Iron in PDB 6vi8: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Superoxo Bound Structure

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

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Superoxo Bound Structure, PDB code: 6vi8 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)	29.02 / 1.95
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.040, 58.040, 231.290, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 26.3

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Superoxo Bound Structure (pdb code 6vi8). 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 Superoxo Bound Structure, PDB code: 6vi8:
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 Superoxo 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 Superoxo Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:26.0 occ:1.00 O A:O204 2.1 23.6 1.0 NE2 A:HIS95 2.1 9.8 1.0 ND1 A:HIS51 2.2 12.2 1.0 OE2 A:GLU57 2.3 13.9 1.0 O11 A:3HA206 2.3 16.9 1.0 OE1 A:GLU57 2.6 11.8 1.0 CD A:GLU57 2.8 13.4 1.0 CE1 A:HIS95 3.0 8.3 1.0 CE1 A:HIS51 3.1 12.5 1.0 O A:O205 3.1 27.8 1.0 CD2 A:HIS95 3.2 10.4 1.0 C4 A:3HA206 3.2 30.9 1.0 CG A:HIS51 3.2 13.0 1.0 N10 A:3HA206 3.3 24.9 1.0 CB A:HIS51 3.6 6.7 1.0 C3 A:3HA206 3.6 26.0 1.0 OE1 A:GLU110 3.7 24.8 1.0 ND1 A:HIS95 4.1 8.7 1.0 NE2 A:HIS51 4.2 12.6 1.0 CG A:HIS95 4.3 8.0 1.0 CG A:GLU57 4.3 12.1 1.0 CD2 A:HIS51 4.3 12.5 1.0 C5 A:3HA206 4.3 29.3 1.0 OD2 A:ASP53 4.5 10.8 1.0 CB A:ASP53 4.6 13.0 1.0 CD A:GLU110 4.7 17.5 1.0 C2 A:3HA206 5.0 24.8 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Superoxo 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 Superoxo Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:22.4 occ:1.00 SG A:CYS128 2.2 34.6 1.0 SG A:CYS162 2.3 23.7 1.0 SG A:CYS125 2.3 27.0 1.0 SG A:CYS165 2.3 33.5 1.0 CB A:CYS125 3.0 23.5 1.0 CB A:CYS162 3.1 18.3 1.0 CB A:CYS128 3.3 32.4 1.0 CB A:CYS165 3.4 30.4 1.0 N A:CYS128 3.8 29.5 1.0 N A:CYS165 3.9 34.0 1.0 CA A:CYS128 4.1 28.6 1.0 CA A:CYS165 4.2 35.9 1.0 CA A:CYS125 4.5 20.9 1.0 CB A:HIS164 4.5 40.8 1.0 CA A:CYS162 4.5 20.1 1.0 CB A:ALA127 4.5 28.7 1.0 CB A:GLN167 4.7 22.3 1.0 O A:HOH393 4.7 20.8 1.0 N A:GLY129 4.7 32.9 1.0 C A:CYS128 4.7 30.5 1.0 C A:CYS165 4.7 32.4 1.0 CB A:HIS130 4.8 27.7 1.0 C A:ALA127 4.8 31.9 1.0 C A:HIS164 4.8 41.4 1.0 N A:HIS130 4.9 25.4 1.0 N A:GLY166 4.9 26.8 1.0 N A:GLN167 5.0 26.4 1.0 CD2 A:HIS164 5.0 41.0 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