Chlorine in PDB 6f9p: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II), PDB code: 6f9p was solved by T.Isabet, E.Stura, P.Legrand, A.Zaparucha, K.Bastard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.43 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.200, 98.870, 165.960, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.3

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) also contains other interesting chemical elements:

Rhenium

(Re)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) (pdb code 6f9p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II), PDB code: 6f9p:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:92.9 occ:1.00 RE A:RE402 2.8 76.5 0.4 O A:HOH555 2.9 81.2 1.0 NH1 A:ARG338 3.4 81.2 1.0 NE2 A:HIS312 3.7 60.3 1.0 CE1 A:PHE191 4.0 62.4 1.0 OE2 A:GLU178 4.1 62.5 1.0 OE1 A:GLU178 4.1 92.8 1.0 CD2 A:HIS312 4.2 60.2 1.0 CD A:ARG338 4.4 61.4 1.0 O A:HOH549 4.5 79.2 1.0 CD A:GLU178 4.5 80.8 1.0 CZ A:PHE191 4.5 62.7 1.0 CZ A:ARG338 4.6 89.4 1.0 NE2 A:HIS176 4.6 66.1 1.0 CD2 A:LEU173 4.8 0.4 1.0 O2 A:SO4403 4.8 0.3 1.0 CE1 A:HIS176 4.9 66.3 1.0 CE1 A:HIS312 4.9 59.2 1.0 CD1 A:PHE191 4.9 62.6 1.0 CA A:GLY166 5.0 0.0 1.0 NE A:ARG338 5.0 66.2 1.0 CE A:MET336 5.0 75.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:92.7 occ:0.52 RE B:RE402 2.8 0.4 0.5 CD B:ARG314 3.5 0.1 1.0 NE2 B:HIS312 3.9 72.0 1.0 O B:GLY313 4.0 94.8 1.0 CD2 B:HIS312 4.0 73.3 1.0 CA B:ARG314 4.1 0.9 1.0 CB B:ARG314 4.1 0.9 1.0 NE2 B:HIS176 4.3 88.9 1.0 CG B:ARG314 4.4 0.7 1.0 NH1 B:ARG314 4.4 0.8 1.0 NE B:ARG314 4.5 0.6 1.0 NH1 B:ARG338 4.7 0.6 1.0 OE2 B:GLU178 4.7 93.1 1.0 C B:GLY313 4.7 96.5 1.0 N B:ARG314 4.8 0.4 1.0 CE1 B:PHE191 4.8 79.8 1.0 CE B:MET336 4.8 0.1 1.0 CZ B:ARG314 4.9 0.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:0.5 occ:0.59 RE C:RE402 2.8 0.1 0.6 NH1 C:ARG338 3.9 0.2 1.0 CD2 C:LEU173 3.9 0.0 1.0 NE2 C:HIS312 4.2 80.8 1.0 CA C:GLY166 4.3 0.5 1.0 NE2 C:HIS176 4.5 94.7 1.0 CD2 C:HIS312 4.5 81.7 1.0 N C:GLY166 4.6 0.4 1.0 CE1 C:HIS176 4.6 96.4 1.0 OE1 C:GLU178 4.6 0.7 1.0 OE2 C:GLU178 4.6 0.9 1.0 CE1 C:PHE191 4.9 84.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:0.4 occ:0.58 RE D:RE402 2.8 0.9 0.6 NH1 D:ARG338 3.8 96.1 1.0 CD2 D:LEU173 4.0 0.2 1.0 NE2 D:HIS312 4.1 76.3 1.0 CA D:GLY166 4.3 0.6 1.0 CD2 D:HIS312 4.5 76.8 1.0 OE1 D:GLU178 4.6 95.2 1.0 OE2 D:GLU178 4.6 87.1 1.0 NE2 D:HIS176 4.6 78.8 1.0 CE1 D:HIS176 4.6 79.5 1.0 N D:GLY166 4.7 0.7 1.0 CE1 D:PHE191 4.9 76.5 1.0

K.Bastard, T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha. Structural Studies Based on Two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity Within the Clavaminate Synthase-Like Family. Sci Rep V. 8 16587 2018.
ISSN: ESSN 2045-2322
PubMed: 30410048
DOI: 10.1038/S41598-018-34795-9