Iron in PDB 9dqq: Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate

The structure of Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate, PDB code: 9dqq was solved by Y.-C.Zheng, W.-C.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.68 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.871, 43.616, 126.201, 90, 106.95, 90
R / Rfree (%)	20.7 / 28

The binding sites of Iron atom in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate (pdb code 9dqq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate, PDB code: 9dqq:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:37.5 occ:1.00 NE2 A:HIS210 2.1 34.2 1.0 O A:HOH423 2.1 39.0 1.0 OD1 A:ASP159 2.2 43.9 1.0 NE2 A:HIS157 2.2 45.7 1.0 O5 A:AKG301 2.4 47.5 1.0 O2 A:AKG301 2.7 61.4 1.0 CG A:ASP159 2.9 32.0 1.0 OD2 A:ASP159 3.0 31.2 1.0 CE1 A:HIS210 3.0 40.1 1.0 CE1 A:HIS157 3.1 43.9 1.0 CD2 A:HIS210 3.1 36.8 1.0 CD2 A:HIS157 3.1 41.9 1.0 C2 A:AKG301 3.2 58.0 1.0 C1 A:AKG301 3.4 65.1 1.0 ND1 A:HIS210 4.2 35.1 1.0 ND1 A:HIS157 4.2 41.5 1.0 CG A:HIS157 4.2 46.4 1.0 CG A:HIS210 4.2 39.8 1.0 CB A:ASP159 4.4 28.8 1.0 C3 A:AKG301 4.7 50.7 1.0 O1 A:AKG301 4.7 61.0 1.0 CA A:ASP159 4.9 37.5 1.0 N A:ASP159 4.9 40.2 1.0 CZ2 A:TRP203 5.0 29.7 1.0 O A:HOH477 5.0 38.1 1.0 O A:HOH405 5.0 56.6 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:118.8 occ:1.00 NH1 B:ARG67 2.0 40.3 0.5 OG1 A:THR195 2.5 40.0 1.0 OD2 A:ASP199 2.5 38.8 1.0 O B:ARG67 2.9 45.4 0.5 O B:ARG67 2.9 44.3 0.5 CZ B:ARG67 3.2 44.6 0.5 CG A:ASP199 3.5 27.4 1.0 O A:CYS193 3.5 29.3 1.0 CB A:THR195 3.8 38.7 1.0 N A:THR195 3.8 27.0 1.0 NH2 B:ARG67 3.8 37.6 0.5 OD1 A:ASP199 3.9 32.1 1.0 C B:ARG67 4.1 38.7 0.5 C B:ARG67 4.1 37.6 0.5 CG2 A:THR195 4.2 41.8 1.0 N A:GLU196 4.2 34.2 1.0 CA A:THR195 4.3 30.2 1.0 NE B:ARG67 4.3 47.4 0.5 CA B:THR68 4.4 33.9 1.0 CD B:ARG67 4.6 44.8 0.5 CB A:ASP199 4.7 35.6 1.0 C A:CYS193 4.7 29.6 1.0 N B:THR68 4.7 33.1 1.0 C A:THR195 4.7 27.1 1.0 CG A:GLU196 4.7 46.7 1.0 C A:LEU194 4.8 27.6 1.0 C B:THR68 4.9 40.2 1.0 CA A:LEU194 4.9 29.5 1.0 O B:THR68 4.9 28.4 1.0 CB A:GLU196 5.0 31.6 1.0 CB A:PRO18 5.0 36.4 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:69.8 occ:1.00 O5 B:AKG301 2.1 68.0 1.0 OD1 B:ASP159 2.2 69.3 1.0 NE2 B:HIS210 2.2 55.7 1.0 O2 B:AKG301 2.5 62.4 1.0 OD2 B:ASP159 2.6 67.2 1.0 CG B:ASP159 2.8 66.6 1.0 C2 B:AKG301 2.9 78.5 1.0 NE2 B:HIS157 2.9 68.7 1.0 CE1 B:HIS210 3.0 56.1 1.0 CE1 B:HIS157 3.1 73.2 1.0 C1 B:AKG301 3.1 74.4 1.0 CD2 B:HIS210 3.3 55.7 1.0 CD2 B:HIS157 4.1 68.8 1.0 ND1 B:HIS210 4.2 54.8 1.0 ND1 B:HIS157 4.2 75.5 1.0 CB B:ASP159 4.3 66.7 1.0 CG B:HIS210 4.3 61.1 1.0 O1 B:AKG301 4.4 69.5 1.0 C3 B:AKG301 4.4 73.1 1.0 OE1 B:GLU154 4.7 91.0 1.0 CG B:HIS157 4.7 69.5 1.0 CA B:ASP159 4.9 67.7 1.0 N B:ASP159 5.0 72.6 1.0 C4 B:AKG301 5.0 66.0 1.0

Y.C.Zheng, X.Li, L.Cha, J.C.Paris, C.Michael, R.Ushimaru, Y.Ogasawara, I.Abe, Y.Guo, W.C.Chang. Comparison of A Nonheme Iron Cyclopropanase with A Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 39901767
DOI: 10.1021/JACS.4C17741