Iron in PDB 9n1e: Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded

The structure of Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded, PDB code: 9n1e was solved by S.S.Skirboll, H.N.Phan, P.D.Swartz, T.M.Makris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.65 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.814, 112.814, 67.882, 90, 90, 120
R / Rfree (%)	18.1 / 21.4

The binding sites of Iron atom in the Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded (pdb code 9n1e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded, PDB code: 9n1e:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded


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 N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:31.3 occ:0.62 OE2 A:GLU194 2.0 30.2 1.0 O A:HOH604 2.0 30.6 0.6 NE2 A:HIS288 2.1 44.8 1.0 ND1 A:HIS204 2.1 28.6 1.0 O A:HOH518 2.2 27.5 0.7 CD A:GLU194 2.7 21.9 1.0 OE1 A:GLU194 2.8 26.2 1.0 CE1 A:HIS204 2.9 31.1 1.0 CD2 A:HIS288 3.0 37.9 1.0 CE1 A:HIS288 3.1 47.6 1.0 CG A:HIS204 3.3 25.1 1.0 O A:HOH557 3.5 37.0 0.7 FE A:FE402 3.7 27.7 0.6 CB A:HIS204 3.8 26.5 1.0 O A:HOH523 3.8 23.8 0.8 NE2 A:HIS204 4.1 31.9 1.0 ND1 A:HIS288 4.1 40.7 1.0 CG A:HIS288 4.1 38.6 1.0 CG A:GLU194 4.2 16.9 1.0 CD2 A:HIS204 4.3 23.9 1.0 O A:HOH614 4.5 29.9 1.0 OD1 A:ASP292 4.6 39.6 1.0 OH A:TYR284 4.8 44.1 1.0 CD2 A:PHE168 4.8 27.1 1.0 CE1 A:TYR284 4.8 40.8 1.0 CB A:GLU194 5.0 17.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded


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 N-Oxygenase Hrmi with the Diferric Cofactor Partially Loaded within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:27.7 occ:0.62 OD1 A:ASP292 2.1 39.6 1.0 O A:HOH523 2.1 23.8 0.8 O A:HOH518 2.1 27.5 0.7 O A:HOH557 2.2 37.0 0.7 ND1 A:HIS295 2.3 33.9 1.0 OE2 A:GLU258 2.4 28.5 1.0 CG A:ASP292 3.1 39.3 1.0 CE1 A:HIS295 3.1 36.0 1.0 CD A:GLU258 3.3 36.1 1.0 CG A:HIS295 3.4 36.2 1.0 OE1 A:GLU258 3.4 32.4 1.0 OE2 A:GLU194 3.5 30.2 1.0 OD2 A:ASP292 3.5 39.4 1.0 FE A:FE401 3.7 31.3 0.6 OD1 A:ASN190 3.8 29.2 1.0 CB A:HIS295 3.8 28.7 1.0 NE2 A:HIS295 4.3 34.5 1.0 CE2 A:PHE168 4.3 38.7 1.0 ND2 A:ASN190 4.3 25.3 1.0 CB A:ASP292 4.4 29.9 1.0 CD2 A:HIS295 4.4 33.4 1.0 CG A:ASN190 4.4 29.3 1.0 CD2 A:HIS288 4.5 37.9 1.0 CA A:ASP292 4.6 35.7 1.0 CG2 A:ILE291 4.6 37.8 1.0 CD A:GLU194 4.6 21.9 1.0 CG A:GLU258 4.7 25.9 1.0 NE2 A:HIS288 4.8 44.8 1.0 CD2 A:PHE168 4.9 27.1 1.0

S.S.Skirboll, M.Gangopadhyay, H.N.Phan, J.Hartsell, A.Mudireddy, D.Hilovsky, P.D.Swartz, X.Liu, Y.Guo, T.M.Makris. The Heme Oxygenase-Like Diiron Enzyme Hrmi Reveals Altered Regulatory Mechanisms For Dioxygen Activation and Substrate N-Oxygenation. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 40774922
DOI: 10.1021/JACS.5C08814