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Cobalt in PDB 4lit: Structure of Ycfd A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and 2-Oxoglutarate.

Protein crystallography data

The structure of Structure of Ycfd A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and 2-Oxoglutarate., PDB code: 4lit 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) 33.16 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.140, 74.140, 208.860, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.6

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Ycfd A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and 2-Oxoglutarate. (pdb code 4lit). 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 2-Oxoglutarate., PDB code: 4lit:

Cobalt binding site 1 out of 1 in 4lit

Go back to Cobalt Binding Sites List in 4lit
Cobalt binding site 1 out of 1 in the Structure of Ycfd A Ribosomal Oxygenase From Escherichia Coli in Complex with Cobalt and 2-Oxoglutarate.


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 2-Oxoglutarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co501

b:44.1
occ:1.00
OD2 A:ASP161 2.0 52.2 1.0
O5 A:AKG502 2.1 52.1 1.0
NE2 A:HIS221 2.1 29.9 1.0
NE2 A:HIS159 2.1 35.4 1.0
O2 A:AKG502 2.2 58.6 1.0
C2 A:AKG502 2.8 56.1 1.0
C1 A:AKG502 2.8 58.9 1.0
CG A:ASP161 2.9 41.5 1.0
CE1 A:HIS221 3.0 34.3 1.0
CE1 A:HIS159 3.1 34.5 1.0
CD2 A:HIS159 3.1 35.1 1.0
OD1 A:ASP161 3.2 49.8 1.0
CD2 A:HIS221 3.2 33.0 1.0
O1 A:AKG502 4.0 55.9 1.0
ND1 A:HIS159 4.2 37.2 1.0
ND1 A:HIS221 4.2 33.8 1.0
C3 A:AKG502 4.2 51.0 1.0
CG A:HIS159 4.2 37.2 1.0
CG A:HIS221 4.3 34.8 1.0
CB A:ASP161 4.3 34.2 1.0

Reference:

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
Page generated: Sun Dec 13 10:45:10 2020

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