Iron in PDB 5ep9: Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis

The structure of Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis, PDB code: 5ep9 was solved by B.Selvaraj, Y.Lindqvist, L.Niiranen, V.Siitonen, M.Metsa-Ketela, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.207, 120.557, 102.879, 90.00, 92.54, 90.00
R / Rfree (%)	17.6 / 20.3

The binding sites of Iron atom in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis (pdb code 5ep9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis, PDB code: 5ep9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis


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 the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:26.2 occ:1.00 O5 A:AKG301 1.9 33.1 1.0 OD1 A:ASP132 2.0 29.8 1.0 O1 A:AKG301 2.1 31.0 1.0 O A:HOH423 2.1 24.3 1.0 NE2 A:HIS213 2.1 30.0 1.0 NE2 A:HIS130 2.2 29.4 1.0 C2 A:AKG301 2.7 36.0 1.0 C1 A:AKG301 2.7 33.7 1.0 CE1 A:HIS213 3.0 30.4 1.0 CG A:ASP132 3.0 29.3 1.0 CE1 A:HIS130 3.0 28.6 1.0 CD2 A:HIS213 3.2 28.3 1.0 CD2 A:HIS130 3.2 28.6 1.0 OD2 A:ASP132 3.4 29.6 1.0 O2 A:AKG301 3.9 32.3 1.0 O A:HOH521 4.0 41.5 1.0 O A:HOH524 4.0 46.1 1.0 ND1 A:HIS213 4.2 29.0 1.0 ND1 A:HIS130 4.2 30.5 1.0 NE2 A:HIS207 4.2 28.5 1.0 C3 A:AKG301 4.2 34.6 1.0 O A:HOH429 4.2 24.8 1.0 CG A:HIS213 4.3 27.7 1.0 CG A:HIS130 4.3 29.6 1.0 CB A:ASP132 4.4 30.9 1.0 CE1 A:HIS207 4.8 26.7 1.0 CA A:ASP132 4.9 32.1 1.0 C4 A:AKG301 4.9 35.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis


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 the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:30.0 occ:1.00 O2 B:AKG301 1.9 26.0 1.0 OD1 B:ASP132 2.0 34.2 1.0 O5 B:AKG301 2.1 31.9 1.0 NE2 B:HIS130 2.1 30.7 1.0 NE2 B:HIS213 2.1 34.2 1.0 O B:HOH424 2.1 31.5 1.0 C2 B:AKG301 2.7 33.7 1.0 C1 B:AKG301 2.7 31.1 1.0 CE1 B:HIS213 3.0 32.7 1.0 CE1 B:HIS130 3.0 31.5 1.0 CG B:ASP132 3.0 36.4 1.0 CD2 B:HIS130 3.1 31.7 1.0 CD2 B:HIS213 3.1 33.8 1.0 OD2 B:ASP132 3.4 35.4 1.0 O1 B:AKG301 4.0 29.8 1.0 ND1 B:HIS213 4.1 32.7 1.0 ND1 B:HIS130 4.1 31.3 1.0 NE2 B:HIS207 4.2 32.1 1.0 C3 B:AKG301 4.2 36.2 1.0 CG B:HIS130 4.2 31.6 1.0 O B:HOH465 4.2 32.4 1.0 CG B:HIS213 4.2 33.9 1.0 O B:HOH505 4.3 35.6 1.0 CB B:ASP132 4.4 34.2 1.0 C4 B:AKG301 4.8 36.4 1.0 CE1 B:HIS207 4.8 32.1 1.0 CA B:ASP132 4.8 36.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis


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 the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:25.4 occ:1.00 O5 C:AKG301 1.9 27.7 1.0 OD1 C:ASP132 2.0 28.0 1.0 O2 C:AKG301 2.1 33.5 1.0 NE2 C:HIS213 2.1 30.9 1.0 NE2 C:HIS130 2.1 29.5 1.0 O C:HOH451 2.2 31.0 1.0 C2 C:AKG301 2.6 29.9 1.0 C1 C:AKG301 2.7 31.9 1.0 CG C:ASP132 3.0 30.4 1.0 CE1 C:HIS213 3.0 30.4 1.0 CE1 C:HIS130 3.1 28.8 1.0 CD2 C:HIS130 3.1 28.9 1.0 CD2 C:HIS213 3.2 28.8 1.0 OD2 C:ASP132 3.3 30.7 1.0 O1 C:AKG301 4.0 29.7 1.0 O C:HOH498 4.1 46.7 1.0 C3 C:AKG301 4.1 29.9 1.0 NE2 C:HIS207 4.1 28.2 1.0 O C:HOH500 4.1 46.8 1.0 ND1 C:HIS213 4.2 32.0 1.0 O C:HOH446 4.2 26.4 1.0 ND1 C:HIS130 4.2 29.6 1.0 O C:HOH497 4.2 60.6 1.0 CG C:HIS130 4.2 28.0 1.0 CG C:HIS213 4.3 29.2 1.0 CB C:ASP132 4.4 31.5 1.0 CE1 C:HIS207 4.8 26.3 1.0 CA C:ASP132 4.8 32.3 1.0 C4 C:AKG301 4.9 29.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Non-Heme Alpha Ketoglutarate Dependent Epimerase Snon From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:32.1 occ:1.00 O1 D:AKG301 1.8 22.6 1.0 NE2 D:HIS130 2.0 34.0 1.0 O D:HOH403 2.0 36.6 1.0 OD1 D:ASP132 2.1 34.3 1.0 O5 D:AKG301 2.2 30.8 1.0 NE2 D:HIS213 2.2 37.3 1.0 C1 D:AKG301 2.7 32.6 1.0 C2 D:AKG301 2.8 31.6 1.0 CE1 D:HIS130 3.0 34.1 1.0 CE1 D:HIS213 3.0 35.8 1.0 CG D:ASP132 3.0 33.2 1.0 CD2 D:HIS130 3.0 35.9 1.0 CD2 D:HIS213 3.2 36.3 1.0 OD2 D:ASP132 3.4 34.5 1.0 O2 D:AKG301 4.0 35.5 1.0 O D:HOH434 4.1 40.1 1.0 ND1 D:HIS130 4.1 35.5 1.0 CG D:HIS130 4.1 35.4 1.0 ND1 D:HIS213 4.2 37.2 1.0 NE2 D:HIS207 4.2 37.5 1.0 O D:HOH467 4.3 58.8 1.0 CG D:HIS213 4.3 35.6 1.0 C3 D:AKG301 4.3 35.0 1.0 CB D:ASP132 4.4 35.2 1.0 CE1 D:HIS207 4.8 36.8 1.0 CA D:ASP132 4.9 36.2 1.0 C4 D:AKG301 4.9 35.9 1.0 N D:ASP132 5.0 35.8 1.0

V.Siitonen, B.Selvaraj, L.Niiranen, Y.Lindqvist, G.Schneider, M.Metsa-Ketela. Divergent Non-Heme Iron Enzymes in the Nogalamycin Biosynthetic Pathway. Proc.Natl.Acad.Sci.Usa V. 113 5251 2016.
ISSN: ESSN 1091-6490
PubMed: 27114534
DOI: 10.1073/PNAS.1525034113