Iron in PDB 6npc: X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate

The structure of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate, PDB code: 6npc 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 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.901, 86.901, 220.613, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22

The binding sites of Iron atom in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate (pdb code 6npc). 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 2-Trimethylaminoethylphosphonate, PDB code: 6npc:
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 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 2-Trimethylaminoethylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:8.0 occ:1.00 OD1 A:ASP200 2.0 5.3 1.0 O1 A:AKG402 2.0 12.3 1.0 O5 A:AKG402 2.2 13.2 1.0 NE2 A:HIS341 2.3 7.9 1.0 NE2 A:HIS198 2.3 5.7 1.0 C1 A:AKG402 2.8 12.6 1.0 C2 A:AKG402 2.9 12.7 1.0 CE1 A:HIS341 3.0 7.9 1.0 CG A:ASP200 3.0 5.3 1.0 CD2 A:HIS198 3.2 5.7 1.0 CE1 A:HIS198 3.3 5.8 1.0 CD2 A:HIS341 3.3 7.8 1.0 OD2 A:ASP200 3.4 5.2 1.0 OE1 A:GLN211 4.0 8.3 1.0 O2 A:AKG402 4.0 12.6 1.0 ND1 A:HIS341 4.1 7.8 1.0 C1 A:KVV403 4.2 6.2 1.0 NE2 A:GLN211 4.2 7.5 1.0 CG A:HIS341 4.3 7.7 1.0 CB A:ASP200 4.4 5.3 1.0 ND1 A:HIS198 4.4 5.7 1.0 CG A:HIS198 4.4 5.7 1.0 C3 A:AKG402 4.4 12.7 1.0 O11 A:KVV403 4.4 6.1 1.0 CD A:GLN211 4.5 7.7 1.0 C5 A:KVV403 4.6 6.6 1.0 NH2 A:ARG288 4.8 6.8 1.0 CA A:ASP200 4.8 5.2 1.0 P4 A:KVV403 4.9 6.1 1.0 C4 A:AKG402 5.0 12.5 1.0

Iron binding site 2 out of 2 in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 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 2-Trimethylaminoethylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:15.2 occ:0.65 O B:HOH660 2.0 17.0 0.7 O B:HOH616 2.1 13.7 0.7 OD1 B:ASP200 2.2 11.2 1.0 O B:HOH694 2.3 16.6 0.7 NE2 B:HIS198 2.4 12.3 1.0 NE2 B:HIS341 2.5 14.1 1.0 CE1 B:HIS341 3.0 14.1 1.0 CG B:ASP200 3.1 11.1 1.0 OD2 B:ASP200 3.3 11.7 1.0 CD2 B:HIS198 3.3 12.1 1.0 CE1 B:HIS198 3.4 12.3 1.0 CD2 B:HIS341 3.6 14.0 1.0 OE1 B:GLN211 4.2 14.6 1.0 ND1 B:HIS341 4.2 13.9 1.0 O3 B:SO4402 4.3 19.6 1.0 CG B:HIS198 4.5 11.9 1.0 ND1 B:HIS198 4.5 12.1 1.0 O4 B:SO4402 4.5 17.8 1.0 CB B:ASP200 4.5 10.7 1.0 NE2 B:GLN211 4.5 13.9 1.0 CG B:HIS341 4.5 13.7 1.0 CD B:GLN211 4.8 13.2 1.0 NH2 B:ARG288 4.9 22.7 1.0 S B:SO4402 5.0 17.8 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