Iron 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:

Magnesium

(Mg)

2 atoms

The binding sites of Iron 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 Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of Ptlh with Akg and Ent-1PL Bound, PDB code: 2rdn:

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe1 b:12.1 occ:1.00 O2 A:AKG279 2.0 5.8 1.0 O A:HOH281 2.1 5.7 1.0 OD1 A:ASP139 2.1 4.9 1.0 NE2 A:HIS137 2.2 5.6 1.0 NE2 A:HIS226 2.2 5.0 1.0 O5 A:AKG279 2.3 5.5 1.0 C1 A:AKG279 2.8 7.0 1.0 C2 A:AKG279 2.9 5.4 1.0 CG A:ASP139 3.1 5.4 1.0 CE1 A:HIS226 3.1 4.7 1.0 CE1 A:HIS137 3.1 5.2 1.0 CD2 A:HIS137 3.2 4.5 1.0 CD2 A:HIS226 3.3 4.5 1.0 OD2 A:ASP139 3.4 6.4 1.0 NH1 A:ARG246 4.0 6.2 1.0 O1 A:AKG279 4.0 7.5 1.0 ND1 A:HIS137 4.2 5.2 1.0 ND1 A:HIS226 4.3 4.8 1.0 OH A:TYR142 4.3 10.2 1.0 O2 A:1PL280 4.3 8.9 1.0 CG A:HIS137 4.3 4.9 1.0 CG A:HIS226 4.4 4.7 1.0 C3 A:AKG279 4.4 5.6 1.0 CB A:ASP139 4.4 4.9 1.0 C12 A:1PL280 4.7 8.9 1.0 CE2 A:TYR142 4.8 10.1 1.0 CA A:ASP139 4.8 4.8 1.0 N A:ASP139 4.8 4.7 1.0 CE1 A:PHE220 4.9 6.7 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