Magnesium in PDB 2i7d: Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+

The structure of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+, PDB code: 2i7d was solved by A.Rinaldo-Matthis, K.Wallden, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.10 / 1.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.623, 47.153, 62.384, 68.92, 81.69, 74.99
R / Rfree (%)	16.6 / 19.6

The structure of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ (pdb code 2i7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+, PDB code: 2i7d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg728 b:4.9 occ:1.00 F1 A:ALF400 2.0 6.9 1.0 OD2 A:ASP10 2.1 5.5 1.0 O A:HOH731 2.1 6.5 1.0 O A:ASP12 2.1 5.5 1.0 OD1 A:ASP145 2.1 5.5 1.0 O A:HOH729 2.1 5.5 1.0 CG A:ASP10 3.1 4.1 1.0 CG A:ASP145 3.1 4.8 1.0 C A:ASP12 3.2 4.9 1.0 OD1 A:ASP10 3.5 5.1 1.0 OD2 A:ASP145 3.5 6.8 1.0 AL A:ALF400 3.5 5.7 1.0 F3 A:ALF400 3.5 9.2 1.0 CA A:ASP12 3.9 5.1 1.0 OD1 A:ASP144 4.0 6.1 1.0 CB A:ASP12 4.0 5.2 1.0 N A:ASP12 4.1 4.8 1.0 N A:GLY13 4.3 4.9 1.0 F4 A:ALF400 4.4 6.5 1.0 CB A:ASP10 4.4 4.8 1.0 N A:ASP145 4.4 4.2 1.0 CB A:ASP145 4.5 4.8 1.0 CE1 A:PHE44 4.5 9.0 1.0 CA A:GLY13 4.6 5.5 1.0 C2' A:DUR300 4.6 9.7 1.0 O2 A:DUR300 4.7 9.5 1.0 O3' A:DUR300 4.7 7.8 1.0 CZ A:PHE44 4.7 10.2 1.0 CG A:ASP144 4.7 5.0 1.0 O A:HOH792 4.8 13.3 1.0 N A:LYS146 4.8 4.9 1.0 C A:MET11 4.9 3.9 1.0 CA A:ASP145 4.9 4.9 1.0 CG2 A:VAL14 4.9 6.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg729 b:6.8 occ:1.00 F4 B:ALF401 2.0 7.8 1.0 OD1 B:ASP145 2.0 7.2 1.0 OD2 B:ASP10 2.1 6.9 1.0 O B:HOH733 2.1 8.7 1.0 O B:HOH730 2.1 7.5 1.0 O B:ASP12 2.1 8.2 1.0 CG B:ASP145 3.1 6.7 1.0 CG B:ASP10 3.1 6.8 1.0 C B:ASP12 3.3 6.6 1.0 OD2 B:ASP145 3.5 8.9 1.0 OD1 B:ASP10 3.5 7.7 1.0 AL B:ALF401 3.5 7.3 1.0 F1 B:ALF401 3.6 10.1 1.0 CA B:ASP12 4.0 6.5 1.0 OD2 B:ASP144 4.0 7.7 1.0 CB B:ASP12 4.0 7.1 1.0 N B:ASP12 4.1 6.3 1.0 N B:GLY13 4.3 7.0 1.0 F2 B:ALF401 4.4 8.1 1.0 N B:ASP145 4.4 6.8 1.0 CB B:ASP145 4.4 7.2 1.0 CB B:ASP10 4.4 6.1 1.0 C2' B:DUR301 4.5 10.7 1.0 CE1 B:PHE44 4.5 11.9 1.0 O2 B:DUR301 4.6 10.2 1.0 CA B:GLY13 4.6 7.3 1.0 O3' B:DUR301 4.6 8.8 1.0 CZ B:PHE44 4.7 12.0 1.0 CG2 B:VAL14 4.8 7.2 1.0 CG B:ASP144 4.8 7.0 1.0 CA B:ASP145 4.8 6.8 1.0 N B:LYS146 4.8 7.1 1.0 O B:HOH770 4.9 14.9 1.0 C B:MET11 4.9 5.9 1.0

K.Wallden, A.Rinaldo-Matthis, B.Ruzzenente, C.Rampazzo, V.Bianchi, P.Nordlund. Structures of Human and Murine Cytosolic Deoxyribonucleotidase: Insights Into Substrate Specificity and Catalysis To Be Published.