Manganese in PDB 9dq1: Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine, PDB code: 9dq1 was solved by Y.-C.Zheng, P.Swartz, W.-C.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.49 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.342, 74.971, 87.295, 90, 90.03, 90
R / Rfree (%)	17.5 / 20.4

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine also contains other interesting chemical elements:

Iodine

(I)

7 atoms

The binding sites of Manganese atom in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine (pdb code 9dq1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine, PDB code: 9dq1:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:9.9 occ:1.00 O2 A:AKG302 1.6 17.4 1.0 O5 A:AKG302 2.2 11.7 1.0 OD1 A:ASP135 2.2 14.7 1.0 NE2 A:HIS186 2.2 7.5 1.0 C1 A:AKG302 2.2 17.0 1.0 NE2 A:HIS133 2.3 9.1 1.0 O A:HOH403 2.4 17.8 1.0 OD2 A:ASP135 2.5 35.2 1.0 C2 A:AKG302 2.6 6.7 1.0 CG A:ASP135 2.7 13.5 1.0 CE1 A:HIS186 3.1 9.1 1.0 CE1 A:HIS133 3.2 7.8 1.0 CD2 A:HIS186 3.2 5.8 1.0 CD2 A:HIS133 3.3 9.9 1.0 O1 A:AKG302 3.5 12.1 1.0 C3 A:AKG302 4.1 9.5 1.0 CB A:ASP135 4.2 9.1 1.0 ND1 A:HIS186 4.3 6.3 1.0 CG A:HIS186 4.3 6.2 1.0 ND1 A:HIS133 4.4 8.1 1.0 CG A:HIS133 4.4 7.7 1.0 CG A:6HN303 4.4 13.4 1.0 N A:6HN303 4.5 12.7 1.0 CA A:ASP135 4.8 9.7 1.0 N A:ASP135 4.9 7.1 1.0 C4 A:AKG302 4.9 11.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:11.3 occ:1.00 O2 B:AKG302 2.1 16.9 1.0 OD1 B:ASP135 2.2 21.5 1.0 NE2 B:HIS133 2.3 12.3 1.0 O5 B:AKG302 2.3 10.7 1.0 NE2 B:HIS186 2.3 13.1 1.0 OD2 B:ASP135 2.4 30.5 1.0 O B:HOH402 2.4 19.2 1.0 CG B:ASP135 2.7 11.8 1.0 C1 B:AKG302 2.9 18.2 1.0 C2 B:AKG302 3.0 14.2 1.0 CE1 B:HIS133 3.2 8.5 1.0 CE1 B:HIS186 3.2 13.0 1.0 CD2 B:HIS133 3.2 8.7 1.0 CD2 B:HIS186 3.3 9.6 1.0 O1 B:AKG302 4.2 11.8 1.0 CB B:ASP135 4.2 8.7 1.0 ND1 B:HIS133 4.3 6.7 1.0 ND1 B:HIS186 4.3 10.5 1.0 CG B:HIS133 4.4 8.3 1.0 CG B:6HN303 4.4 14.1 1.0 CG B:HIS186 4.4 9.7 1.0 N B:6HN303 4.4 11.7 1.0 C3 B:AKG302 4.5 9.4 1.0 CA B:ASP135 4.8 11.2 1.0 N B:ASP135 4.9 9.5 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