Fluorine in PDB 5k91: Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride, PDB code: 5k91 was solved by D.Puehringer, I.Schaffner, G.Mlynek, C.Obinger, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 1.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.146, 54.697, 94.266, 99.06, 94.84, 99.04
R / Rfree (%)	19 / 22.2

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride (pdb code 5k91). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride, PDB code: 5k91:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:35.4 occ:1.00 FE A:HEM201 2.6 13.1 1.0 O A:HOH330 2.8 30.2 1.0 ND A:HEM201 2.8 12.7 1.0 O A:HOH440 2.9 25.9 1.0 NA A:HEM201 3.1 12.5 1.0 HD2 A:ARG127 3.1 20.0 1.0 NC A:HEM201 3.2 11.9 1.0 NB A:HEM201 3.3 13.5 1.0 HB2 A:LEU129 3.4 15.0 1.0 C1D A:HEM201 3.6 11.0 1.0 C4D A:HEM201 3.6 11.9 1.0 HZ A:PHE145 3.7 16.9 1.0 HE1 A:PHE145 3.7 17.0 1.0 C1A A:HEM201 3.7 12.5 1.0 HE A:ARG127 3.8 19.0 1.0 HD13 A:LEU129 3.8 15.9 1.0 C4C A:HEM201 3.9 12.0 1.0 C4B A:HEM201 4.0 12.6 1.0 CHA A:HEM201 4.0 12.4 1.0 C1B A:HEM201 4.0 12.8 1.0 CD A:ARG127 4.0 16.6 1.0 C4A A:HEM201 4.0 13.4 1.0 C1C A:HEM201 4.0 13.7 1.0 HB2 A:ARG127 4.1 17.6 1.0 CHD A:HEM201 4.1 11.5 1.0 HB A:THR143 4.2 15.2 1.0 CZ A:PHE145 4.3 14.1 1.0 CE1 A:PHE145 4.3 14.2 1.0 HG3 A:ARG127 4.3 18.9 1.0 NE A:ARG127 4.3 15.8 1.0 HG22 A:THR143 4.3 17.1 1.0 HD22 A:LEU129 4.3 17.2 1.0 CHC A:HEM201 4.3 13.0 1.0 CHB A:HEM201 4.3 13.1 1.0 CB A:LEU129 4.4 12.5 1.0 HG21 A:THR143 4.5 17.1 1.0 CG A:ARG127 4.6 15.8 1.0 NE2 A:HIS114 4.6 14.1 1.0 C3D A:HEM201 4.6 12.0 1.0 CD1 A:LEU129 4.6 13.3 1.0 C2D A:HEM201 4.7 11.6 1.0 HA A:LEU129 4.7 14.4 1.0 HD3 A:ARG127 4.7 20.0 1.0 CB A:ARG127 4.8 14.6 1.0 CG2 A:THR143 4.8 14.2 1.0 HHA A:HEM201 4.9 14.9 1.0 C2A A:HEM201 4.9 13.5 1.0 C2B A:HEM201 4.9 13.6 1.0 CG A:LEU129 4.9 13.5 1.0 C3B A:HEM201 4.9 12.9 1.0 HD12 A:LEU129 4.9 15.9 1.0 HB3 A:LEU129 4.9 15.0 1.0 C3C A:HEM201 5.0 13.3 1.0 CB A:THR143 5.0 12.7 1.0 C3A A:HEM201 5.0 14.5 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:29.7 occ:1.00 FE B:HEM201 2.3 12.8 1.0 O B:HOH451 2.8 25.1 1.0 ND B:HEM201 2.8 12.5 1.0 NA B:HEM201 2.9 12.4 1.0 NB B:HEM201 3.0 12.9 1.0 O B:HOH339 3.0 28.5 1.0 NC B:HEM201 3.0 11.6 1.0 HD2 B:ARG127 3.1 19.3 1.0 HB2 B:LEU129 3.6 13.1 1.0 C4D B:HEM201 3.6 12.2 1.0 C1A B:HEM201 3.6 12.8 1.0 HZ B:PHE145 3.6 16.9 1.0 HE B:ARG127 3.6 19.1 1.0 C1D B:HEM201 3.7 12.3 1.0 C4B B:HEM201 3.7 12.8 1.0 C4A B:HEM201 3.8 12.5 1.0 HE1 B:PHE145 3.8 17.1 1.0 C1B B:HEM201 3.8 12.9 1.0 C1C B:HEM201 3.8 13.1 1.0 C4C B:HEM201 3.8 12.8 1.0 CHA B:HEM201 3.9 13.4 1.0 HD13 B:LEU129 3.9 16.9 1.0 CD B:ARG127 4.0 16.1 1.0 CHC B:HEM201 4.0 13.0 1.0 CHD B:HEM201 4.1 12.1 1.0 CHB B:HEM201 4.1 13.1 1.0 NE B:ARG127 4.2 16.0 1.0 CZ B:PHE145 4.3 14.0 1.0 HB2 B:ARG127 4.3 18.4 1.0 HD22 B:LEU129 4.3 15.8 1.0 CE1 B:PHE145 4.3 14.3 1.0 HG3 B:ARG127 4.3 18.9 1.0 HB B:THR143 4.3 15.8 1.0 NE2 B:HIS114 4.3 13.8 1.0 HG22 B:THR143 4.5 16.2 1.0 CB B:LEU129 4.6 10.9 1.0 HG21 B:THR143 4.6 16.2 1.0 CG B:ARG127 4.6 15.8 1.0 C3D B:HEM201 4.7 12.3 1.0 HHA B:HEM201 4.7 16.1 1.0 HD3 B:ARG127 4.7 19.3 1.0 C3B B:HEM201 4.7 13.3 1.0 C2D B:HEM201 4.7 13.1 1.0 C3A B:HEM201 4.7 12.9 1.0 C2A B:HEM201 4.8 12.3 1.0 C2B B:HEM201 4.8 12.9 1.0 CD1 B:LEU129 4.8 14.1 1.0 HHC B:HEM201 4.9 15.6 1.0 C2C B:HEM201 4.9 13.0 1.0 C3C B:HEM201 4.9 13.1 1.0 CG2 B:THR143 4.9 13.5 1.0 HHB B:HEM201 4.9 15.7 1.0 HHD B:HEM201 4.9 14.6 1.0 CB B:ARG127 4.9 15.3 1.0 HA B:LEU129 5.0 13.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ C:F202 b:34.3 occ:1.00 FE C:HEM201 2.4 12.9 1.0 ND C:HEM201 2.9 11.7 1.0 NA C:HEM201 2.9 12.8 1.0 O C:HOH442 3.0 20.4 1.0 HD2 C:ARG127 3.0 18.4 1.0 NB C:HEM201 3.1 11.6 1.0 O C:HOH322 3.1 25.3 1.0 NC C:HEM201 3.1 11.9 1.0 HB2 C:LEU129 3.6 15.2 1.0 C4D C:HEM201 3.7 12.3 1.0 HZ C:PHE145 3.7 15.7 1.0 C1A C:HEM201 3.7 13.4 1.0 HE C:ARG127 3.7 18.5 1.0 C4A C:HEM201 3.7 13.4 1.0 C1D C:HEM201 3.8 12.4 1.0 HE1 C:PHE145 3.8 16.6 1.0 C4B C:HEM201 3.8 12.6 1.0 CHA C:HEM201 3.8 12.7 1.0 C1B C:HEM201 3.9 12.6 1.0 C1C C:HEM201 3.9 12.2 1.0 C4C C:HEM201 3.9 13.4 1.0 HD13 C:LEU129 3.9 16.2 1.0 CD C:ARG127 3.9 15.3 1.0 CHD C:HEM201 4.1 12.7 1.0 CHB C:HEM201 4.1 13.0 1.0 HB2 C:ARG127 4.1 15.2 1.0 CHC C:HEM201 4.1 11.7 1.0 NE C:ARG127 4.2 15.4 1.0 CZ C:PHE145 4.3 13.1 1.0 CE1 C:PHE145 4.3 13.9 1.0 HD22 C:LEU129 4.3 17.9 1.0 HG3 C:ARG127 4.4 17.0 1.0 HB C:THR143 4.4 14.6 1.0 NE2 C:HIS114 4.4 14.0 1.0 HG22 C:THR143 4.5 15.3 1.0 CB C:LEU129 4.6 12.6 1.0 CG C:ARG127 4.6 14.2 1.0 HG21 C:THR143 4.6 15.3 1.0 HHA C:HEM201 4.6 15.3 1.0 HD3 C:ARG127 4.6 18.4 1.0 C3D C:HEM201 4.7 11.9 1.0 C2A C:HEM201 4.7 13.0 1.0 C3A C:HEM201 4.8 13.7 1.0 C3B C:HEM201 4.8 12.8 1.0 C2D C:HEM201 4.8 12.6 1.0 CD1 C:LEU129 4.8 13.5 1.0 CB C:ARG127 4.8 12.6 1.0 C2B C:HEM201 4.9 13.1 1.0 CG2 C:THR143 4.9 12.8 1.0 C2C C:HEM201 5.0 13.2 1.0 C3C C:HEM201 5.0 13.5 1.0 HA C:LEU129 5.0 14.3 1.0 HHB C:HEM201 5.0 15.6 1.0 HHD C:HEM201 5.0 15.3 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ D:F202 b:33.6 occ:1.00 FE D:HEM201 2.5 12.6 1.0 O D:HOH346 2.9 28.5 1.0 ND D:HEM201 2.9 12.2 1.0 O D:HOH430 2.9 20.9 1.0 NA D:HEM201 3.0 12.6 1.0 HD2 D:ARG127 3.1 18.8 1.0 NB D:HEM201 3.1 12.6 1.0 NC D:HEM201 3.2 12.0 1.0 HB2 D:LEU129 3.6 15.3 1.0 HE1 D:PHE145 3.7 16.5 1.0 C4D D:HEM201 3.7 11.9 1.0 HE D:ARG127 3.7 19.4 1.0 HZ D:PHE145 3.7 16.5 1.0 C1D D:HEM201 3.7 11.7 1.0 C1A D:HEM201 3.8 12.2 1.0 C4B D:HEM201 3.8 12.7 1.0 HD13 D:LEU129 3.9 17.3 1.0 C4C D:HEM201 3.9 12.8 1.0 C4A D:HEM201 3.9 12.6 1.0 C1B D:HEM201 3.9 12.6 1.0 C1C D:HEM201 3.9 12.0 1.0 CHA D:HEM201 4.0 11.1 1.0 CD D:ARG127 4.0 15.7 1.0 CHD D:HEM201 4.1 12.4 1.0 HB2 D:ARG127 4.2 17.2 1.0 CHC D:HEM201 4.2 12.0 1.0 CHB D:HEM201 4.2 12.6 1.0 NE D:ARG127 4.2 16.1 1.0 CE1 D:PHE145 4.2 13.8 1.0 CZ D:PHE145 4.3 13.7 1.0 HB D:THR143 4.3 16.1 1.0 HD22 D:LEU129 4.3 17.4 1.0 HG3 D:ARG127 4.3 17.4 1.0 HG22 D:THR143 4.3 17.0 1.0 NE2 D:HIS114 4.5 13.9 1.0 CB D:LEU129 4.5 12.8 1.0 HG21 D:THR143 4.5 17.0 1.0 CG D:ARG127 4.6 14.5 1.0 HD3 D:ARG127 4.7 18.8 1.0 C3D D:HEM201 4.7 11.4 1.0 C2D D:HEM201 4.8 12.1 1.0 CD1 D:LEU129 4.8 14.4 1.0 HHA D:HEM201 4.8 13.3 1.0 C3B D:HEM201 4.8 13.0 1.0 CG2 D:THR143 4.8 14.2 1.0 CB D:ARG127 4.8 14.3 1.0 C2B D:HEM201 4.8 13.3 1.0 C2A D:HEM201 4.9 13.3 1.0 C3C D:HEM201 4.9 13.9 1.0 C3A D:HEM201 4.9 13.7 1.0 HA D:LEU129 4.9 14.2 1.0 HHD D:HEM201 4.9 14.8 1.0 C2C D:HEM201 4.9 13.5 1.0

I.Schaffner, G.Mlynek, N.Flego, D.Puhringer, J.Libiseller-Egger, L.Coates, S.Hofbauer, M.Bellei, P.G.Furtmuller, G.Battistuzzi, G.Smulevich, K.Djinovic-Carugo, C.Obinger. Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights From Structural and Kinetic Studies. Acs Catal V. 7 7962 2017.
ISSN: ESSN 2155-5435
PubMed: 29142780
DOI: 10.1021/ACSCATAL.7B01749