Manganese in PDB 5ncj: Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine

The structure of Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine, PDB code: 5ncj 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)	51.91 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.740, 56.061, 73.802, 90.00, 112.46, 90.00
R / Rfree (%)	15.5 / 17.3

The binding sites of Manganese atom in the Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine (pdb code 5ncj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine, PDB code: 5ncj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:22.6 occ:1.00 OD1 A:ASP112 2.1 25.3 1.0 HD1 A:HL5303 2.2 26.1 0.9 O3 A:SIN302 2.2 27.5 1.0 OD A:HL5303 2.2 21.8 0.9 NE2 A:HIS110 2.3 21.5 1.0 NE2 A:HIS210 2.3 19.6 1.0 O4 A:SIN302 2.7 34.2 1.0 C4 A:SIN302 2.8 26.8 1.0 O A:HOH404 3.0 30.4 1.0 CG A:ASP112 3.0 22.1 1.0 CE1 A:HIS210 3.1 20.9 1.0 CE1 A:HIS110 3.1 21.4 1.0 HE1 A:HIS210 3.2 25.1 1.0 HE1 A:HIS110 3.2 25.7 1.0 OD2 A:ASP112 3.3 22.9 1.0 CD2 A:HIS110 3.3 21.7 1.0 CD2 A:HIS210 3.3 19.6 1.0 CD1 A:HL5303 3.4 21.3 0.9 HD13 A:HL5303 3.5 25.5 0.9 HD2 A:HIS110 3.6 26.0 1.0 HD2 A:HIS210 3.6 23.5 1.0 HD21 A:HL5303 3.8 26.1 0.9 HD23 A:HL5303 3.9 26.1 0.9 O A:HOH408 3.9 35.8 1.0 HD12 A:HL5303 4.1 25.5 0.9 HE2 A:PHE204 4.1 23.6 1.0 CD2 A:HL5303 4.2 21.8 0.9 ND1 A:HIS210 4.3 19.9 1.0 ND1 A:HIS110 4.3 20.3 1.0 C3 A:SIN302 4.3 20.9 1.0 CG A:HL5303 4.3 20.7 0.9 CG A:HIS110 4.4 19.3 1.0 CG A:HIS210 4.4 19.1 1.0 CB A:ASP112 4.4 20.4 1.0 HA A:ASP112 4.4 25.2 1.0 HE3 A:LYS95 4.5 27.8 1.0 HZ1 A:LYS95 4.5 32.9 1.0 HG1 A:HL5303 4.6 24.9 0.9 H22 A:SIN302 4.7 23.3 1.0 H32 A:SIN302 4.8 25.0 1.0 CA A:ASP112 4.8 21.0 1.0 H21 A:SIN302 4.9 23.3 1.0 HB3 A:ASP112 4.9 24.5 1.0 HZ A:PHE204 4.9 24.4 1.0 C2 A:SIN302 4.9 19.4 1.0 H31 A:SIN302 4.9 25.0 1.0 HB3 A:PRO172 5.0 31.2 1.0 HB2 A:ASP112 5.0 24.5 1.0 HD1 A:HIS210 5.0 23.9 1.0 N A:ASP112 5.0 20.4 1.0 HD1 A:HIS110 5.0 24.4 1.0 CE2 A:PHE204 5.0 19.7 1.0

Manganese binding site 2 out of 2 in the Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Grie in Complex with Manganese, Succinate and (2S,4R)-5-Hydroxyleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:22.9 occ:1.00 OD1 B:ASP112 2.1 21.5 1.0 HD1 B:HL5303 2.1 24.1 0.9 NE2 B:HIS110 2.2 16.6 1.0 OD B:HL5303 2.3 20.1 0.9 NE2 B:HIS210 2.3 18.2 1.0 O1 B:SIN302 2.3 24.7 1.0 O2 B:SIN302 2.5 27.6 1.0 C1 B:SIN302 2.8 23.6 1.0 CG B:ASP112 3.1 18.8 1.0 CE1 B:HIS110 3.1 17.1 1.0 O B:HOH417 3.1 27.3 1.0 CE1 B:HIS210 3.1 19.2 1.0 HE1 B:HIS110 3.2 20.5 1.0 HE1 B:HIS210 3.2 23.0 1.0 CD2 B:HIS110 3.3 17.4 1.0 CD2 B:HIS210 3.3 17.5 1.0 OD2 B:ASP112 3.3 19.5 1.0 CD1 B:HL5303 3.4 19.6 0.9 HD13 B:HL5303 3.4 23.5 0.9 HD2 B:HIS110 3.5 20.9 1.0 HD2 B:HIS210 3.6 21.0 1.0 HD21 B:HL5303 3.7 24.2 0.9 O B:HOH415 3.9 27.7 1.0 HD23 B:HL5303 4.0 24.2 0.9 HD12 B:HL5303 4.1 23.5 0.9 CD2 B:HL5303 4.2 20.2 0.9 HE2 B:PHE204 4.2 21.8 1.0 ND1 B:HIS110 4.3 17.2 1.0 ND1 B:HIS210 4.3 18.1 1.0 C2 B:SIN302 4.3 18.8 1.0 CG B:HL5303 4.3 18.4 0.9 CG B:HIS110 4.4 17.7 1.0 CG B:HIS210 4.4 15.8 1.0 HG3 B:PRO172 4.5 34.0 1.0 HA B:ASP112 4.5 20.2 1.0 CB B:ASP112 4.5 16.8 1.0 HZ1 B:LYS95 4.5 23.2 1.0 HG1 B:HL5303 4.6 22.1 0.9 HE3 B:LYS95 4.6 21.5 1.0 H21 B:SIN302 4.7 22.5 1.0 H32 B:SIN302 4.8 21.2 1.0 CA B:ASP112 4.8 16.9 1.0 H22 B:SIN302 4.9 22.5 1.0 HZ B:PHE204 4.9 21.5 1.0 HB3 B:ASP112 4.9 20.1 1.0 H31 B:SIN302 4.9 21.2 1.0 N B:ASP112 4.9 17.9 1.0 H B:ASP112 4.9 21.5 1.0 C3 B:SIN302 5.0 17.7 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