Magnesium in PDB 5epa: Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis

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

Resolution Low / High (Å)	47.70 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.009, 83.151, 271.677, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.8

The structure of Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

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

Magnesium binding site 1 out of 3 in the Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:30.0 occ:1.00 O B:HOH456 1.9 22.0 1.0 O B:HOH407 2.1 27.9 1.0 O B:HOH513 2.1 25.9 1.0 OD2 B:ASP62 4.0 61.1 1.0 OD1 B:ASP62 4.1 58.4 1.0 OE2 B:GLU61 4.2 74.9 1.0 CG B:ASP62 4.5 58.8 1.0 CD B:GLU61 4.7 71.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:36.1 occ:1.00 O D:HOH424 1.9 35.9 1.0 OE1 D:GLU50 4.0 53.8 1.0 O D:GLU50 4.2 36.4 1.0 O D:HOH498 4.4 27.7 1.0 O D:LEU49 4.5 29.8 1.0 CA D:GLU50 4.5 37.0 1.0 NH1 D:ARG54 4.8 33.2 1.0 C D:GLU50 4.8 37.3 1.0 CD D:GLU50 5.0 50.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Non-Heme Alpha Ketoglutarate Dependent Carbocyclase Snok From Nogalamycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:41.3 occ:1.00 O D:HOH415 1.9 30.0 1.0 O D:HOH458 2.1 28.2 1.0 O D:HOH432 2.2 40.2 1.0 OD2 D:ASP62 4.0 36.4 1.0 OE2 D:GLU61 4.1 35.9 1.0 OD1 D:ASP62 4.2 35.0 1.0 CG D:ASP62 4.5 35.0 1.0 CD D:GLU61 4.6 35.3 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