Iron in PDB 6vi6: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Substrate Monodentately Bound Structure

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

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Substrate Monodentately Bound Structure, PDB code: 6vi6 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)	29.00 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.990, 57.990, 231.860, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 25.4

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Substrate Monodentately Bound Structure (pdb code 6vi6). 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 Substrate Monodentately Bound Structure, PDB code: 6vi6:
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 Substrate Monodentately 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 Substrate Monodentately Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:30.4 occ:1.00 NE2 A:HIS95 2.2 16.0 1.0 ND1 A:HIS51 2.2 16.4 1.0 O11 A:3HA204 2.3 23.3 1.0 OE1 A:GLU57 2.3 19.3 1.0 O A:HOH406 2.5 26.0 1.0 OE2 A:GLU57 2.5 19.4 1.0 CD A:GLU57 2.8 23.2 1.0 CE1 A:HIS51 3.0 16.4 1.0 CE1 A:HIS95 3.1 16.6 1.0 C4 A:3HA204 3.1 40.6 1.0 CD2 A:HIS95 3.2 16.2 1.0 N10 A:3HA204 3.2 33.2 1.0 CG A:HIS51 3.3 17.3 1.0 C3 A:3HA204 3.6 39.4 1.0 CB A:HIS51 3.7 17.6 1.0 OE1 A:GLU110 3.9 29.1 1.0 NE2 A:HIS51 4.2 22.4 1.0 ND1 A:HIS95 4.3 17.2 1.0 C5 A:3HA204 4.3 40.8 1.0 CG A:HIS95 4.3 17.0 1.0 CG A:GLU57 4.3 22.1 1.0 CD2 A:HIS51 4.3 21.9 1.0 OD2 A:ASP53 4.5 16.0 1.0 CD A:GLU110 4.7 23.9 1.0 CB A:ASP53 4.7 17.1 1.0 C2 A:3HA204 4.9 38.0 1.0 OE2 A:GLU110 5.0 22.7 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Substrate Monodentately 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 Substrate Monodentately Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:39.2 occ:1.00 SG A:CYS128 2.3 42.8 1.0 SG A:CYS165 2.3 47.3 1.0 SG A:CYS125 2.3 39.7 1.0 SG A:CYS162 2.3 38.4 1.0 CB A:CYS125 3.1 40.1 1.0 CB A:CYS162 3.1 40.9 1.0 CB A:CYS165 3.3 49.0 1.0 CB A:CYS128 3.4 49.4 1.0 N A:CYS165 3.7 53.3 1.0 N A:CYS128 3.8 46.8 1.0 CA A:CYS165 4.0 52.0 1.0 CA A:CYS128 4.1 49.8 1.0 CA A:CYS125 4.6 36.1 1.0 CB A:ALA127 4.6 40.6 1.0 CA A:CYS162 4.6 41.4 1.0 CB A:GLN167 4.6 45.2 1.0 C A:CYS165 4.6 52.7 1.0 N A:GLY166 4.8 49.2 1.0 C A:CYS128 4.8 51.6 1.0 CD2 A:HIS164 4.8 71.6 1.0 C A:ALA127 4.8 53.2 1.0 C A:HIS164 4.8 54.6 1.0 CB A:HIS130 4.8 51.7 1.0 N A:GLY129 4.9 51.2 1.0 N A:GLN167 4.9 42.0 1.0 CB A:HIS164 4.9 62.6 1.0 O A:HOH393 4.9 36.6 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