Iron in PDB 5nku: Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425

The structure of Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425, PDB code: 5nku 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)	N/A / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.427, 53.015, 55.337, 107.30, 98.54, 109.86
R / Rfree (%)	23.9 / 25.3

The structure of Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 (pdb code 5nku). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425, PDB code: 5nku:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:37.6 occ:1.00 FE A:HEM500 0.0 37.6 1.0 NA A:HEM500 1.9 32.9 1.0 NC A:HEM500 2.0 38.8 1.0 NB A:HEM500 2.1 41.0 1.0 NE2 A:HIS114 2.1 41.3 1.0 ND A:HEM500 2.1 31.3 1.0 O A:OH501 2.4 42.5 1.0 C1A A:HEM500 2.9 38.1 1.0 C1C A:HEM500 3.0 40.0 1.0 C4D A:HEM500 3.0 25.1 1.0 HO A:OH501 3.0 51.0 0.6 C4B A:HEM500 3.0 37.4 1.0 CD2 A:HIS114 3.0 39.2 1.0 CE1 A:HIS114 3.1 37.6 1.0 C4A A:HEM500 3.1 33.7 1.0 DO A:OH501 3.1 51.0 0.4 C1B A:HEM500 3.1 34.1 1.0 C4C A:HEM500 3.1 44.5 1.0 C1D A:HEM500 3.1 35.6 1.0 HD2 A:HIS114 3.2 47.1 1.0 CHA A:HEM500 3.2 31.3 1.0 HE1 A:HIS114 3.3 45.1 1.0 CHC A:HEM500 3.3 33.3 1.0 CHB A:HEM500 3.5 35.1 1.0 CHD A:HEM500 3.6 35.8 1.0 ND1 A:HIS114 4.1 43.9 1.0 CG A:HIS114 4.2 42.6 1.0 C2A A:HEM500 4.2 38.5 1.0 C2C A:HEM500 4.2 32.3 1.0 HHA A:HEM500 4.2 37.6 1.0 C3A A:HEM500 4.2 40.1 1.0 C3D A:HEM500 4.2 33.2 1.0 HHC A:HEM500 4.3 40.0 1.0 C3B A:HEM500 4.3 44.3 1.0 C3C A:HEM500 4.3 35.9 1.0 C2D A:HEM500 4.3 31.1 1.0 C2B A:HEM500 4.3 38.2 1.0 HD2 A:ARG127 4.4 89.4 1.0 D1 A:HOH604 4.4 71.0 1.0 HHB A:HEM500 4.4 42.1 1.0 HZ A:PHE145 4.5 49.0 1.0 O A:HOH604 4.5 59.1 1.0 HHD A:HEM500 4.5 42.9 1.0 HE1 A:PHE108 4.7 49.7 1.0 HE A:ARG127 4.8 94.0 0.0 DE A:ARG127 4.8 94.0 1.0 HZ A:PHE108 4.8 51.7 1.0 HE1 A:PHE145 4.8 61.2 1.0 HE3 A:MET162 4.9 82.1 1.0 HD1 A:HIS114 4.9 52.7 0.0 DD1 A:HIS114 4.9 52.7 1.0 HG21 A:THR143 4.9 48.2 1.0

Iron binding site 2 out of 2 in the Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Joint Neutron/X-Ray Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:31.4 occ:1.00 FE B:HEM203 0.0 31.4 1.0 NA B:HEM203 1.9 25.8 1.0 NB B:HEM203 1.9 32.2 1.0 NC B:HEM203 2.0 31.4 1.0 ND B:HEM203 2.0 29.4 1.0 NE2 B:HIS114 2.2 29.0 1.0 O B:OH204 2.2 34.6 1.0 DO B:OH204 2.7 41.5 1.0 C1B B:HEM203 2.9 33.3 1.0 C4A B:HEM203 3.0 29.8 1.0 C4B B:HEM203 3.0 30.9 1.0 C1A B:HEM203 3.0 32.4 1.0 C1C B:HEM203 3.0 31.2 1.0 C1D B:HEM203 3.1 26.9 1.0 C4C B:HEM203 3.1 33.2 1.0 C4D B:HEM203 3.1 27.3 1.0 CE1 B:HIS114 3.1 30.0 1.0 HO B:OH204 3.1 41.5 0.0 CD2 B:HIS114 3.2 32.6 1.0 HE1 B:HIS114 3.2 36.0 1.0 CHB B:HEM203 3.4 35.5 1.0 CHC B:HEM203 3.4 28.6 1.0 HD2 B:HIS114 3.4 39.1 1.0 CHA B:HEM203 3.4 30.9 1.0 CHD B:HEM203 3.5 24.6 1.0 HE1 B:MET162 3.7 0.9 1.0 C2B B:HEM203 4.1 35.0 1.0 C3B B:HEM203 4.2 34.2 1.0 C3A B:HEM203 4.2 36.3 1.0 C2A B:HEM203 4.2 32.9 1.0 ND1 B:HIS114 4.2 35.2 1.0 D1 B:HOH308 4.3 58.4 1.0 C3D B:HEM203 4.3 28.5 1.0 C2D B:HEM203 4.3 31.8 1.0 HHB B:HEM203 4.3 42.6 1.0 CG B:HIS114 4.3 30.3 1.0 C2C B:HEM203 4.3 31.7 1.0 C3C B:HEM203 4.3 31.9 1.0 HHC B:HEM203 4.4 34.4 1.0 HHA B:HEM203 4.4 37.1 1.0 HHD B:HEM203 4.4 29.6 1.0 D2 B:HOH308 4.4 58.4 1.0 HD2 B:ARG127 4.5 62.1 1.0 O B:HOH308 4.5 48.7 1.0 HZ B:PHE145 4.6 34.8 1.0 HE1 B:PHE108 4.6 36.3 1.0 DE B:ARG127 4.6 69.8 1.0 CE B:MET162 4.6 0.2 1.0 HE1 B:PHE145 4.8 46.2 1.0 HE3 B:MET162 4.8 0.9 1.0 HE B:ARG127 4.9 69.8 0.0 HG21 B:THR143 4.9 43.1 1.0 HD1 B:HIS114 5.0 42.2 0.0 DD1 B:HIS114 5.0 42.2 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