Iron in PDB 6vi5: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

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

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure, PDB code: 6vi5 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)	46.03 / 1.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.930, 57.930, 231.440, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.9

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure (pdb code 6vi5). 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 Resting State Structure, PDB code: 6vi5:
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 Resting State 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 Resting State Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:17.4 occ:1.00 NE2 A:HIS95 2.2 9.7 1.0 ND1 A:HIS51 2.2 14.5 1.0 O A:HOH314 2.3 14.7 1.0 OE2 A:GLU57 2.3 16.6 1.0 O A:HOH488 2.6 27.3 1.0 OE1 A:GLU57 2.6 15.9 1.0 CD A:GLU57 2.8 17.2 1.0 CE1 A:HIS95 3.1 8.5 1.0 CE1 A:HIS51 3.1 12.4 1.0 CD2 A:HIS95 3.2 10.6 1.0 CG A:HIS51 3.3 18.0 1.0 CB A:HIS51 3.6 11.2 1.0 O A:HOH482 4.0 58.9 1.0 OE1 A:GLU110 4.0 29.4 1.0 ND1 A:HIS95 4.3 9.4 1.0 O A:HOH460 4.3 55.7 1.0 NE2 A:HIS51 4.3 11.7 1.0 O A:HOH520 4.3 39.0 1.0 CG A:GLU57 4.3 12.4 1.0 CG A:HIS95 4.3 8.7 1.0 CD2 A:HIS51 4.4 14.1 1.0 OD2 A:ASP53 4.5 13.1 1.0 CB A:ASP53 4.8 8.6 1.0 CD A:GLU110 4.8 21.2 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State 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 Resting State Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:26.2 occ:1.00 SG A:CYS165 2.3 34.2 1.0 SG A:CYS125 2.3 27.6 1.0 SG A:CYS128 2.3 37.4 1.0 SG A:CYS162 2.3 26.1 1.0 CB A:CYS125 3.1 22.6 1.0 CB A:CYS162 3.1 25.0 1.0 CB A:CYS128 3.4 39.3 1.0 CB A:CYS165 3.4 33.2 1.0 N A:CYS165 3.7 33.2 1.0 N A:CYS128 3.8 36.9 1.0 CA A:CYS165 4.1 34.0 1.0 CA A:CYS128 4.1 39.0 1.0 CB A:GLN167 4.5 34.9 0.6 CB A:HIS164 4.5 45.2 1.0 CA A:CYS125 4.6 20.3 1.0 CA A:CYS162 4.6 24.7 1.0 CB A:GLN167 4.6 35.4 0.4 CB A:ALA127 4.6 27.6 1.0 C A:CYS128 4.7 40.0 1.0 CB A:HIS130 4.7 33.4 1.0 C A:CYS165 4.7 34.7 1.0 O A:HOH419 4.7 26.9 1.0 N A:GLY166 4.8 29.9 1.0 C A:ALA127 4.8 42.7 1.0 C A:HIS164 4.8 38.0 1.0 N A:GLN167 4.8 29.6 1.0 N A:GLY129 4.8 30.9 1.0 N A:HIS130 4.9 26.7 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