Cobalt in PDB 5yka: Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II)

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II), PDB code: 5yka was solved by H.S.Chung, C.W.Pemble, S.H.Joo, C.R.Raetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.64 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.802, 59.607, 116.438, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.9

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cobalt atom in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II) (pdb code 5yka). 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 Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II), PDB code: 5yka:

Cobalt binding site 1 out of 1 in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Cobalt(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:13.2 occ:1.00 O A:HOH534 2.1 14.6 1.0 OD1 A:ASP148 2.1 12.3 1.0 O A:HOH536 2.1 15.0 1.0 NE2 A:HIS146 2.2 12.9 1.0 NE2 A:HIS260 2.2 11.3 1.0 O A:HOH623 2.2 15.7 1.0 CE1 A:HIS260 3.1 11.6 1.0 CE1 A:HIS146 3.1 12.0 1.0 CG A:ASP148 3.1 12.9 1.0 CD2 A:HIS146 3.1 10.6 1.0 CD2 A:HIS260 3.2 11.7 1.0 OD2 A:ASP148 3.4 12.6 1.0 OD1 A:ASP142 3.8 26.5 1.0 O2 A:SO4402 4.1 23.8 0.8 ND1 A:HIS260 4.2 10.4 1.0 ND1 A:HIS146 4.2 12.1 1.0 CG A:HIS146 4.3 11.6 1.0 CG A:HIS260 4.3 11.2 1.0 O A:HOH715 4.3 20.1 1.0 O A:HOH574 4.4 28.8 1.0 CG A:ASP142 4.5 26.3 1.0 CB A:ASP148 4.5 12.3 1.0 CA A:ASP148 4.8 11.5 1.0 OD2 A:ASP142 4.8 21.2 1.0 N A:ASP148 4.9 10.9 1.0 NH1 A:ARG162 5.0 21.8 1.0

S.H.Joo, C.W.Pemble, E.G.Yang, C.R.H.Raetz, H.S.Chung. Biochemical and Structural Insights Into An Fe(II)/ Alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (Kdoo). J. Mol. Biol. V. 430 4036 2018.
ISSN: ESSN 1089-8638
PubMed: 30092253
DOI: 10.1016/J.JMB.2018.07.029