Iron in PDB 9n1x: Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor

The structure of Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor, PDB code: 9n1x 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)	18.06 / 2.14
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.639, 112.639, 68.215, 90, 90, 120
R / Rfree (%)	16.9 / 22

The binding sites of Iron atom in the Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor (pdb code 9n1x). 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 Diferrous Cofactor, PDB code: 9n1x:
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 Diferrous Cofactor


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 Diferrous Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:34.3 occ:1.00 O A:HOH664 1.9 29.0 0.8 OE2 A:GLU194 2.0 32.7 1.0 NE2 A:HIS288 2.2 31.8 1.0 O A:HOH616 2.2 35.5 1.0 ND1 A:HIS204 2.3 37.2 1.0 CD A:GLU194 2.7 30.8 1.0 OE1 A:GLU194 2.7 29.7 1.0 O A:HOH669 3.0 38.5 1.0 CE1 A:HIS204 3.0 36.9 1.0 CD2 A:HIS288 3.1 27.3 1.0 CE1 A:HIS288 3.2 37.2 1.0 CG A:HIS204 3.3 34.8 1.0 CB A:HIS204 3.7 28.7 1.0 O A:HOH512 4.0 31.4 1.0 CG A:GLU194 4.2 24.7 1.0 NE2 A:HIS204 4.2 37.8 1.0 O A:HOH513 4.2 23.2 1.0 CG A:HIS288 4.3 29.7 1.0 ND1 A:HIS288 4.3 31.1 1.0 CD2 A:HIS204 4.3 34.9 1.0 O A:HOH592 4.3 31.5 1.0 OH A:TYR284 4.5 34.4 1.0 FE A:FE2402 4.5 27.4 1.0 CD2 A:PHE168 4.6 32.5 0.5 CD2 A:PHE168 4.7 30.5 0.6 CE1 A:TYR284 4.9 35.9 1.0 CG A:PHE168 5.0 28.1 0.6

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


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 Diferrous Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:27.4 occ:1.00 O A:HOH512 2.1 31.4 1.0 OD1 A:ASP292 2.1 27.4 1.0 O A:HOH513 2.1 23.2 1.0 OE2 A:GLU258 2.2 19.6 1.0 O A:HOH669 2.2 38.5 1.0 ND1 A:HIS295 2.2 24.8 1.0 CD A:GLU258 3.1 26.4 1.0 CE1 A:HIS295 3.1 25.8 1.0 CG A:ASP292 3.1 27.6 1.0 OE1 A:GLU258 3.3 24.1 1.0 CG A:HIS295 3.3 27.1 1.0 OD2 A:ASP292 3.5 29.0 1.0 CB A:HIS295 3.7 20.0 1.0 OE2 A:GLU194 3.8 32.7 1.0 OD1 A:ASN190 3.8 20.7 1.0 ND2 A:ASN190 4.0 18.2 1.0 NE2 A:HIS295 4.3 23.7 1.0 O A:HOH664 4.3 29.0 0.8 CG A:ASN190 4.3 21.2 1.0 CD2 A:HIS295 4.4 22.7 1.0 CB A:ASP292 4.4 24.1 1.0 CE2 A:PHE168 4.5 36.0 0.6 CG A:GLU258 4.5 18.8 1.0 FE A:FE2401 4.5 34.3 1.0 CG2 A:ILE291 4.7 33.1 1.0 CD2 A:HIS288 4.7 27.3 1.0 CA A:ASP292 4.7 28.7 1.0 CD A:GLU194 4.9 30.8 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