Iron in PDB 9n2a: Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor and Substrate Bound

The structure of Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor and Substrate Bound, PDB code: 9n2a 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)	17.92 / 2.14
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.089, 112.089, 67.255, 90, 90, 120
R / Rfree (%)	16.6 / 20.1

The binding sites of Iron atom in the Crystal Structure of N-Oxygenase Hrmi with the Diferrous Cofactor and Substrate Bound (pdb code 9n2a). 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 and Substrate Bound, PDB code: 9n2a:
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 and Substrate Bound


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 and Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:34.5 occ:1.00 OE2 A:GLU194 2.0 28.4 1.0 NE2 A:HIS288 2.1 29.8 1.0 O A:HOH556 2.2 33.1 1.0 ND1 A:HIS204 2.3 35.1 1.0 NZ A:LYS403 2.4 31.7 0.9 O A:HOH501 2.5 24.7 1.0 OE1 A:GLU194 2.7 25.5 1.0 CD A:GLU194 2.7 29.7 1.0 CE1 A:HIS288 3.0 33.1 1.0 CD2 A:HIS288 3.1 24.5 1.0 CE1 A:HIS204 3.2 32.1 1.0 CG A:HIS204 3.3 27.8 1.0 CB A:HIS204 3.7 29.6 1.0 O A:HOH512 3.8 27.9 1.0 CE A:LYS403 3.9 43.2 0.9 O A:HOH545 4.0 22.5 1.0 ND1 A:HIS288 4.1 26.5 1.0 CG A:GLU194 4.1 24.3 1.0 CG A:HIS288 4.2 30.1 1.0 NE2 A:HIS204 4.3 34.1 1.0 CD2 A:HIS204 4.4 32.5 1.0 OH A:TYR284 4.4 39.8 1.0 FE A:FE2402 4.4 25.1 1.0 O A:HOH514 4.5 36.8 1.0 CE1 A:TYR284 4.7 36.5 1.0 CD2 A:PHE168 4.8 33.2 1.0 CZ A:TYR284 4.9 38.6 1.0 CD A:LYS403 5.0 38.2 0.9

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


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 and Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:25.1 occ:1.00 OD1 A:ASP292 2.0 26.0 1.0 O A:HOH545 2.1 22.5 1.0 O A:HOH512 2.1 27.9 1.0 ND1 A:HIS295 2.2 19.8 1.0 O A:HOH501 2.2 24.7 1.0 OE2 A:GLU258 2.2 19.7 1.0 CG A:ASP292 3.0 28.6 1.0 CD A:GLU258 3.1 22.2 1.0 CE1 A:HIS295 3.1 23.2 1.0 OE1 A:GLU258 3.2 22.9 1.0 CG A:HIS295 3.3 24.5 1.0 OD2 A:ASP292 3.4 29.3 1.0 CB A:HIS295 3.6 18.7 1.0 OE2 A:GLU194 3.8 28.4 1.0 OD1 A:ASN190 3.9 21.6 1.0 ND2 A:ASN190 4.1 20.1 1.0 NE2 A:HIS295 4.2 22.7 1.0 CG2 A:ILE291 4.3 32.3 1.0 CD2 A:HIS295 4.3 21.9 1.0 CB A:ASP292 4.4 26.6 1.0 CG A:ASN190 4.4 18.9 1.0 FE A:FE2401 4.4 34.5 1.0 CG A:GLU258 4.5 19.5 1.0 CD2 A:HIS288 4.5 24.5 1.0 CA A:ASP292 4.6 28.8 1.0 NZ A:LYS403 4.6 31.7 0.9 CE2 A:PHE168 4.8 31.5 1.0 CD A:GLU194 4.9 29.7 1.0 NE2 A:HIS288 4.9 29.8 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