Nickel in PDB 5erl: Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro

The structure of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro, PDB code: 5erl 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)	48.80 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.324, 117.784, 160.964, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.4

The binding sites of Nickel atom in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro (pdb code 5erl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro, PDB code: 5erl:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni300 b:12.0 occ:1.00 O2 A:SIN301 1.9 12.3 1.0 OD2 A:ASP132 1.9 50.1 1.0 NE2 A:HIS130 2.0 48.7 1.0 O A:HOH401 2.0 35.0 1.0 NE2 A:HIS213 2.1 46.2 1.0 CG A:ASP132 2.7 50.1 1.0 C1 A:SIN301 2.7 13.9 1.0 CE1 A:HIS130 2.7 48.5 1.0 OD1 A:ASP132 2.8 50.2 1.0 CE1 A:HIS213 3.0 46.2 1.0 O1 A:SIN301 3.1 11.8 1.0 CD2 A:HIS130 3.1 49.7 1.0 CD2 A:HIS213 3.2 45.6 1.0 ND1 A:HIS130 3.9 49.6 1.0 C2 A:SIN301 4.1 14.0 1.0 CB A:ASP132 4.1 50.7 1.0 CG A:HIS130 4.1 50.5 1.0 ND1 A:HIS213 4.2 46.5 1.0 O A:HOH407 4.3 40.4 1.0 CG A:HIS213 4.3 45.9 1.0 NE2 A:HIS207 4.3 48.3 1.0 C3 A:SIN301 4.6 13.7 1.0 CE1 A:HIS207 4.8 49.1 1.0 CA A:ASP132 5.0 52.1 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni300 b:18.2 occ:1.00 O1 B:SIN301 1.9 14.8 1.0 O B:HOH401 1.9 52.4 1.0 OD2 B:ASP132 2.0 72.1 1.0 NE2 B:HIS130 2.0 67.5 1.0 NE2 B:HIS213 2.0 64.2 1.0 CE1 B:HIS130 2.7 66.8 1.0 CG B:ASP132 2.8 72.4 1.0 C1 B:SIN301 2.9 13.9 1.0 CE1 B:HIS213 2.9 62.6 1.0 OD1 B:ASP132 3.0 73.5 1.0 CD2 B:HIS213 3.2 62.3 1.0 CD2 B:HIS130 3.2 67.8 1.0 O2 B:SIN301 3.3 13.4 1.0 ND1 B:HIS130 3.9 66.7 1.0 ND1 B:HIS213 4.1 61.0 1.0 CB B:ASP132 4.2 72.2 1.0 C2 B:SIN301 4.2 13.5 1.0 CG B:HIS130 4.2 66.9 1.0 CG B:HIS213 4.2 60.3 1.0 NE2 B:HIS207 4.2 63.3 1.0 C3 B:SIN301 4.6 13.2 1.0 CE1 B:HIS207 4.7 63.9 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni300 b:16.2 occ:1.00 O2 C:SIN301 1.9 14.1 1.0 OD2 C:ASP132 1.9 77.5 1.0 O C:HOH401 2.0 49.9 1.0 NE2 C:HIS213 2.0 69.4 1.0 NE2 C:HIS130 2.0 74.9 1.0 C1 C:SIN301 2.7 13.0 1.0 CG C:ASP132 2.7 78.9 1.0 CE1 C:HIS130 2.8 75.4 1.0 CE1 C:HIS213 2.8 68.0 1.0 O1 C:SIN301 2.9 11.4 1.0 OD1 C:ASP132 2.9 81.9 1.0 CD2 C:HIS213 3.2 68.6 1.0 CD2 C:HIS130 3.2 75.7 1.0 ND1 C:HIS130 3.9 76.4 1.0 ND1 C:HIS213 4.0 67.1 1.0 C2 C:SIN301 4.0 13.1 1.0 CB C:ASP132 4.1 76.4 1.0 CG C:HIS130 4.2 76.6 1.0 CG C:HIS213 4.2 67.1 1.0 NE2 C:HIS207 4.2 62.1 1.0 C3 C:SIN301 4.5 13.1 1.0 CE1 C:HIS207 4.8 62.5 1.0 CA C:ASP132 4.9 76.6 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni300 b:17.2 occ:1.00 O1 D:SIN301 1.9 14.7 1.0 OD2 D:ASP132 1.9 86.8 1.0 NE2 D:HIS213 2.0 79.2 1.0 O D:HOH403 2.0 59.6 1.0 NE2 D:HIS130 2.1 83.9 1.0 CG D:ASP132 2.7 87.9 1.0 C1 D:SIN301 2.8 13.4 1.0 CE1 D:HIS130 2.8 84.3 1.0 CE1 D:HIS213 2.8 76.4 1.0 O2 D:SIN301 2.9 12.8 1.0 OD1 D:ASP132 3.0 90.1 1.0 CD2 D:HIS213 3.1 78.2 1.0 CD2 D:HIS130 3.3 82.9 1.0 ND1 D:HIS130 4.0 83.9 1.0 ND1 D:HIS213 4.0 74.3 1.0 NE2 D:HIS207 4.1 78.3 1.0 CB D:ASP132 4.1 85.1 1.0 CG D:HIS213 4.2 75.1 1.0 C2 D:SIN301 4.2 12.9 1.0 CG D:HIS130 4.2 83.1 1.0 C3 D:SIN301 4.6 12.6 1.0 CE1 D:HIS207 4.6 80.1 1.0 O D:HOH401 5.0 50.5 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