Aluminium 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
Magnesium	(Mg)	2 atoms

The binding sites of Aluminium 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 Aluminium atom.
In total 2 binding sites of Aluminium where determined in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+, PDB code: 2i7d:
Jump to Aluminium binding site number: 1; 2;

Aluminium 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 Aluminium with other atoms in the Al 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:Al400 b:5.7 occ:1.00 AL A:ALF400 0.0 5.7 1.0 F2 A:ALF400 1.8 9.6 1.0 F1 A:ALF400 1.8 6.9 1.0 F3 A:ALF400 1.8 9.2 1.0 F4 A:ALF400 1.8 6.5 1.0 OD1 A:ASP10 2.1 5.1 1.0 O3' A:DUR300 2.1 7.8 1.0 CG A:ASP10 3.1 4.1 1.0 C3' A:DUR300 3.1 7.8 1.0 OD2 A:ASP10 3.5 5.5 1.0 MG A:MG728 3.5 4.9 1.0 O A:HOH729 3.7 5.5 1.0 C2' A:DUR300 3.7 9.7 1.0 NZ A:LYS134 3.8 6.1 1.0 OG1 A:THR99 3.9 7.2 1.0 N A:ASP12 3.9 4.8 1.0 OD2 A:ASP12 4.0 7.3 1.0 N A:MET11 4.2 4.7 1.0 N A:SER100 4.3 7.1 1.0 CB A:ASP12 4.3 5.2 1.0 CB A:ASP10 4.4 4.8 1.0 C4' A:DUR300 4.5 9.6 1.0 O A:ASP12 4.5 5.5 1.0 CA A:THR99 4.5 6.2 1.0 CG A:ASP12 4.6 6.1 1.0 CA A:ASP12 4.6 5.1 1.0 O A:HOH731 4.7 6.5 1.0 CB A:THR99 4.7 6.2 1.0 C1' A:DUR300 4.8 9.3 1.0 C A:MET11 4.8 3.9 1.0 CE A:LYS134 4.8 6.2 1.0 CA A:MET11 4.9 5.1 1.0 CA A:ASP10 4.9 4.6 1.0 C A:THR99 5.0 6.0 1.0

Aluminium 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 Aluminium with other atoms in the Al 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:Al401 b:7.3 occ:1.00 AL B:ALF401 0.0 7.3 1.0 F3 B:ALF401 1.8 10.4 1.0 F1 B:ALF401 1.8 10.1 1.0 F4 B:ALF401 1.8 7.8 1.0 F2 B:ALF401 1.8 8.1 1.0 O3' B:DUR301 2.0 8.8 1.0 OD1 B:ASP10 2.0 7.7 1.0 CG B:ASP10 3.1 6.8 1.0 C3' B:DUR301 3.1 9.8 1.0 OD2 B:ASP10 3.5 6.9 1.0 MG B:MG729 3.5 6.8 1.0 C2' B:DUR301 3.7 10.7 1.0 O B:HOH730 3.7 7.5 1.0 NZ B:LYS134 3.9 7.6 1.0 OG1 B:THR99 3.9 7.1 1.0 N B:ASP12 4.0 6.3 1.0 OD2 B:ASP12 4.0 8.5 1.0 N B:MET11 4.2 6.6 1.0 N B:SER100 4.3 7.8 1.0 CB B:ASP12 4.3 7.1 1.0 CB B:ASP10 4.4 6.1 1.0 C4' B:DUR301 4.4 10.8 1.0 CA B:THR99 4.6 6.3 1.0 O B:ASP12 4.6 8.2 1.0 CG B:ASP12 4.6 6.9 1.0 CA B:ASP12 4.7 6.5 1.0 CB B:THR99 4.7 6.6 1.0 O B:HOH733 4.7 8.7 1.0 C1' B:DUR301 4.7 10.6 1.0 C B:MET11 4.8 5.9 1.0 CA B:ASP10 4.8 6.0 1.0 CA B:MET11 4.9 6.6 1.0 CE B:LYS134 4.9 6.4 1.0 O B:SER100 4.9 9.9 1.0 C B:THR99 5.0 6.7 1.0 C B:ASP10 5.0 6.7 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.