Chlorine 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:

Cobalt

(Co)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where 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:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl419 b:24.6 occ:0.81 OH A:TYR213 3.2 27.2 1.0 N A:PHE202 3.2 18.8 1.0 O A:HOH581 3.2 19.1 1.0 CA A:GLY199 3.4 23.4 1.0 C A:GLY199 3.6 24.0 1.0 N A:GLY199 3.6 24.1 1.0 CB A:PHE202 3.7 22.0 1.0 N A:ARG201 3.8 18.4 1.0 CB A:ARG201 3.9 18.7 1.0 CA A:PHE202 4.0 18.1 1.0 O A:GLY199 4.0 25.1 1.0 N A:LYS200 4.0 21.3 1.0 C A:ARG201 4.0 17.6 1.0 O A:HOH642 4.1 38.9 1.0 CA A:ARG201 4.1 17.4 1.0 NH2 A:ARG201 4.1 22.9 1.0 CZ A:TYR213 4.2 24.7 1.0 CE2 A:TYR213 4.2 22.6 1.0 NE A:ARG201 4.3 18.5 1.0 CZ A:ARG201 4.4 20.6 1.0 C A:LYS200 4.6 21.4 1.0 C A:PRO198 4.8 23.8 1.0 CG A:ARG201 4.9 16.6 1.0 CG A:PHE202 5.0 25.7 1.0 CA A:LYS200 5.0 21.6 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl420 b:23.7 occ:0.69 O A:HOH723 3.0 36.5 1.0 O A:HOH693 3.0 19.2 1.0 N A:ASP17 3.2 16.8 1.0 CD1 A:ILE29 3.6 26.7 1.0 CA A:PHE16 3.6 14.9 1.0 CD2 A:PHE16 3.9 17.9 1.0 C A:PHE16 3.9 17.5 1.0 CB A:PHE16 3.9 14.7 1.0 CB A:ASP17 4.1 22.1 1.0 CA A:ASP17 4.2 17.7 1.0 CG A:PHE16 4.3 14.6 1.0 CG1 A:ILE29 4.3 22.7 1.0 CG2 A:ILE29 4.3 18.8 1.0 OD2 A:ASP17 4.4 49.1 1.0 CG A:ASP17 4.4 40.4 1.0 O A:GLN15 4.5 19.3 1.0 O4 A:PG4412 4.8 56.4 1.0 N A:PHE16 4.8 13.3 1.0 CE2 A:PHE16 4.8 19.7 1.0 O A:HOH753 4.9 32.2 1.0 N A:ALA18 5.0 17.6 1.0 CB A:ILE29 5.0 17.0 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