Iron in PDB 7v4m: Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction

The structure of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction, PDB code: 7v4m was solved by T.L.Li, M.Z.Saeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.184, 77.568, 68.118, 90, 90, 90
R / Rfree (%)	18.7 / 23.3

The structure of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Iron atom in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction (pdb code 7v4m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction, PDB code: 7v4m:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:22.8 occ:1.00 O5 B:AKG301 2.0 21.3 1.0 OD2 B:ASP117 2.1 22.1 1.0 O B:HOH464 2.1 22.0 1.0 O1 B:AKG301 2.1 23.6 1.0 NE2 B:HIS115 2.3 16.0 1.0 NE2 B:HIS160 2.3 13.9 1.0 C2 B:AKG301 2.7 23.2 1.0 C1 B:AKG301 2.8 25.0 1.0 CG B:ASP117 3.0 23.5 1.0 CE1 B:HIS160 3.1 13.7 1.0 CE1 B:HIS115 3.1 16.0 1.0 OD1 B:ASP117 3.3 27.4 1.0 CD2 B:HIS115 3.3 18.6 1.0 CD2 B:HIS160 3.5 9.1 1.0 NH2 B:ARG121 4.0 27.7 1.0 O2 B:AKG301 4.0 20.2 1.0 C3 B:AKG301 4.2 21.3 1.0 ND1 B:HIS115 4.2 15.3 1.0 ND1 B:HIS160 4.3 10.8 1.0 CG B:HIS115 4.4 17.3 1.0 CB B:ASP117 4.4 20.8 1.0 CG2 B:THR156 4.4 14.6 1.0 CB B:THR156 4.4 14.8 1.0 CG B:HIS160 4.5 9.9 1.0 CZ B:ARG121 4.7 31.9 1.0 C4 B:AKG301 5.0 23.4 1.0

Iron binding site 2 out of 2 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:22.7 occ:1.00 O B:HOH422 2.9 9.9 1.0 O B:HOH480 3.1 9.3 1.0 N B:ILE145 3.3 10.9 1.0 CA B:ARG133 3.6 11.1 1.0 O B:ALA132 3.7 8.5 1.0 C B:ARG133 3.7 11.1 1.0 C B:ALA132 3.7 10.3 1.0 N B:ARG133 3.7 10.8 1.0 N B:PHE134 3.8 8.5 1.0 CB B:ILE145 3.9 11.2 1.0 CA B:HIS144 4.0 12.6 1.0 O B:LEU143 4.0 16.4 1.0 CE1 B:HIS172 4.0 8.0 1.0 ND1 B:HIS144 4.1 10.1 1.0 CB B:ALA132 4.1 9.4 1.0 CA B:ILE145 4.1 8.6 1.0 C B:HIS144 4.1 13.0 1.0 CG1 B:ILE145 4.1 11.6 1.0 O B:ARG133 4.2 7.7 1.0 NE2 B:HIS172 4.4 7.0 1.0 CD1 B:ILE145 4.4 14.6 1.0 O B:ILE145 4.4 9.1 1.0 CB B:PHE134 4.4 12.2 1.0 CA B:ALA132 4.6 9.6 1.0 CA B:PHE134 4.7 10.4 1.0 C B:ILE145 4.7 8.1 1.0 CE1 B:HIS144 4.8 9.8 1.0 CG B:HIS144 4.8 9.1 1.0 C B:LEU143 4.8 14.1 1.0 CB B:HIS144 4.9 11.1 1.0 N B:HIS144 4.9 10.4 1.0 OG1 B:THR128 4.9 11.7 1.0 CD B:ARG170 5.0 10.3 1.0

S.M.Zadeh, M.H.Chen, Z.C.Wang, E.K.Astani, I.W.Lo, K.H.Lin, N.S.Hsu, K.Adhikari, S.Y.Lyu, H.Y.Tsai, Y.Terasawa, M.Yabe, K.Yamamoto, S.Ichikawa, T.L.Li. Beta-Hydroxylation of Alpha-Amino-Beta-Hydroxylbutanoyl-Glycyluridine Catalyzed By A Nonheme Hydroxylase Ensures the Maturation of Caprazamycin Commun Chem V. 5 87 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00703-6