Sodium in PDB 5nci: Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine

The structure of Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine, PDB code: 5nci was solved by P.Lukat, W.Blankenfeldt, R.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.97 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.720, 56.061, 73.534, 90.00, 111.95, 90.00
R / Rfree (%)	14 / 16.9

The structure of Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Sodium atom in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine (pdb code 5nci). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine, PDB code: 5nci:

Sodium binding site 1 out of 1 in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:42.6 occ:1.00 O B:HOH401 2.4 39.0 1.0 O B:GLY259 2.7 44.1 1.0 OG B:SER74 2.9 37.9 1.0 HA B:SER74 2.9 31.0 1.0 O B:HOH529 3.0 43.1 1.0 HH11 B:ARG76 3.0 36.6 1.0 O B:ARG257 3.1 31.8 1.0 HB2 B:SER74 3.2 38.9 1.0 HG B:SER74 3.2 45.5 1.0 CB B:SER74 3.4 32.4 1.0 HA B:SER258 3.5 47.1 1.0 H B:GLY259 3.5 49.5 1.0 N B:GLY259 3.6 41.2 1.0 CA B:SER74 3.6 25.8 1.0 H B:ASP75 3.7 35.8 1.0 HD23 B:LEU261 3.7 37.3 1.0 C B:GLY259 3.7 42.2 1.0 HD21 B:LEU261 3.8 37.3 1.0 HE B:ARG76 3.8 32.4 1.0 C B:SER258 3.8 40.7 1.0 NH1 B:ARG76 3.9 30.5 1.0 C B:ARG257 3.9 34.0 1.0 CA B:SER258 4.0 39.3 1.0 OD1 B:ASP75 4.1 58.9 1.0 CD2 B:LEU261 4.2 31.1 1.0 CA B:GLY259 4.2 43.1 1.0 N B:ASP75 4.3 29.8 1.0 HB3 B:SER74 4.3 38.9 1.0 HB2 B:ARG257 4.4 50.4 1.0 N B:SER258 4.4 36.1 1.0 O B:SER258 4.4 45.2 1.0 HH12 B:ARG76 4.4 36.6 1.0 C B:SER74 4.5 26.4 1.0 NE B:ARG76 4.5 27.0 1.0 H B:ARG76 4.5 30.1 1.0 HA3 B:GLY259 4.6 51.7 1.0 N B:SER74 4.7 23.6 1.0 CZ B:ARG76 4.7 30.1 1.0 O B:HOH470 4.7 41.0 1.0 HE1 B:PHE23 4.8 28.7 1.0 HD22 B:LEU261 4.8 37.3 1.0 N B:PRO260 4.9 40.8 1.0 O B:GLN70 5.0 22.1 1.0 CB B:ARG257 5.0 42.0 1.0 HA B:PRO260 5.0 45.4 1.0 HB3 B:ARG257 5.0 50.4 1.0

P.Lukat, Y.Katsuyama, S.Wenzel, T.Binz, C.Konig, W.Blankenfeldt, M.Bronstrup, R.Muller. Biosynthesis of Methyl-Proline Containing Griselimycins, Natural Products with Anti-Tuberculosis Activity. Chem Sci V. 8 7521 2017.
ISSN: ISSN 2041-6520
PubMed: 29163906
DOI: 10.1039/C7SC02622F