Iron in PDB 5ofq: Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium

The structure of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium, PDB code: 5ofq was solved by I.K.Jozwik, A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.93 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.125, 155.534, 158.151, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.5

The binding sites of Iron atom in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium (pdb code 5ofq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium, PDB code: 5ofq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


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 Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:40.4 occ:1.00 FE A:HEM501 0.0 40.4 1.0 NB A:HEM501 1.9 42.7 1.0 NA A:HEM501 1.9 44.5 1.0 ND A:HEM501 2.0 44.1 1.0 NC A:HEM501 2.1 42.7 1.0 SG A:CYS351 2.3 41.7 1.0 C1B A:HEM501 2.8 42.4 1.0 C4A A:HEM501 2.9 44.0 1.0 C1A A:HEM501 2.9 45.6 1.0 C4B A:HEM501 3.0 42.0 1.0 C4D A:HEM501 3.0 44.6 1.0 C1D A:HEM501 3.1 43.7 1.0 C4C A:HEM501 3.1 42.8 1.0 C1C A:HEM501 3.1 41.9 1.0 CHB A:HEM501 3.2 42.7 1.0 CHA A:HEM501 3.3 44.9 1.0 CHD A:HEM501 3.4 43.1 1.0 CHC A:HEM501 3.5 41.8 1.0 CB A:CYS351 3.5 42.1 1.0 O A:ALA241 3.9 41.2 1.0 C2B A:HEM501 4.1 41.1 1.0 C3A A:HEM501 4.1 44.3 1.0 C3B A:HEM501 4.1 41.0 1.0 C2A A:HEM501 4.2 44.9 1.0 CA A:CYS351 4.2 42.6 1.0 C3D A:HEM501 4.2 44.4 1.0 C2D A:HEM501 4.3 44.2 1.0 CB A:ALA241 4.3 41.2 1.0 C2C A:HEM501 4.4 41.7 1.0 C3C A:HEM501 4.4 42.1 1.0 C A:ALA241 4.6 41.0 1.0 N A:GLY353 4.9 41.5 1.0 CA A:ALA241 4.9 40.7 1.0 C A:CYS351 5.0 42.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:49.5 occ:1.00 FE B:HEM501 0.0 49.5 1.0 NA B:HEM501 1.9 45.3 1.0 NB B:HEM501 2.0 44.4 1.0 ND B:HEM501 2.0 45.3 1.0 NC B:HEM501 2.1 44.2 1.0 SG B:CYS351 2.2 42.8 1.0 C4A B:HEM501 2.8 44.9 1.0 C1B B:HEM501 2.9 44.0 1.0 C1A B:HEM501 3.0 45.4 1.0 C4C B:HEM501 3.0 44.5 1.0 C1D B:HEM501 3.0 45.1 1.0 C4B B:HEM501 3.1 43.7 1.0 C4D B:HEM501 3.1 45.4 1.0 C1C B:HEM501 3.1 43.8 1.0 CHB B:HEM501 3.2 44.1 1.0 CHD B:HEM501 3.4 44.8 1.0 CHA B:HEM501 3.4 45.3 1.0 CB B:CYS351 3.5 43.1 1.0 CHC B:HEM501 3.5 43.4 1.0 O B:ALA241 3.8 43.7 1.0 C3A B:HEM501 4.1 44.9 1.0 C2A B:HEM501 4.2 45.3 1.0 C2B B:HEM501 4.2 43.3 1.0 CA B:CYS351 4.2 43.1 1.0 C3B B:HEM501 4.2 42.9 1.0 C2D B:HEM501 4.2 45.3 1.0 C3D B:HEM501 4.3 45.0 1.0 C3C B:HEM501 4.3 44.2 1.0 C2C B:HEM501 4.3 43.8 1.0 CB B:ALA241 4.3 44.0 1.0 C B:ALA241 4.6 43.6 1.0 N B:GLY353 5.0 41.2 1.0 CA B:ALA241 5.0 43.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:49.8 occ:1.00 FE C:HEM503 0.0 49.8 1.0 NA C:HEM503 1.9 51.7 1.0 ND C:HEM503 2.0 50.6 1.0 NB C:HEM503 2.1 49.6 1.0 SG C:CYS351 2.1 47.3 1.0 NC C:HEM503 2.1 49.1 1.0 C1A C:HEM503 3.0 51.1 1.0 C4A C:HEM503 3.0 51.0 1.0 C4D C:HEM503 3.0 50.5 1.0 C1B C:HEM503 3.0 49.5 1.0 C1D C:HEM503 3.1 50.0 1.0 C4C C:HEM503 3.1 49.1 1.0 C4B C:HEM503 3.1 48.6 1.0 C1C C:HEM503 3.2 48.4 1.0 CHA C:HEM503 3.3 51.0 1.0 CHB C:HEM503 3.3 49.9 1.0 CHD C:HEM503 3.4 49.0 1.0 CB C:CYS351 3.5 47.6 1.0 CHC C:HEM503 3.5 47.9 1.0 CB C:ALA241 4.1 46.7 1.0 CA C:CYS351 4.1 47.1 1.0 C3A C:HEM503 4.2 50.7 1.0 C2A C:HEM503 4.2 50.9 1.0 O C:ALA241 4.2 46.0 1.0 C3D C:HEM503 4.2 49.5 1.0 C2D C:HEM503 4.3 49.9 1.0 C2B C:HEM503 4.3 48.6 1.0 C3B C:HEM503 4.3 47.9 1.0 C3C C:HEM503 4.3 48.9 1.0 C2C C:HEM503 4.4 48.1 1.0 C C:ALA241 4.7 45.5 1.0 N C:GLY353 4.9 46.2 1.0 C C:CYS351 4.9 46.3 1.0 N C:LEU352 4.9 46.4 1.0 OG1 C:THR245 5.0 45.9 1.0 CA C:ALA241 5.0 44.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:47.1 occ:1.00 FE D:HEM501 0.0 47.1 1.0 NA D:HEM501 1.9 51.4 1.0 NB D:HEM501 1.9 48.5 1.0 ND D:HEM501 2.1 51.8 1.0 SG D:CYS351 2.2 49.3 1.0 NC D:HEM501 2.2 49.5 1.0 C4A D:HEM501 2.8 50.3 1.0 C1B D:HEM501 2.9 48.3 1.0 C1A D:HEM501 2.9 52.2 1.0 C4D D:HEM501 3.0 52.7 1.0 C4B D:HEM501 3.0 47.6 1.0 C1D D:HEM501 3.1 52.1 1.0 CHB D:HEM501 3.2 48.9 1.0 C1C D:HEM501 3.2 48.4 1.0 C4C D:HEM501 3.2 49.9 1.0 CHA D:HEM501 3.4 52.9 1.0 CB D:CYS351 3.4 49.7 1.0 CHC D:HEM501 3.5 47.4 1.0 CHD D:HEM501 3.6 51.0 1.0 O D:ALA241 4.0 46.9 1.0 C3A D:HEM501 4.0 50.9 1.0 CA D:CYS351 4.1 50.6 1.0 C2A D:HEM501 4.1 51.7 1.0 C2B D:HEM501 4.1 46.8 1.0 C3B D:HEM501 4.2 46.4 1.0 CB D:ALA241 4.3 48.8 1.0 C3D D:HEM501 4.3 53.3 1.0 C2D D:HEM501 4.3 53.4 1.0 C3C D:HEM501 4.4 49.1 1.0 C2C D:HEM501 4.4 48.4 1.0 C D:ALA241 4.7 46.7 1.0 C D:CYS351 4.9 51.0 1.0 N D:GLY353 4.9 50.5 1.0 N D:LEU352 4.9 51.9 1.0 CA D:ALA241 5.0 46.9 1.0

A.Abdulmughni, I.K.Jozwik, E.Brill, F.Hannemann, A.W.H.Thunnissen, R.Bernhardt. Biochemical and Structural Characterization of CYP109A2, A Vitamin D3 25-Hydroxylase From Bacillus Megaterium. Febs J. V. 284 3881 2017.
ISSN: ISSN 1742-4658
PubMed: 28940959
DOI: 10.1111/FEBS.14276