O D:HOH531 2.0 29.7 1.0 O D:HOH491 2.1 25.3 1.0 O D:HOH318 2.1 18.0 1.0 O D:HOH330 2.2 15.9 1.0 O D:HOH496 3.8 27.4 1.0 O D:HOH393 4.1 17.5 1.0 O D:HOH472 4.1 30.9 1.0 OD1 D:ASP55 4.1 14.9 1.0 OD2 D:ASP55 4.4 15.1 1.0 NZ D:LYS48 4.7 18.0 1.0 CG D:ASP55 4.7 11.9 1.0 O D:HOH511 4.7 19.9 0.6 CE2 D:PHE60 4.9 7.8 1.0 CE D:LYS48 5.0 22.3 1.0

D.G.Conrady, J.K.Yano, D.Lorimer, T.E.Edwards. Crystal Structure of A Nucleoside Diphosphate Kinase From Naegleria Fowleri To Be Published.