Iron in PDB 8zbd: Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis

The structure of Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis, PDB code: 8zbd was solved by A.G.Gabdulkhakov, T.V.Tishchenko, T.S.Rudenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.51 / 2.33
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.997, 66.997, 245.03, 90, 90, 90
R / Rfree (%)	18.9 / 24.6

The binding sites of Iron atom in the Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis (pdb code 8zbd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis, PDB code: 8zbd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis


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 Persulfide Dioxygenase From Beggiatoa Leptomitoformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:32.5 occ:1.00 OD2 A:ASP134 2.1 33.2 1.0 O A:HOH409 2.2 23.3 1.0 O A:HOH441 2.3 32.1 1.0 NE2 A:HIS113 2.4 28.4 1.0 NE2 A:HIS57 2.4 27.3 1.0 O A:HOH452 2.9 24.2 1.0 CG A:ASP134 3.2 29.1 1.0 CE1 A:HIS57 3.2 26.1 1.0 CD2 A:HIS113 3.2 25.7 1.0 CE1 A:HIS113 3.4 28.2 1.0 CD2 A:HIS57 3.5 27.7 1.0 CB A:ASP134 3.7 30.2 1.0 CE1 A:HIS175 4.2 24.4 1.0 OD1 A:ASP61 4.2 32.0 1.0 OD1 A:ASP134 4.2 29.5 1.0 CG A:HIS113 4.4 27.1 1.0 ND1 A:HIS57 4.4 26.5 1.0 ND1 A:HIS59 4.4 25.2 1.0 ND1 A:HIS113 4.4 28.1 1.0 CG A:HIS57 4.5 25.0 1.0 N A:ALA60 4.7 23.6 1.0 ND1 A:HIS175 4.8 27.6 1.0 CA A:HIS59 4.8 24.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Persulfide Dioxygenase From Beggiatoa Leptomitoformis


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 Persulfide Dioxygenase From Beggiatoa Leptomitoformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:34.1 occ:1.00 OD2 B:ASP134 2.1 38.2 1.0 NE2 B:HIS57 2.3 26.7 1.0 O B:HOH443 2.3 39.8 1.0 O B:HOH402 2.4 29.8 1.0 NE2 B:HIS113 2.4 31.9 1.0 O B:HOH445 3.0 33.9 1.0 CE1 B:HIS57 3.2 27.8 1.0 CG B:ASP134 3.2 30.6 1.0 CD2 B:HIS113 3.2 27.2 1.0 CD2 B:HIS57 3.4 27.3 1.0 CE1 B:HIS113 3.5 33.8 1.0 CB B:ASP134 3.8 29.2 1.0 OD1 B:ASP61 4.0 38.6 1.0 CE1 B:HIS175 4.3 28.6 1.0 OD1 B:ASP134 4.3 31.1 1.0 ND1 B:HIS57 4.3 26.2 1.0 ND1 B:HIS59 4.4 29.3 1.0 CG B:HIS113 4.4 30.0 1.0 CG B:HIS57 4.5 25.2 1.0 ND1 B:HIS113 4.5 33.2 1.0 N B:ALA60 4.8 36.5 1.0 CA B:HIS59 4.8 30.7 1.0 ND1 B:HIS175 4.8 32.5 1.0

T.S.Rudenko, L.I.Trubitsina, V.V.Terentyev, I.V.Trubitsin, V.I.Borshchevskiy, S.V.Tishchenko, A.G.Gabdulkhakov, A.A.Leontievsky, M.Y.Grabovich. Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa Leptomitoformis , Where Persulfide Dioxygenase Plays A Key Role. Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
PubMed: 39456744
DOI: 10.3390/IJMS252010962