Iron in PDB 5lmc: Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain

The structure of Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain, PDB code: 5lmc was solved by C.V.Romao, P.T.Borges, J.B.Vicente, M.A.Carrondo, M.Teixeira, C.Frazao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.07 / 1.90
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	150.471, 150.471, 95.361, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 16.6

The structure of Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Iron atom in the Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain (pdb code 5lmc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain, PDB code: 5lmc:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE1 A:FEO501 0.0 21.7 1.0 O A:FEO501 2.0 19.6 1.0 NE2 A:HIS84 2.0 20.8 1.0 O1 A:PO4503 2.1 27.2 1.0 OD1 A:ASP166 2.1 19.3 1.0 NE2 A:HIS227 2.2 24.1 1.0 OD2 A:ASP83 2.3 25.1 1.0 CE1 A:HIS84 3.0 23.4 1.0 CD2 A:HIS227 3.0 23.8 1.0 CG A:ASP166 3.0 19.9 1.0 CD2 A:HIS84 3.1 25.2 1.0 P A:PO4503 3.2 48.3 1.0 CE1 A:HIS227 3.2 22.3 1.0 CG A:ASP83 3.3 26.7 1.0 OD2 A:ASP166 3.3 21.9 1.0 FE2 A:FEO501 3.5 21.9 1.0 O4 A:PO4503 3.5 53.4 1.0 OD1 A:ASP83 3.6 24.2 1.0 O3 A:PO4503 3.6 42.5 1.0 ND1 A:HIS84 4.1 27.7 1.0 CG A:HIS84 4.2 23.2 1.0 CG A:HIS227 4.2 21.7 1.0 ND1 A:HIS227 4.3 20.8 1.0 OG A:SER226 4.4 24.3 1.0 CB A:ASP166 4.4 19.0 1.0 O2 A:PO4503 4.5 48.6 1.0 CB A:ASP83 4.6 26.4 1.0 OH A:TYR194 4.6 70.1 1.0 OE2 A:GLU81 4.7 24.1 1.0 CD2 A:HIS79 4.7 20.0 1.0 NE2 A:HIS79 4.9 19.2 1.0 CA A:ASP166 5.0 23.5 1.0

Iron binding site 2 out of 3 in the Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.9 occ:1.00 FE2 A:FEO501 0.0 21.9 1.0 O A:FEO501 1.9 19.6 1.0 OD2 A:ASP166 2.1 21.9 1.0 OE2 A:GLU81 2.2 24.1 1.0 NE2 A:HIS79 2.2 19.2 1.0 NE2 A:HIS147 2.2 25.9 1.0 O3 A:PO4503 2.7 42.5 1.0 CD2 A:HIS79 3.0 20.0 1.0 CE1 A:HIS147 3.1 27.6 1.0 CG A:ASP166 3.2 19.9 1.0 CD2 A:HIS147 3.2 22.5 1.0 CE1 A:HIS79 3.3 19.8 1.0 CD A:GLU81 3.3 27.7 1.0 FE1 A:FEO501 3.5 21.7 1.0 OD1 A:ASP166 3.6 19.3 1.0 P A:PO4503 3.8 48.3 1.0 CB A:GLU81 3.8 17.5 1.0 O1 A:PO4503 3.9 27.2 1.0 O4 A:PO4503 4.1 53.4 1.0 CG A:GLU81 4.1 23.9 1.0 CG A:HIS79 4.2 22.9 1.0 OE1 A:GLU81 4.2 31.2 1.0 ND1 A:HIS147 4.3 26.9 1.0 ND1 A:HIS79 4.3 17.6 1.0 CG A:HIS147 4.3 24.0 1.0 CB A:ASP166 4.4 19.0 1.0 OD1 A:ASP83 4.4 24.2 1.0 O A:HOH619 4.4 24.7 1.0 CD2 A:HIS84 4.4 25.2 1.0 NE2 A:HIS84 4.4 20.8 1.0 OD2 A:ASP83 4.8 25.1 1.0 OD1 A:ASN165 5.0 36.0 1.0

Iron binding site 3 out of 3 in the Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Flavodiiron Core of Escherichia Coli Flavorubredoxin, Including the Fe-4SG Atoms From Its Rubredoxin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:52.5 occ:0.50 SG A:CYS461 2.2 44.5 0.5 SG A:CYS464 2.3 58.5 0.5 SG A:CYS431 2.5 44.7 0.5 SG A:CYS428 2.5 47.5 0.5 O A:HOH864 5.0 61.2 1.0 NE2 A:GLN137 5.0 56.2 1.0

C.V.Romao, J.B.Vicente, P.T.Borges, B.L.Victor, P.Lamosa, E.Silva, L.Pereira, T.M.Bandeiras, C.M.Soares, M.A.Carrondo, D.Turner, M.Teixeira, C.Frazao. Structure of Escherichia Coli Flavodiiron Nitric Oxide Reductase. J.Mol.Biol. V. 428 4686 2016.
ISSN: ESSN 1089-8638
PubMed: 27725182
DOI: 10.1016/J.JMB.2016.10.008