Chlorine in PDB 5y9i: Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Co(II)

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Co(II), PDB code: 5y9i was solved by H.S.Chung, C.W.Pemble, S.H.Joo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.263, 59.566, 116.950, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.5

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Co(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 Co(II) (pdb code 5y9i). 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 Co(II), PDB code: 5y9i:
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 Co(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 Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:23.5 occ:1.00 O A:HOH649 2.9 32.8 1.0 NE A:ARG174 3.0 12.3 1.0 NE1 A:TRP176 3.1 10.0 1.0 O A:HOH840 3.4 27.6 1.0 O A:HOH517 3.5 32.1 1.0 CG2 A:VAL262 3.6 19.9 1.0 CD A:ARG174 3.8 15.2 1.0 CE2 A:TRP176 3.8 11.1 1.0 CD2 A:LEU268 3.8 16.1 1.0 CZ2 A:TRP176 3.8 12.1 1.0 CG1 A:VAL262 3.8 16.2 1.0 CZ A:ARG174 3.9 16.8 1.0 NH2 A:ARG174 3.9 11.8 1.0 CE2 A:PHE164 4.2 11.0 1.0 CD2 A:PHE164 4.2 11.4 1.0 CD1 A:TRP176 4.3 13.4 1.0 CB A:VAL262 4.4 14.2 1.0 CG A:ARG174 4.5 13.4 1.0 CD1 A:LEU268 4.8 11.7 1.0 CZ2 A:TRP251 4.8 9.7 1.0 CG A:LEU268 4.9 12.4 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 Co(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 Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:40.6 occ:1.00 OG A:SER152 3.1 25.8 1.0 CD A:PRO151 3.3 18.6 1.0 N A:SER152 3.4 14.2 1.0 CB A:SER152 3.6 22.1 1.0 N A:PRO151 3.7 12.9 1.0 CB A:PHE150 4.1 19.3 1.0 C A:PHE150 4.1 13.0 1.0 CA A:SER152 4.1 14.7 1.0 CG A:PRO151 4.2 20.2 1.0 NZ A:LYS140 4.2 43.4 1.0 CA A:PHE150 4.3 16.6 1.0 C A:PRO151 4.4 15.3 1.0 CA A:PRO151 4.4 15.3 1.0 CB A:PRO151 4.5 15.7 1.0 O A:PHE150 4.8 13.1 1.0 C A:SER152 5.0 14.9 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 Co(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 Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:22.8 occ:1.00 OH A:TYR213 3.0 21.9 1.0 O A:HOH646 3.1 12.4 1.0 N A:PHE202 3.2 16.6 1.0 O A:HOH775 3.4 31.3 1.0 CA A:GLY199 3.5 20.6 1.0 N A:GLY199 3.5 16.2 1.0 C A:GLY199 3.7 23.0 1.0 CB A:PHE202 3.7 16.1 1.0 N A:ARG201 3.8 13.5 1.0 CB A:ARG201 3.9 14.2 1.0 CZ A:TYR213 4.0 18.0 1.0 N A:LYS200 4.0 19.7 1.0 CA A:PHE202 4.0 18.7 1.0 O A:GLY199 4.1 20.2 1.0 CE2 A:TYR213 4.1 18.1 1.0 C A:ARG201 4.1 16.6 1.0 CA A:ARG201 4.1 15.5 1.0 NH2 A:ARG201 4.2 20.0 1.0 NE A:ARG201 4.3 11.7 1.0 O A:HOH632 4.4 27.4 1.0 CZ A:ARG201 4.4 17.8 1.0 C A:LYS200 4.6 17.6 1.0 C A:PRO198 4.8 19.1 1.0 CG A:ARG201 4.9 13.6 1.0 CA A:LYS200 4.9 18.0 1.0 CG A:PHE202 5.0 21.8 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.