Cobalt in PDB 4liv: Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid.

The structure of Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid., PDB code: 4liv was solved by N.C.Brissett, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.04 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.010, 75.010, 209.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25

The binding sites of Cobalt atom in the Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid. (pdb code 4liv). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid., PDB code: 4liv:

Cobalt binding site 1 out of 1 in the Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Ycfd, A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and Succinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:43.7 occ:1.00 OD2 A:ASP161 2.0 57.1 1.0 NE2 A:HIS159 2.0 44.5 1.0 NE2 A:HIS221 2.1 33.8 1.0 O2 A:SIN502 2.3 39.8 1.0 O1 A:SIN502 2.4 39.9 1.0 CE1 A:HIS159 2.5 37.5 1.0 C1 A:SIN502 2.7 39.3 1.0 CD2 A:HIS221 3.1 33.6 1.0 CG A:ASP161 3.1 52.9 1.0 CE1 A:HIS221 3.2 30.1 1.0 CD2 A:HIS159 3.3 37.4 1.0 OD1 A:ASP161 3.6 60.7 1.0 ND1 A:HIS159 3.8 25.3 1.0 CG A:HIS159 4.2 25.8 1.0 C2 A:SIN502 4.2 36.6 1.0 CG A:HIS221 4.2 32.8 1.0 ND1 A:HIS221 4.2 31.3 1.0 CB A:ASP161 4.3 39.9 1.0 C3 A:SIN502 4.9 30.7 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.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Delft, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 509 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263