Magnesium in PDB 2rdn: Crystal Structure of Ptlh with Akg and Ent-1PL Bound

The structure of Crystal Structure of Ptlh with Akg and Ent-1PL Bound, PDB code: 2rdn was solved by Z.You, S.Omura, H.Ikeda, D.E.Cane, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.499, 70.106, 48.725, 90.00, 92.49, 90.00
R / Rfree (%)	17.2 / 19.6

The structure of Crystal Structure of Ptlh with Akg and Ent-1PL Bound also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Ptlh with Akg and Ent-1PL Bound (pdb code 2rdn). 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 Ptlh with Akg and Ent-1PL Bound, PDB code: 2rdn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ptlh with Akg and Ent-1PL Bound


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 Ptlh with Akg and Ent-1PL Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg277 b:13.5 occ:1.00 O A:HOH283 2.0 18.9 1.0 O A:HOH285 2.0 11.5 1.0 O A:HOH407 2.0 14.8 1.0 O A:HOH284 2.1 16.5 1.0 O A:HOH282 2.3 15.6 1.0 OD2 A:ASP60 4.0 11.8 1.0 O A:HOH776 4.3 30.9 1.0 OD1 A:ASP60 4.4 9.8 1.0 CB A:HIS62 4.6 8.1 1.0 CG A:ASP60 4.6 10.3 1.0 O A:HOH676 4.6 35.7 1.0 CD2 A:HIS62 5.0 8.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ptlh with Akg and Ent-1PL Bound


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 Ptlh with Akg and Ent-1PL Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg278 b:10.0 occ:1.00 O A:HOH286 2.1 10.7 1.0 O A:HOH288 2.1 11.8 1.0 O A:HOH290 2.1 12.4 1.0 O A:HOH287 2.1 10.4 1.0 O A:HOH289 2.1 12.1 1.0 O A:HOH349 2.1 7.1 1.0 O A:HOH805 3.3 0.1 1.0 N A:GLY176 4.0 8.3 1.0 O A:HOH302 4.2 11.9 1.0 ND1 A:HIS223 4.2 6.4 1.0 O A:HOH807 4.3 30.2 1.0 CA A:GLY176 4.4 8.4 1.0 O A:HIS173 4.4 7.5 1.0 O A:ARG174 4.5 9.3 1.0 C A:ARG174 4.6 8.7 1.0 CE1 A:HIS223 4.6 5.6 1.0 O A:HOH768 4.6 0.0 1.0 CA A:ARG174 4.8 8.0 1.0 N A:ARG175 4.9 8.8 1.0

Z.You, S.Omura, H.Ikeda, D.E.Cane, G.Jogl. Crystal Structure of the Non-Heme Iron Dioxygenase Ptlh in Pentalenolactone Biosynthesis. J.Biol.Chem. V. 282 36552 2007.
ISSN: ISSN 0021-9258
PubMed: 17942405
DOI: 10.1074/JBC.M706358200