Iron in PDB 5equ: Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro

The structure of Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro, PDB code: 5equ was solved by B.Selvaraj, Y.Lindqvist, 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)	95.75 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.908, 119.742, 159.447, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.8

The binding sites of Iron atom in the Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro (pdb code 5equ). 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 Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro, PDB code: 5equ:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro


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 Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:26.2 occ:1.00 NE2 A:HIS130 1.9 42.2 1.0 O A:HOH401 2.0 37.7 1.0 NE2 A:HIS213 2.0 40.7 1.0 OD2 A:ASP132 2.0 38.4 1.0 O5 A:AKG301 2.0 26.0 1.0 O2 A:AKG301 2.1 28.8 1.0 C2 A:AKG301 2.7 28.7 1.0 C1 A:AKG301 2.8 28.8 1.0 CE1 A:HIS130 2.8 42.7 1.0 CG A:ASP132 2.8 40.6 1.0 CE1 A:HIS213 2.9 40.1 1.0 OD1 A:ASP132 3.0 41.5 1.0 CD2 A:HIS130 3.1 42.7 1.0 CD2 A:HIS213 3.1 39.9 1.0 ND1 A:HIS130 3.9 43.5 1.0 O1 A:AKG301 4.0 30.3 1.0 ND1 A:HIS213 4.0 38.1 1.0 O A:HOH443 4.1 46.2 1.0 CG A:HIS130 4.1 42.8 1.0 CG A:HIS213 4.2 38.9 1.0 C3 A:AKG301 4.2 28.0 1.0 CB A:ASP132 4.2 40.1 1.0 NE2 A:HIS207 4.3 38.0 1.0 C4 A:AKG301 4.8 28.0 1.0 CE1 A:HIS207 4.9 39.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro


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 Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:25.6 occ:1.00 NE2 B:HIS130 1.8 49.9 1.0 NE2 B:HIS213 2.0 47.6 1.0 O B:HOH414 2.0 43.5 1.0 OD2 B:ASP132 2.1 46.2 1.0 O5 B:AKG301 2.1 26.8 1.0 O1 B:AKG301 2.1 27.3 1.0 CE1 B:HIS130 2.7 52.4 1.0 C2 B:AKG301 2.8 27.8 1.0 C1 B:AKG301 2.8 29.8 1.0 CE1 B:HIS213 2.8 46.4 1.0 CG B:ASP132 2.9 48.0 1.0 CD2 B:HIS130 3.0 50.8 1.0 CD2 B:HIS213 3.1 46.5 1.0 OD1 B:ASP132 3.2 49.4 1.0 ND1 B:HIS130 3.8 51.8 1.0 ND1 B:HIS213 4.0 44.8 1.0 O2 B:AKG301 4.0 29.5 1.0 CG B:HIS130 4.0 50.4 1.0 CG B:HIS213 4.1 44.8 1.0 O B:HOH404 4.2 56.0 1.0 C3 B:AKG301 4.2 27.8 1.0 NE2 B:HIS207 4.3 44.4 1.0 CB B:ASP132 4.4 47.2 1.0 O B:HOH433 4.4 44.7 1.0 C4 B:AKG301 4.8 26.8 1.0 CE1 B:HIS207 4.8 44.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro


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 Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe300 b:23.7 occ:1.00 NE2 C:HIS130 1.8 42.5 1.0 O2 C:AKG301 2.0 20.4 1.0 O C:HOH406 2.0 36.2 1.0 OD2 C:ASP132 2.0 43.1 1.0 NE2 C:HIS213 2.0 43.4 1.0 O5 C:AKG301 2.1 26.2 1.0 CE1 C:HIS130 2.6 45.0 1.0 C1 C:AKG301 2.8 25.1 1.0 C2 C:AKG301 2.8 26.2 1.0 CE1 C:HIS213 2.9 43.2 1.0 CG C:ASP132 3.0 46.1 1.0 CD2 C:HIS130 3.1 43.6 1.0 CD2 C:HIS213 3.1 44.0 1.0 OD1 C:ASP132 3.3 48.1 1.0 ND1 C:HIS130 3.8 45.7 1.0 O C:HOH425 3.9 39.6 1.0 O1 C:AKG301 4.0 26.2 1.0 ND1 C:HIS213 4.0 43.0 1.0 CG C:HIS130 4.1 44.2 1.0 CG C:HIS213 4.1 42.6 1.0 C3 C:AKG301 4.3 25.9 1.0 CB C:ASP132 4.4 44.5 1.0 NE2 C:HIS207 4.4 44.6 1.0 C4 C:AKG301 4.9 25.8 1.0 CE1 C:HIS207 4.9 45.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro


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 Epimerase Snon in Complex with FE3+, Alpha Ketoglutarate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe300 b:24.7 occ:1.00 NE2 D:HIS130 1.8 48.0 1.0 OD2 D:ASP132 2.0 49.1 1.0 O D:HOH404 2.0 46.3 1.0 O5 D:AKG301 2.0 23.8 1.0 NE2 D:HIS213 2.1 48.8 1.0 O1 D:AKG301 2.1 23.7 1.0 CE1 D:HIS130 2.6 49.0 1.0 C2 D:AKG301 2.8 24.6 1.0 C1 D:AKG301 2.8 24.4 1.0 CE1 D:HIS213 2.9 48.4 1.0 CG D:ASP132 2.9 51.6 1.0 CD2 D:HIS130 3.0 48.3 1.0 CD2 D:HIS213 3.1 48.1 1.0 OD1 D:ASP132 3.2 53.2 1.0 ND1 D:HIS130 3.8 49.5 1.0 ND1 D:HIS213 4.0 47.2 1.0 O D:HOH405 4.0 47.0 1.0 CG D:HIS130 4.1 48.4 1.0 O2 D:AKG301 4.1 24.6 1.0 CG D:HIS213 4.1 46.6 1.0 O D:HOH420 4.3 47.5 1.0 C3 D:AKG301 4.3 24.7 1.0 CB D:ASP132 4.3 50.4 1.0 NE2 D:HIS207 4.4 45.2 1.0 C4 D:AKG301 4.9 24.6 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