Iron in PDB 5k8z: Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5)

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5), PDB code: 5k8z 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)	44.43 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.858, 72.833, 112.494, 90.00, 94.57, 90.00
R / Rfree (%)	19.8 / 22.8

The binding sites of Iron atom in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5) (pdb code 5k8z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5), PDB code: 5k8z:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:17.0 occ:1.00 FE A:HEM202 0.0 17.0 1.0 ND A:HEM202 2.0 16.6 1.0 NB A:HEM202 2.1 18.6 1.0 NC A:HEM202 2.1 18.2 1.0 NA A:HEM202 2.1 17.6 1.0 NE2 A:HIS114 2.3 25.1 1.0 O A:OH203 2.4 24.1 1.0 HO A:OH203 2.9 28.9 1.0 C1D A:HEM202 3.1 15.7 1.0 C4C A:HEM202 3.1 16.4 1.0 C1B A:HEM202 3.1 18.8 1.0 CE1 A:HIS114 3.1 25.2 1.0 C4B A:HEM202 3.1 20.0 1.0 C4D A:HEM202 3.1 16.7 1.0 C1C A:HEM202 3.1 19.1 1.0 C4A A:HEM202 3.1 18.0 1.0 C1A A:HEM202 3.1 18.2 1.0 HE1 A:HIS114 3.1 30.2 1.0 CD2 A:HIS114 3.4 25.6 1.0 CHD A:HEM202 3.4 15.6 1.0 CHB A:HEM202 3.5 19.1 1.0 CHC A:HEM202 3.5 18.6 1.0 CHA A:HEM202 3.5 17.2 1.0 HE1 A:MET162 3.5 70.4 0.2 HD2 A:HIS114 3.6 30.7 1.0 ND1 A:HIS114 4.3 25.7 1.0 HD2 A:ARG127 4.3 35.7 1.0 C2D A:HEM202 4.3 16.5 1.0 C3D A:HEM202 4.3 15.7 1.0 C2B A:HEM202 4.3 19.9 1.0 C3B A:HEM202 4.3 22.6 1.0 C3C A:HEM202 4.3 19.1 1.0 C2C A:HEM202 4.3 20.2 1.0 HE1 A:MET162 4.3 68.1 0.8 C3A A:HEM202 4.3 17.8 1.0 C2A A:HEM202 4.3 18.4 1.0 HHD A:HEM202 4.4 18.7 1.0 CG A:HIS114 4.4 25.9 1.0 HHB A:HEM202 4.4 22.9 1.0 HHC A:HEM202 4.4 22.3 1.0 HHA A:HEM202 4.4 20.7 1.0 CE A:MET162 4.4 58.7 0.2 O A:HOH356 4.4 19.4 1.0 HZ A:PHE145 4.4 29.7 1.0 HE1 A:PHE145 4.5 30.0 1.0 HE3 A:MET162 4.6 70.4 0.2 HZ A:PHE108 4.8 28.6 1.0 HE A:ARG127 4.9 38.6 1.0 HE1 A:PHE108 4.9 28.7 1.0 HE2 A:MET162 5.0 70.4 0.2 HD1 A:HIS114 5.0 30.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:15.1 occ:1.00 FE B:HEM202 0.0 15.1 1.0 NC B:HEM202 2.0 12.3 1.0 NA B:HEM202 2.0 13.7 1.0 NB B:HEM202 2.0 13.5 1.0 ND B:HEM202 2.1 13.1 1.0 NE2 B:HIS114 2.3 20.2 1.0 O B:OH203 2.5 13.2 1.0 C4A B:HEM202 3.1 16.4 1.0 C4C B:HEM202 3.1 12.5 1.0 C4B B:HEM202 3.1 13.3 1.0 C1D B:HEM202 3.1 13.5 1.0 C1B B:HEM202 3.1 15.0 1.0 C1C B:HEM202 3.1 12.7 1.0 HO B:OH203 3.1 15.8 1.0 C1A B:HEM202 3.1 15.9 1.0 C4D B:HEM202 3.1 13.7 1.0 CE1 B:HIS114 3.2 20.1 1.0 HE1 B:HIS114 3.3 24.1 1.0 CD2 B:HIS114 3.3 20.6 1.0 CHD B:HEM202 3.4 12.7 1.0 CHC B:HEM202 3.4 12.9 1.0 CHB B:HEM202 3.4 15.4 1.0 CHA B:HEM202 3.5 14.0 1.0 HD2 B:HIS114 3.5 24.7 1.0 HE1 B:MET162 3.7 27.7 1.0 C3A B:HEM202 4.3 18.5 1.0 C3B B:HEM202 4.3 14.8 1.0 C2A B:HEM202 4.3 19.0 1.0 C2B B:HEM202 4.3 14.6 1.0 C3C B:HEM202 4.3 13.3 1.0 C2C B:HEM202 4.3 12.9 1.0 C2D B:HEM202 4.3 13.7 1.0 C3D B:HEM202 4.3 12.0 1.0 ND1 B:HIS114 4.3 20.4 1.0 HD2 B:ARG127 4.3 41.1 1.0 O B:HOH352 4.4 23.9 1.0 HZ B:PHE145 4.4 20.4 1.0 HHD B:HEM202 4.4 15.3 1.0 HHB B:HEM202 4.4 18.5 1.0 HHC B:HEM202 4.4 15.5 1.0 CG B:HIS114 4.4 20.8 1.0 HHA B:HEM202 4.4 16.8 1.0 HE1 B:PHE145 4.6 22.7 1.0 CE B:MET162 4.6 23.1 1.0 HE B:ARG127 4.7 53.9 1.0 HZ B:PHE108 4.8 23.1 1.0 HE1 B:PHE108 4.8 22.9 1.0 HE3 B:MET162 4.9 27.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:12.3 occ:1.00 FE C:HEM202 0.0 12.3 1.0 NB C:HEM202 2.0 9.4 1.0 NC C:HEM202 2.1 11.1 1.0 ND C:HEM202 2.1 11.7 1.0 NA C:HEM202 2.1 12.3 1.0 NE2 C:HIS114 2.2 12.5 1.0 O C:OH203 2.4 17.0 1.0 HO C:OH203 3.0 20.4 1.0 C1B C:HEM202 3.0 9.4 1.0 C4A C:HEM202 3.1 11.7 1.0 C1D C:HEM202 3.1 10.8 1.0 C4C C:HEM202 3.1 11.4 1.0 C1C C:HEM202 3.1 11.5 1.0 C4B C:HEM202 3.1 12.2 1.0 C4D C:HEM202 3.1 10.8 1.0 C1A C:HEM202 3.1 11.6 1.0 CE1 C:HIS114 3.2 14.2 1.0 CD2 C:HIS114 3.2 13.3 1.0 HE1 C:HIS114 3.3 17.0 1.0 CHB C:HEM202 3.4 10.4 1.0 HD2 C:HIS114 3.4 16.0 1.0 CHD C:HEM202 3.4 11.2 1.0 CHC C:HEM202 3.4 11.9 1.0 CHA C:HEM202 3.5 11.0 1.0 HE3 C:MET162 3.7 29.7 1.0 C2B C:HEM202 4.3 10.7 1.0 C3A C:HEM202 4.3 13.2 1.0 C3B C:HEM202 4.3 10.8 1.0 ND1 C:HIS114 4.3 13.6 1.0 C2C C:HEM202 4.3 12.4 1.0 C3C C:HEM202 4.3 13.1 1.0 C2D C:HEM202 4.3 11.7 1.0 C2A C:HEM202 4.3 11.5 1.0 C3D C:HEM202 4.3 11.5 1.0 HD2 C:ARG127 4.3 22.4 1.0 CG C:HIS114 4.4 13.3 1.0 HHB C:HEM202 4.4 12.4 1.0 HZ C:PHE145 4.4 17.2 1.0 HHD C:HEM202 4.4 13.5 1.0 O C:HOH394 4.4 15.2 1.0 HHC C:HEM202 4.4 14.3 1.0 HHA C:HEM202 4.5 13.2 1.0 HE1 C:PHE145 4.6 15.8 1.0 CE C:MET162 4.6 24.7 1.0 HZ C:PHE108 4.7 14.3 1.0 HE2 C:MET162 4.8 29.7 1.0 HE C:ARG127 4.8 23.8 1.0 O C:HOH343 5.0 22.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:12.6 occ:1.00 FE D:HEM202 0.0 12.6 1.0 NC D:HEM202 2.0 10.8 1.0 NA D:HEM202 2.1 10.6 1.0 NB D:HEM202 2.1 10.8 1.0 ND D:HEM202 2.1 10.6 1.0 NE2 D:HIS114 2.3 11.6 1.0 O D:OH203 2.6 10.2 1.0 C4C D:HEM202 3.1 10.1 1.0 C4A D:HEM202 3.1 12.0 1.0 C4B D:HEM202 3.1 11.0 1.0 C1D D:HEM202 3.1 10.4 1.0 C1A D:HEM202 3.1 10.2 1.0 C1C D:HEM202 3.1 10.3 1.0 C1B D:HEM202 3.1 11.8 1.0 C4D D:HEM202 3.1 11.2 1.0 HO D:OH203 3.1 12.2 1.0 CE1 D:HIS114 3.1 10.8 1.0 HE1 D:HIS114 3.2 13.0 1.0 CD2 D:HIS114 3.3 10.7 1.0 CHD D:HEM202 3.4 10.2 1.0 CHC D:HEM202 3.4 10.5 1.0 CHA D:HEM202 3.4 10.2 1.0 CHB D:HEM202 3.4 11.3 1.0 HD2 D:HIS114 3.6 12.8 1.0 HE1 D:MET162 3.7 18.7 1.0 C3A D:HEM202 4.3 12.2 1.0 C2A D:HEM202 4.3 11.4 1.0 C3C D:HEM202 4.3 10.4 1.0 C3B D:HEM202 4.3 11.6 1.0 C2C D:HEM202 4.3 10.4 1.0 ND1 D:HIS114 4.3 10.6 1.0 C2B D:HEM202 4.3 12.0 1.0 C2D D:HEM202 4.3 11.6 1.0 C3D D:HEM202 4.3 10.3 1.0 HZ D:PHE145 4.4 15.0 1.0 O D:HOH338 4.4 16.0 1.0 HHD D:HEM202 4.4 12.2 1.0 HHB D:HEM202 4.4 13.6 1.0 HHC D:HEM202 4.4 12.6 1.0 CG D:HIS114 4.4 11.3 1.0 HHA D:HEM202 4.4 12.2 1.0 HD2 D:ARG127 4.4 30.7 1.0 HE1 D:PHE145 4.6 17.1 1.0 CE D:MET162 4.6 15.6 1.0 HE1 D:PHE108 4.8 19.4 1.0 HE3 D:MET162 4.8 18.7 1.0 HE D:ARG127 4.9 38.5 1.0 HZ D:PHE108 4.9 17.3 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