Magnesium in PDB 2rdq: Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate Bound

The structure of Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate Bound, PDB code: 2rdq 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 / 1.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.817, 70.869, 48.769, 90.00, 98.21, 90.00
R / Rfree (%)	17.8 / 20.2

The structure of Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate Bound also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate Bound (pdb code 2rdq). 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 Fe/Alpha Ketoglutarate Bound, PDB code: 2rdq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate 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 Fe/Alpha Ketoglutarate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg267 b:10.8 occ:1.00 O A:HOH275 2.0 12.9 1.0 O A:HOH274 2.1 9.4 1.0 O A:HOH272 2.1 16.0 1.0 O A:HOH273 2.1 14.2 1.0 O A:HOH271 2.2 13.4 1.0 O A:HOH858 2.2 39.1 1.0 O A:HOH781 3.7 70.2 1.0 O A:HOH875 3.9 56.2 1.0 OD2 A:ASP60 4.0 10.7 1.0 O A:HOH800 4.3 0.2 1.0 OD1 A:ASP60 4.3 7.3 1.0 O A:HOH849 4.4 50.8 1.0 CB A:HIS62 4.6 6.9 1.0 CG A:ASP60 4.6 8.6 1.0 O A:HOH560 4.6 28.8 1.0 CD2 A:HIS62 5.0 6.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ptlh with Fe/Alpha Ketoglutarate 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 Fe/Alpha Ketoglutarate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg268 b:7.0 occ:1.00 O A:HOH279 2.0 8.1 1.0 O A:HOH280 2.0 9.6 1.0 O A:HOH278 2.0 8.3 1.0 O A:HOH277 2.1 8.5 1.0 O A:HOH276 2.1 8.4 1.0 O A:HOH281 2.1 5.9 1.0 N A:GLY176 4.1 6.2 1.0 O A:HOH346 4.1 8.5 1.0 O A:HOH607 4.1 24.2 1.0 O A:HOH487 4.2 18.4 1.0 ND1 A:HIS223 4.2 5.3 1.0 O A:HIS173 4.4 5.2 1.0 CA A:GLY176 4.4 6.3 1.0 O A:HOH629 4.5 17.7 1.0 O A:HOH435 4.5 14.6 1.0 O A:ARG174 4.5 7.1 1.0 C A:ARG174 4.6 7.0 1.0 CE1 A:HIS223 4.6 4.4 1.0 O A:HOH490 4.7 16.5 1.0 CA A:ARG174 4.8 6.2 1.0 N A:ARG175 4.9 6.2 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