Cobalt 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:

Sodium

(Na)

1 atom

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine, PDB code: 5nci:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 A:Co301 b:17.3 occ:1.00 OD1 A:ASP112 2.0 18.4 1.0 NE2 A:HIS210 2.1 15.5 1.0 O1 A:AKG302 2.1 22.0 1.0 NE2 A:HIS110 2.1 16.6 1.0 O5 A:AKG302 2.2 20.1 1.0 C1 A:AKG302 2.8 23.5 1.0 C2 A:AKG302 2.9 20.9 1.0 CE1 A:HIS210 2.9 16.9 1.0 CG A:ASP112 3.0 18.0 1.0 CE1 A:HIS110 3.0 17.4 1.0 HE1 A:HIS210 3.1 20.3 1.0 HE1 A:HIS110 3.1 20.8 1.0 CD2 A:HIS210 3.1 16.1 1.0 CD2 A:HIS110 3.1 16.7 1.0 OD2 A:ASP112 3.2 18.2 1.0 HD2 A:HIS210 3.4 19.3 1.0 HD2 A:HIS110 3.4 20.0 1.0 HD21 A:LEU303 3.4 25.3 1.0 HD11 A:LEU303 3.4 23.3 1.0 HE2 A:PHE204 4.0 21.0 1.0 ND1 A:HIS210 4.1 15.5 1.0 O2 A:AKG302 4.1 25.0 1.0 ND1 A:HIS110 4.1 16.9 1.0 O A:HOH517 4.1 24.8 1.0 CG A:HIS210 4.2 13.4 1.0 CG A:HIS110 4.2 14.6 1.0 CD2 A:LEU303 4.3 21.1 1.0 CD1 A:LEU303 4.4 19.4 1.0 C3 A:AKG302 4.4 19.8 1.0 CB A:ASP112 4.4 16.4 1.0 HA A:ASP112 4.5 17.8 1.0 HG3 A:PRO172 4.5 27.6 1.0 HG A:LEU303 4.6 24.0 1.0 CG A:LEU303 4.7 20.0 1.0 H31 A:AKG302 4.7 23.7 1.0 HG2 A:PRO172 4.7 27.6 1.0 H42 A:AKG302 4.8 23.0 1.0 HZ A:PHE204 4.8 18.0 1.0 HD22 A:LEU303 4.8 25.3 1.0 CA A:ASP112 4.8 14.8 1.0 HD1 A:HIS210 4.8 18.6 1.0 HD13 A:LEU303 4.8 23.3 1.0 H A:ASP112 4.8 16.1 1.0 N A:ASP112 4.8 13.4 1.0 HB3 A:ASP112 4.8 19.7 1.0 HD1 A:HIS110 4.9 20.3 1.0 CE2 A:PHE204 4.9 17.5 1.0 HD23 A:LEU303 4.9 25.3 1.0 H32 A:AKG302 4.9 23.7 1.0 HB2 A:ASP112 4.9 19.7 1.0 HD12 A:LEU303 5.0 23.3 1.0 H41 A:AKG302 5.0 23.0 1.0 C4 A:AKG302 5.0 19.2 1.0

Cobalt binding site 2 out of 2 in the Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Grie in Complex with Cobalt, Alpha-Ketoglutarate and L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:20.9 occ:1.00 OD1 B:ASP112 2.0 18.8 1.0 NE2 B:HIS110 2.1 20.8 1.0 O2 B:AKG302 2.1 22.8 1.0 NE2 B:HIS210 2.1 18.0 1.0 O5 B:AKG302 2.1 22.3 1.0 C1 B:AKG302 2.8 25.0 1.0 C2 B:AKG302 2.8 24.8 1.0 CE1 B:HIS210 2.9 18.7 1.0 CE1 B:HIS110 2.9 19.6 1.0 HE1 B:HIS210 2.9 22.4 1.0 HE1 B:HIS110 3.0 23.5 1.0 CG B:ASP112 3.0 19.2 1.0 CD2 B:HIS110 3.2 19.4 1.0 OD2 B:ASP112 3.2 20.0 1.0 CD2 B:HIS210 3.2 18.6 1.0 HD21 B:LEU303 3.4 27.2 1.0 HD2 B:HIS110 3.5 23.3 1.0 HD2 B:HIS210 3.5 22.4 1.0 HD11 B:LEU303 3.5 30.3 1.0 ND1 B:HIS210 4.0 17.2 1.0 ND1 B:HIS110 4.0 18.8 1.0 HE2 B:PHE204 4.0 18.7 1.0 O1 B:AKG302 4.1 25.0 1.0 O B:HOH434 4.1 29.2 1.0 CG B:HIS110 4.2 17.7 1.0 CG B:HIS210 4.2 14.2 1.0 C3 B:AKG302 4.3 24.3 1.0 CD2 B:LEU303 4.4 22.6 1.0 CB B:ASP112 4.4 17.4 1.0 HG3 B:PRO172 4.4 34.1 1.0 CD1 B:LEU303 4.4 25.2 1.0 HA B:ASP112 4.5 19.7 1.0 HG B:LEU303 4.5 28.8 1.0 H31 B:AKG302 4.6 29.2 1.0 CG B:LEU303 4.7 24.0 1.0 HD1 B:HIS210 4.8 20.7 1.0 HZ B:PHE204 4.8 19.4 1.0 HD1 B:HIS110 4.8 22.6 1.0 H42 B:AKG302 4.8 29.3 1.0 CA B:ASP112 4.9 16.4 1.0 HD22 B:LEU303 4.9 27.2 1.0 H32 B:AKG302 4.9 29.2 1.0 HB3 B:ASP112 4.9 20.8 1.0 CE2 B:PHE204 4.9 15.6 1.0 H41 B:AKG302 4.9 29.3 1.0 HD13 B:LEU303 4.9 30.3 1.0 HD23 B:LEU303 4.9 27.2 1.0 HB2 B:ASP112 4.9 20.8 1.0 N B:ASP112 4.9 16.1 1.0 C4 B:AKG302 5.0 24.4 1.0 HB3 B:PRO172 5.0 29.7 1.0 HD12 B:LEU303 5.0 30.3 1.0 H B:ASP112 5.0 19.4 1.0 HG2 B:PRO172 5.0 34.1 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