Magnesium in PDB 4nwi: Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine

All present enzymatic activity of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine:
3.1.3.5;

The structure of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine, PDB code: 4nwi was solved by T.Monecke, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.88 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.600, 99.350, 72.810, 90.00, 92.46, 90.00
R / Rfree (%)	22.8 / 24.6

The structure of Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine (pdb code 4nwi). 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 Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine, PDB code: 4nwi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine


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 Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.8 occ:1.00 OD2 A:ASP55 1.9 17.2 1.0 O A:HOH629 2.0 18.3 1.0 O A:HOH630 2.0 18.6 1.0 O A:HOH628 2.0 21.7 1.0 OD1 A:ASP245 2.1 15.9 1.0 O A:ASP57 2.2 18.1 1.0 CG A:ASP55 3.0 17.6 1.0 CG A:ASP245 3.1 20.5 1.0 OD2 A:ASP245 3.4 24.1 1.0 C A:ASP57 3.4 19.0 1.0 OD1 A:ASP55 3.4 17.2 1.0 OD2 A:ASP249 3.9 13.2 1.0 OG1 A:THR59 4.0 13.0 1.0 CA A:ASP57 4.1 16.4 1.0 OG A:SER246 4.1 22.8 1.0 CB A:ASP55 4.2 17.1 1.0 O A:HOH551 4.2 26.0 1.0 N A:ASP57 4.2 15.4 1.0 CB A:ASP57 4.3 15.0 1.0 O A:HOH645 4.4 24.9 1.0 CB A:ASP245 4.4 20.0 1.0 N A:TYR58 4.5 20.1 1.0 N A:ASP245 4.6 23.5 1.0 N A:THR59 4.6 15.7 1.0 C A:TYR58 4.7 19.6 1.0 CB A:TYR58 4.7 21.9 1.0 CG A:ASP249 4.7 16.0 1.0 OD1 A:ASP249 4.8 18.2 1.0 CA A:TYR58 4.8 21.0 1.0 C A:PHE56 4.8 15.7 1.0 CB A:THR59 4.9 13.6 1.0 CL A:CL403 4.9 19.3 1.0 CA A:ASP245 5.0 21.4 1.0 O A:HOH512 5.0 22.1 1.0 CD2 A:TYR58 5.0 22.8 1.0 N A:SER246 5.0 23.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine


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 Cytosolic 5'-Nucleotidase Iiib (Cn-Iiib) Bound to Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:21.4 occ:1.00 O B:HOH638 2.0 10.7 1.0 O B:HOH637 2.0 19.8 1.0 OD1 B:ASP245 2.0 26.6 1.0 O B:ASP57 2.0 23.3 1.0 OD2 B:ASP55 2.0 23.1 1.0 O B:HOH636 2.4 26.8 1.0 CG B:ASP245 3.0 24.2 1.0 CG B:ASP55 3.1 21.8 1.0 C B:ASP57 3.2 22.7 1.0 OD2 B:ASP245 3.4 25.1 1.0 OD1 B:ASP55 3.6 15.3 1.0 OG1 B:THR59 3.8 14.9 1.0 O B:HOH501 3.9 30.8 1.0 OD2 B:ASP249 4.0 17.1 1.0 CA B:ASP57 4.0 21.3 1.0 OG B:SER246 4.1 24.9 1.0 N B:ASP57 4.2 19.2 1.0 CB B:ASP57 4.2 23.2 1.0 N B:TYR58 4.2 23.6 1.0 O B:HOH561 4.3 42.6 1.0 C B:TYR58 4.3 23.1 1.0 CB B:ASP245 4.4 21.4 1.0 N B:THR59 4.4 22.9 1.0 CB B:ASP55 4.4 19.1 1.0 CB B:TYR58 4.4 22.4 1.0 CA B:TYR58 4.5 22.6 1.0 N B:ASP245 4.6 16.7 1.0 O B:TYR58 4.8 24.7 1.0 C B:PHE56 4.8 19.5 1.0 CB B:THR59 4.8 17.7 1.0 CD2 B:TYR58 4.9 24.3 1.0 O B:HOH650 4.9 40.6 1.0 CA B:ASP245 4.9 18.0 1.0 N B:SER246 5.0 16.1 1.0

T.Monecke, J.Buschmann, P.Neumann, E.Wahle, R.Ficner. Crystal Structures of the Novel Cytosolic 5'-Nucleotidase Iiib Explain Its Preference For M7GMP Plos One V. 9 90915 2014.
ISSN: ESSN 1932-6203
PubMed: 24603684
DOI: 10.1371/JOURNAL.PONE.0090915