Chlorine in PDB 5y9x: Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(II)

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(II), PDB code: 5y9x 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)	24.36 / 1.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.038, 59.263, 116.253, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.8

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(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 Alphaketoglutarate and Coblat(II) (pdb code 5y9x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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 Alphaketoglutarate and Coblat(II), PDB code: 5y9x:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(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 Alphaketoglutarate and Coblat(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl417 b:24.0 occ:1.00 O A:HOH751 2.9 34.4 1.0 O A:HOH715 3.0 13.1 1.0 N A:ASP17 3.2 9.8 1.0 NZ A:LYS32 3.5 24.2 0.5 CD1 A:ILE29 3.6 20.2 1.0 CA A:PHE16 3.6 8.2 1.0 CD2 A:PHE16 3.9 11.7 1.0 C A:PHE16 3.9 8.5 1.0 CB A:PHE16 4.0 9.0 1.0 CB A:ASP17 4.0 16.2 1.0 CA A:ASP17 4.2 12.0 1.0 CG A:PHE16 4.3 8.8 1.0 CG2 A:ILE29 4.3 14.8 1.0 CG1 A:ILE29 4.3 15.7 1.0 CE A:LYS32 4.3 24.0 1.0 CG A:ASP17 4.3 23.5 1.0 OD2 A:ASP17 4.3 27.4 1.0 O A:HOH798 4.6 47.0 1.0 O A:GLN15 4.6 13.9 1.0 CE2 A:PHE16 4.8 11.6 1.0 N A:PHE16 4.8 7.9 1.0 O A:HOH765 4.9 32.6 1.0 N A:ALA18 4.9 9.8 1.0 CB A:ILE29 5.0 11.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(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 Alphaketoglutarate and Coblat(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl418 b:30.4 occ:1.00 O A:ACT414 3.1 59.2 1.0 N A:PHE202 3.2 14.0 1.0 OH A:TYR213 3.2 22.4 1.0 O A:HOH605 3.3 14.7 1.0 C A:ACT414 3.5 25.8 1.0 CA A:GLY199 3.6 19.7 1.0 CB A:PHE202 3.6 16.4 1.0 N A:GLY199 3.7 19.8 1.0 C A:GLY199 3.7 19.1 1.0 N A:ARG201 3.8 13.6 1.0 CB A:ARG201 4.0 12.3 1.0 CH3 A:ACT414 4.0 39.5 1.0 O A:GLY199 4.0 19.6 1.0 CA A:PHE202 4.0 14.1 1.0 C A:ARG201 4.1 12.9 1.0 OXT A:ACT414 4.1 33.6 1.0 N A:LYS200 4.1 17.5 1.0 CA A:ARG201 4.2 12.3 1.0 CZ A:TYR213 4.2 20.1 1.0 NH2 A:ARG201 4.3 19.7 1.0 CE2 A:TYR213 4.3 18.6 1.0 NE A:ARG201 4.4 16.6 1.0 CZ A:ARG201 4.5 18.0 1.0 C A:LYS200 4.7 14.5 1.0 C A:PRO198 4.9 20.7 1.0 CG A:ARG201 4.9 14.6 1.0 CG A:PHE202 4.9 20.7 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Coblat(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl419 b:58.8 occ:1.00 N A:SER87 3.3 16.5 1.0 O A:HOH705 3.5 19.9 1.0 CA A:LYS86 3.7 16.2 1.0 OG A:SER87 3.8 27.2 1.0 C A:LYS86 4.0 15.3 1.0 CB A:LYS86 4.1 18.7 1.0 CB A:SER87 4.1 21.5 1.0 CA A:SER87 4.3 17.1 1.0 CG A:LYS86 4.4 20.6 1.0 N A:LYS86 4.9 14.4 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.