Iron in PDB 6npd: X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate

The structure of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate, PDB code: 6npd was solved by L.J.Rajakovich, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.78
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.564, 87.564, 221.119, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 21.7

The binding sites of Iron atom in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate (pdb code 6npd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate, PDB code: 6npd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:20.3 occ:0.70 OD1 A:ASP200 1.9 11.7 1.0 O1 A:KVP402 2.2 11.7 0.7 NE2 A:HIS198 2.3 11.3 1.0 NE2 A:HIS341 2.6 12.9 1.0 CG A:ASP200 2.9 11.6 1.0 CD2 A:HIS198 3.1 11.3 1.0 CE1 A:HIS341 3.2 12.9 1.0 OD2 A:ASP200 3.2 12.1 1.0 CE1 A:HIS198 3.4 11.4 1.0 C1 A:KVP402 3.5 12.0 1.0 CD2 A:HIS341 3.7 12.9 1.0 O9 A:KVP402 4.0 12.2 1.0 C5 A:KVP402 4.1 12.5 1.0 CB A:ASP200 4.2 11.3 1.0 C2 A:KVP402 4.3 12.3 1.0 P4 A:KVP402 4.3 11.8 1.0 OE1 A:GLN211 4.3 15.9 1.0 CG A:HIS198 4.3 11.1 1.0 ND1 A:HIS341 4.4 12.5 1.0 O11 A:KVP402 4.4 12.1 1.0 ND1 A:HIS198 4.4 11.3 1.0 NE2 A:GLN211 4.5 14.0 1.0 NH2 A:ARG288 4.6 13.2 1.0 CG A:HIS341 4.6 12.4 1.0 CA A:ASP200 4.6 10.9 1.0 N3 A:KVP402 4.8 12.5 1.0 CD A:GLN211 4.9 14.3 1.0 N A:ASP200 5.0 10.8 1.0

Iron binding site 2 out of 2 in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and (R)-1-Hydroxy-2- Trimethylaminoethylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.2 occ:0.40 OD1 B:ASP200 2.3 18.1 1.0 NE2 B:HIS198 2.6 17.5 1.0 NE2 B:HIS341 2.8 19.4 1.0 CG B:ASP200 3.2 17.9 1.0 CE1 B:HIS341 3.3 19.4 1.0 CD2 B:HIS198 3.4 17.1 1.0 OD2 B:ASP200 3.4 18.6 1.0 CE1 B:HIS198 3.6 17.6 1.0 CD2 B:HIS341 3.9 19.3 1.0 NE2 B:GLN211 4.4 20.2 1.0 ND1 B:HIS341 4.5 18.9 1.0 CG B:HIS198 4.6 16.8 1.0 CB B:ASP200 4.6 17.0 1.0 OE1 B:GLN211 4.6 20.2 1.0 ND1 B:HIS198 4.7 17.2 1.0 CG B:HIS341 4.8 18.7 1.0

L.J.Rajakovich, M.E.Pandelia, A.J.Mitchell, W.C.Chang, B.Zhang, A.K.Boal, C.Krebs, J.M.Bollinger Jr.. A New Microbial Pathway For Organophosphonate Degradation Catalyzed By Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry V. 58 1627 2019.
ISSN: ISSN 1520-4995
PubMed: 30789718
DOI: 10.1021/ACS.BIOCHEM.9B00044