Iron in PDB 6vi9: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure

All present enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure:
1.13.11.6;

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure, PDB code: 6vi9 was solved by Y.Wang, F.Liu, Y.Yang, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.55 / 2.31
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.790, 57.790, 231.440, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 27.5

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure (pdb code 6vi9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure, PDB code: 6vi9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:35.7 occ:1.00 SG A:CYS128 2.2 43.3 1.0 SG A:CYS162 2.6 31.1 1.0 SG A:CYS125 2.7 44.1 1.0 SG A:CYS165 2.7 52.6 1.0 CB A:CYS125 3.0 40.9 1.0 CB A:CYS128 3.0 45.9 1.0 N A:CYS128 3.3 41.4 1.0 CB A:CYS162 3.4 30.9 1.0 CB A:CYS165 3.6 36.2 1.0 CA A:CYS128 3.7 45.1 1.0 N A:CYS165 4.2 43.0 1.0 C A:CYS128 4.3 46.6 1.0 N A:GLY129 4.3 50.0 1.0 CA A:CYS165 4.4 44.2 1.0 CA A:CYS125 4.4 39.7 1.0 CB A:ALA127 4.5 36.3 1.0 C A:ALA127 4.5 43.8 1.0 N A:HIS130 4.7 43.3 1.0 CB A:HIS130 4.8 46.7 1.0 CA A:CYS162 4.9 37.5 1.0 C A:CYS125 4.9 39.5 1.0 CA A:ALA127 4.9 48.5 1.0 N A:ALA127 4.9 48.6 1.0 CB A:HIS164 5.0 51.9 1.0 CB A:GLN167 5.0 37.6 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Alkylperoxo Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:36.8 occ:1.00 FE A:QXM302 0.0 36.8 1.0 O02 A:QXM302 2.3 32.0 1.0 NE2 A:HIS95 2.4 19.6 1.0 OE1 A:GLU57 2.4 25.9 1.0 ND1 A:HIS51 2.5 28.0 1.0 O11 A:QXM302 2.5 30.8 1.0 OE2 A:GLU57 2.6 22.4 1.0 C10 A:QXM302 2.7 38.2 1.0 O01 A:QXM302 2.8 43.9 1.0 CD A:GLU57 2.8 23.9 1.0 N01 A:QXM302 3.0 28.2 1.0 C02 A:QXM302 3.3 38.9 1.0 CD2 A:HIS95 3.3 21.8 1.0 CE1 A:HIS51 3.3 25.0 1.0 CE1 A:HIS95 3.4 20.7 1.0 CG A:HIS51 3.4 26.5 1.0 CB A:HIS51 3.8 19.2 1.0 OE2 A:GLU110 3.8 31.1 1.0 C09 A:QXM302 4.2 44.9 1.0 CG A:GLU57 4.3 22.5 1.0 NE2 A:HIS51 4.4 29.4 1.0 CG A:HIS95 4.5 20.5 1.0 ND1 A:HIS95 4.5 18.1 1.0 CD2 A:HIS51 4.5 27.1 1.0 OD2 A:ASP53 4.5 26.3 1.0 C03 A:QXM302 4.7 37.6 1.0 CB A:ASP53 4.8 19.5 1.0 CD A:GLU110 4.8 27.7 1.0

Y.Wang, F.Liu, Y.Yang, A.Liu. Probing Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Reaction Cycle Intermediates Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2005327117