Manganese in PDB 4cug: Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment

The structure of Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment, PDB code: 4cug was solved by M.A.Mcdonough, R.Sekirnik, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.74 / 2.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.220, 117.470, 120.280, 90.00, 90.00, 90.00
R / Rfree (%)	21.01 / 22.7

The binding sites of Manganese atom in the Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment (pdb code 4cug). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment, PDB code: 4cug:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1390 b:82.4 occ:1.00 OD2 A:ASP135 2.0 92.2 1.0 NE2 A:HIS196 2.2 76.2 1.0 O1 A:OGA1391 2.3 96.5 1.0 NE2 A:HIS133 2.5 80.2 1.0 C1 A:OGA1391 3.0 97.2 1.0 O2' A:OGA1391 3.0 97.0 1.0 CE1 A:HIS196 3.1 78.3 1.0 CG A:ASP135 3.2 90.6 1.0 C2 A:OGA1391 3.3 98.5 1.0 CD2 A:HIS196 3.3 78.4 1.0 CE1 A:HIS133 3.4 82.5 1.0 CD2 A:HIS133 3.4 81.4 1.0 OD1 A:ASP135 3.7 92.0 1.0 O2 A:OGA1391 3.9 97.4 1.0 ND1 A:HIS196 4.2 80.8 1.0 CB A:ASP135 4.4 86.1 1.0 CG A:HIS196 4.4 80.9 1.0 ND1 A:HIS133 4.4 85.5 1.0 CG A:HIS133 4.5 84.7 1.0 CB E:ARG82 4.6 0.6 1.0 N1 A:OGA1391 4.6 0.5 1.0

Manganese binding site 2 out of 2 in the Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rhodothermus Marinus Ycfd-Like Ribosomal Protein L16 Arginyl Hydroxylase in Complex Substrate Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1389 b:96.6 occ:1.00 OD2 B:ASP135 1.9 95.5 1.0 O2' B:OGA1390 2.2 0.7 1.0 O1 B:OGA1390 2.3 0.2 1.0 NE2 B:HIS196 2.3 98.9 1.0 NE2 B:HIS133 2.6 0.1 1.0 C1 B:OGA1390 2.7 0.2 1.0 C2 B:OGA1390 2.8 0.5 1.0 CG B:ASP135 3.1 94.4 1.0 CE1 B:HIS196 3.2 97.8 1.0 CD2 B:HIS196 3.3 1.0 1.0 CD2 B:HIS133 3.4 0.7 1.0 CE1 B:HIS133 3.5 1.0 1.0 OD1 B:ASP135 3.8 94.4 1.0 O2 B:OGA1390 3.8 0.1 1.0 N1 B:OGA1390 4.2 0.8 1.0 CB B:ASP135 4.2 93.7 1.0 ND1 B:HIS196 4.4 98.8 1.0 CG B:HIS196 4.4 0.5 1.0 ND1 B:HIS133 4.5 0.2 1.0 CG B:HIS133 4.5 0.2 1.0 CB F:ARG82 4.7 1.0 1.0 C4 B:OGA1390 5.0 0.5 1.0

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.-H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Deflt, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263