Cobalt in PDB 5y9y: Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Succinate and Co(II)

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Succinate and Co(II), PDB code: 5y9y 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)	23.57 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.762, 59.316, 116.429, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.4

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

Chlorine

(Cl)

1 atom

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 Succinate and Co(II) (pdb code 5y9y). 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 Succinate and Co(II), PDB code: 5y9y:

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 Succinate and Co(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 Succinate and Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:15.6 occ:1.00 OD1 A:ASP148 2.1 16.1 1.0 NE2 A:HIS260 2.1 13.6 1.0 NE2 A:HIS146 2.1 16.6 1.0 O1 A:SIN402 2.1 26.1 1.0 O A:HOH643 2.3 23.1 1.0 O2 A:SIN402 2.3 18.4 1.0 C1 A:SIN402 2.6 19.5 1.0 CE1 A:HIS146 3.0 16.3 1.0 CE1 A:HIS260 3.1 13.0 1.0 CD2 A:HIS260 3.1 13.0 1.0 CG A:ASP148 3.1 18.6 1.0 CD2 A:HIS146 3.2 15.6 1.0 O A:HOH507 3.5 26.0 1.0 OD2 A:ASP148 3.5 19.4 1.0 C2 A:SIN402 4.1 21.9 1.0 ND1 A:HIS146 4.2 16.9 1.0 ND1 A:HIS260 4.2 13.7 1.0 CG A:HIS260 4.2 13.2 1.0 O A:HOH694 4.2 27.4 1.0 CG A:HIS146 4.3 16.5 1.0 OD2 A:ASP142 4.3 31.4 1.0 OXT A:ACT412 4.3 29.9 1.0 CB A:ASP148 4.4 14.8 1.0 CG A:ASP142 4.6 34.2 1.0 CA A:ASP148 4.7 13.3 1.0 OD1 A:ASP142 4.8 30.2 1.0 O A:HOH533 4.8 32.1 1.0 N A:ASP148 4.9 13.9 1.0 C3 A:SIN402 5.0 21.3 1.0

H.S.Chung, C.W.Pemble Iv, S.H.Joo. Biochemical and Structural Insights of Fe(II)/Alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdoo From Methylacidiphilum Infernorum V4 To Be Published.