Iron in PDB 7v4f: 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: 7v4f 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)	26.46 / 1.98
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.049, 82.049, 103.893, 90, 90, 90
R / Rfree (%)	19.1 / 25.1

The binding sites of Iron atom in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction (pdb code 7v4f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction, PDB code: 7v4f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 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:Fe204 b:64.4 occ:1.00 O2 B:CO2203 1.9 34.5 1.0 OG1 B:5KC201 2.3 44.0 1.0 NE2 B:HIS115 2.3 25.6 1.0 OD1 B:ASP117 2.4 34.4 1.0 HG1 B:5KC201 2.6 52.8 1.0 OD2 B:ASP117 2.6 25.4 1.0 CG B:ASP117 2.8 29.8 1.0 CE1 B:HIS115 2.9 22.9 1.0 C B:CO2203 3.0 40.9 1.0 O B:5KC201 3.1 49.4 1.0 CB B:5KC201 3.3 49.3 1.0 CG2 B:5KC201 3.4 41.9 1.0 NE2 B:HIS160 3.5 23.4 1.0 CD2 B:HIS115 3.5 22.6 1.0 CE1 B:HIS160 3.6 21.1 1.0 C B:5KC201 3.7 49.8 1.0 CA B:5KC201 4.0 51.9 1.0 H1 B:5KC201 4.1 61.1 1.0 ND1 B:HIS115 4.1 22.6 1.0 O1 B:CO2203 4.2 40.5 1.0 CB B:ASP117 4.3 25.3 1.0 CG B:HIS115 4.5 20.0 1.0 N B:5KC201 4.6 50.9 1.0 O1 B:SIN202 4.6 36.3 1.0 OXT B:5KC201 4.7 46.7 1.0 CD2 B:HIS160 4.8 22.0 1.0 NAL B:5KC201 4.8 46.7 1.0 CD2 B:TYR112 4.8 28.4 1.0 N B:ASP117 4.9 18.1 1.0 ND1 B:HIS160 4.9 18.5 1.0 C1 B:SIN202 4.9 35.5 1.0 CB B:THR156 4.9 20.6 1.0 CA B:ASP117 5.0 22.0 1.0 CE2 B:TYR112 5.0 29.7 1.0

Iron binding site 2 out of 4 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:Fe205 b:42.5 occ:0.50 OD2 B:ASP92 2.4 22.2 1.0 OE1 B:GLU89 2.4 19.1 1.0 CG B:ASP92 3.4 23.2 1.0 CD B:GLU89 3.6 27.3 1.0 CB B:ASP92 3.9 25.8 1.0 OE2 B:GLU89 4.3 31.6 1.0 CA B:GLU89 4.3 27.0 1.0 OD1 B:ASP92 4.4 25.9 1.0 CB B:GLU89 4.5 26.4 1.0 CG B:GLU89 4.6 30.8 1.0 O B:HOH378 4.8 35.3 1.0 N B:GLU89 5.0 22.1 1.0

Iron binding site 3 out of 4 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 3 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 A:Fe202 b:65.9 occ:1.00 NE2 A:HIS160 2.6 25.5 1.0 OD2 A:ASP117 2.7 40.7 1.0 O1 A:SIN201 2.9 47.0 1.0 OD1 A:ASP117 3.0 39.1 1.0 NE2 A:HIS115 3.0 30.5 1.0 CE1 A:HIS160 3.2 24.3 1.0 CG A:ASP117 3.2 41.6 1.0 CE1 A:HIS115 3.3 23.7 1.0 OH A:TYR112 3.5 32.5 1.0 C1 A:SIN201 3.6 48.0 1.0 CD2 A:HIS160 3.8 22.8 1.0 CZ A:TYR112 3.9 25.8 1.0 O2 A:SIN201 4.0 36.9 1.0 CE1 A:TYR112 4.1 24.2 1.0 CD2 A:HIS115 4.2 27.7 1.0 CB A:THR156 4.4 29.1 1.0 ND1 A:HIS160 4.4 25.6 1.0 CG2 A:THR156 4.4 32.5 1.0 ND1 A:HIS115 4.5 27.8 1.0 C2 A:SIN201 4.5 32.2 1.0 CB A:ASP117 4.7 29.9 1.0 CE2 A:TYR112 4.8 23.0 1.0 CG A:HIS160 4.8 20.6 1.0 OG1 A:THR156 4.9 34.0 1.0 CG A:HIS115 5.0 26.5 1.0

Iron binding site 4 out of 4 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 4 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 A:Fe203 b:33.0 occ:1.00 O A:ASP140 2.4 20.7 1.0 O A:HOH340 2.5 28.7 1.0 O A:HOH336 2.6 32.1 1.0 C A:ASP140 3.5 20.4 1.0 CD A:LYS141 4.0 34.3 1.0 OD2 A:ASP140 4.0 31.4 1.0 CB A:ASP140 4.3 19.8 1.0 CG A:ASP140 4.3 23.1 1.0 NZ A:LYS141 4.3 42.3 1.0 N A:LYS141 4.4 17.7 1.0 CA A:LYS141 4.5 20.2 1.0 O A:HOH351 4.5 37.4 1.0 CA A:ASP140 4.5 23.3 1.0 O A:HIS139 4.6 22.4 1.0 CE A:LYS141 4.7 37.5 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