Iron in PDB 8xht: The Apo Structure of Pabcmg

The structure of The Apo Structure of Pabcmg, PDB code: 8xht was solved by L.Wu, G.L.Tang, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.06 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.331, 103.396, 91.072, 90, 89.97, 90
R / Rfree (%)	19.9 / 23.6

The binding sites of Iron atom in the The Apo Structure of Pabcmg (pdb code 8xht). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Apo Structure of Pabcmg, PDB code: 8xht:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Apo Structure of Pabcmg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Apo Structure of Pabcmg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:31.4 occ:0.66 O A:HOH634 2.4 29.1 1.0 NE2 A:HIS172 2.4 40.8 1.0 NE2 A:HIS230 2.4 26.1 1.0 O2 A:AKG403 2.5 46.0 1.0 O5 A:AKG403 2.5 53.2 1.0 OD1 A:ASP174 2.7 22.2 1.0 CD2 A:HIS230 3.0 29.1 1.0 C1 A:AKG403 3.2 45.4 1.0 C2 A:AKG403 3.3 46.5 1.0 CE1 A:HIS172 3.3 37.1 1.0 CD2 A:HIS172 3.3 38.2 1.0 CG A:ASP174 3.5 21.6 1.0 OD2 A:ASP174 3.6 18.3 1.0 CE1 A:HIS230 3.6 31.0 1.0 O A:HOH665 3.8 25.3 1.0 CG A:HIS230 4.3 26.2 1.0 CE2 A:PHE248 4.3 13.2 1.0 O A:HOH685 4.4 28.6 1.0 ND1 A:HIS172 4.4 36.4 1.0 O1 A:AKG403 4.4 45.0 1.0 CG A:HIS172 4.5 33.2 1.0 ND1 A:HIS230 4.5 24.2 1.0 CZ A:PHE248 4.6 17.4 1.0 C3 A:AKG403 4.7 31.4 1.0 CB A:ASP174 5.0 19.6 1.0

Iron binding site 2 out of 4 in the The Apo Structure of Pabcmg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Apo Structure of Pabcmg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:63.4 occ:1.00 O B:HOH532 2.4 28.0 1.0 NE2 B:HIS230 2.5 30.5 1.0 NE2 B:HIS172 2.6 50.4 1.0 CD2 B:HIS230 3.1 23.6 1.0 CE1 B:HIS172 3.3 50.6 1.0 OD1 B:ASP174 3.3 24.0 1.0 O B:HOH683 3.7 35.0 1.0 CD2 B:HIS172 3.7 45.1 1.0 CE1 B:HIS230 3.7 23.3 1.0 O B:HOH700 3.8 36.2 1.0 OD2 B:ASP174 4.0 18.2 1.0 CG B:ASP174 4.1 22.7 1.0 CZ B:PHE248 4.2 15.7 1.0 CE2 B:PHE248 4.3 14.8 1.0 CG B:HIS230 4.4 22.1 1.0 ND1 B:HIS172 4.5 43.1 1.0 ND1 B:HIS230 4.7 21.8 1.0 CG B:HIS172 4.7 37.0 1.0 O B:HOH651 4.7 27.8 1.0

Iron binding site 3 out of 4 in the The Apo Structure of Pabcmg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Apo Structure of Pabcmg within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:56.7 occ:1.00 O C:HOH536 2.4 27.9 1.0 NE2 C:HIS230 2.5 28.9 1.0 NE2 C:HIS172 2.6 48.9 1.0 O5 C:AKG403 2.6 44.5 0.6 O1 C:AKG403 2.8 46.9 0.6 C1 C:AKG403 3.1 44.0 0.6 CD2 C:HIS230 3.1 21.4 1.0 CE1 C:HIS172 3.1 39.9 1.0 OD1 C:ASP174 3.2 25.3 1.0 C2 C:AKG403 3.2 42.5 0.6 CE1 C:HIS230 3.6 23.1 1.0 OD2 C:ASP174 3.8 17.2 1.0 CD2 C:HIS172 3.8 41.5 1.0 CG C:ASP174 3.9 22.2 1.0 O2 C:AKG403 4.0 38.1 0.6 CZ C:PHE248 4.2 14.8 1.0 CE2 C:PHE248 4.3 17.1 1.0 CG C:HIS230 4.4 22.2 1.0 ND1 C:HIS172 4.4 34.5 1.0 ND1 C:HIS230 4.6 19.4 1.0 C3 C:AKG403 4.6 34.4 0.6 O C:HOH680 4.7 27.4 1.0 CG C:HIS172 4.8 36.1 1.0

Iron binding site 4 out of 4 in the The Apo Structure of Pabcmg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Apo Structure of Pabcmg within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:29.2 occ:0.62 NE2 D:HIS230 2.4 27.1 1.0 NE2 D:HIS172 2.4 43.4 1.0 O D:HOH592 2.4 30.1 1.0 O2 D:AKG403 2.5 39.3 1.0 O5 D:AKG403 2.5 41.4 1.0 OD1 D:ASP174 2.7 28.2 1.0 CD2 D:HIS230 3.0 26.6 1.0 C1 D:AKG403 3.2 42.2 1.0 C2 D:AKG403 3.2 41.0 1.0 CD2 D:HIS172 3.3 36.0 1.0 CE1 D:HIS172 3.4 39.5 1.0 CG D:ASP174 3.5 26.4 1.0 CE1 D:HIS230 3.6 25.3 1.0 OD2 D:ASP174 3.6 20.5 1.0 O D:HOH699 3.8 26.6 1.0 O D:HOH691 4.2 26.6 1.0 CG D:HIS230 4.2 25.5 1.0 CE2 D:PHE248 4.4 13.1 1.0 O1 D:AKG403 4.4 38.7 1.0 CG D:HIS172 4.5 35.6 1.0 ND1 D:HIS172 4.5 39.7 1.0 ND1 D:HIS230 4.5 24.7 1.0 CZ D:PHE248 4.6 16.1 1.0 C3 D:AKG403 4.7 29.7 1.0 CB D:ASP174 5.0 21.2 1.0

L.Wu, J.B.He, W.Wei, H.X.Pan, X.Wang, S.Yang, Y.Liang, G.L.Tang, J.Zhou. Three Distinct Strategies Lead to Programmable Aliphatic C-H Oxidation in Bicyclomycin Biosynthesis. Nat Commun V. 16 4651 2025.
ISSN: ESSN 2041-1723
PubMed: 40389404
DOI: 10.1038/S41467-025-58997-8