Iron in PDB 6via: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Seven-Membered Lactone Bound Structure

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

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Seven-Membered Lactone Bound Structure, PDB code: 6via 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)	30.73 / 1.59
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.517, 58.517, 231.902, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.6

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Seven-Membered Lactone Bound Structure (pdb code 6via). 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 - A Seven-Membered Lactone Bound Structure, PDB code: 6via:
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 - A Seven-Membered Lactone 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 - A Seven-Membered Lactone Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:42.7 occ:1.00 SG A:CYS128 2.2 46.2 1.0 SG A:CYS165 2.2 53.2 1.0 SG A:CYS125 2.3 44.8 1.0 SG A:CYS162 2.3 44.8 1.0 CB A:CYS125 3.0 35.3 1.0 CB A:CYS162 3.1 47.4 1.0 CB A:CYS165 3.2 54.8 1.0 CB A:CYS128 3.4 51.2 1.0 N A:CYS165 3.6 58.9 1.0 CA A:CYS165 3.9 56.2 1.0 N A:CYS128 4.0 51.0 1.0 CA A:CYS128 4.2 50.3 1.0 CA A:CYS125 4.5 34.3 1.0 C A:CYS165 4.6 49.7 1.0 CA A:CYS162 4.6 42.8 1.0 CB A:HIS164 4.6 53.0 1.0 CB A:GLN167 4.6 47.0 1.0 CB A:ALA127 4.6 54.3 1.0 N A:GLY166 4.6 48.7 1.0 C A:HIS164 4.7 59.1 1.0 CB A:HIS130 4.7 46.8 1.0 N A:GLN167 4.8 43.7 1.0 O A:HOH370 4.8 37.8 1.0 C A:CYS128 4.8 49.4 1.0 C A:ALA127 4.9 60.2 1.0 N A:HIS164 5.0 55.1 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Seven-Membered Lactone 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 - A Seven-Membered Lactone Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:36.2 occ:0.80 OE2 A:GLU57 2.1 28.4 1.0 NE2 A:HIS95 2.1 26.3 1.0 ND1 A:HIS51 2.2 27.9 1.0 O A:OH205 2.2 38.8 0.8 OE1 A:GLU57 2.2 29.7 1.0 O12 A:EAY206 2.3 36.3 0.8 CD A:GLU57 2.5 28.3 1.0 CE1 A:HIS51 2.9 25.7 1.0 CE1 A:HIS95 3.0 25.7 1.0 CD2 A:HIS95 3.2 27.0 1.0 CG A:HIS51 3.3 26.2 1.0 C11 A:EAY206 3.5 46.4 0.8 OE1 A:GLU110 3.6 49.0 1.0 N01 A:EAY206 3.7 38.2 0.8 CB A:HIS51 3.8 27.3 1.0 C02 A:EAY206 4.0 38.2 0.8 CG A:GLU57 4.1 22.7 1.0 NE2 A:HIS51 4.1 26.0 1.0 ND1 A:HIS95 4.2 24.9 1.0 CG A:HIS95 4.3 25.6 1.0 CD2 A:HIS51 4.3 25.5 1.0 OD2 A:ASP53 4.5 27.2 1.0 CD A:GLU110 4.6 41.0 1.0 CB A:ASP53 4.6 27.3 1.0 O10 A:EAY206 4.6 42.4 0.8

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