Iron in PDB 6vib: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - Enol Tautomers of Acms Bidentately Bound Structure

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

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - Enol Tautomers of Acms Bidentately Bound Structure, PDB code: 6vib 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)	42.29 / 1.84
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.330, 58.330, 232.040, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.6

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - Enol Tautomers of Acms Bidentately Bound Structure (pdb code 6vib). 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 - Enol Tautomers of Acms Bidentately Bound Structure, PDB code: 6vib:
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 - Enol Tautomers of Acms Bidentately 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 - Enol Tautomers of Acms Bidentately Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:35.1 occ:0.80 NE2 A:HIS95 2.2 20.3 1.0 O A:2FO204 2.2 24.8 0.8 OE2 A:GLU57 2.3 23.1 1.0 ND1 A:HIS51 2.3 21.0 1.0 O1 A:2FO204 2.3 35.5 0.8 C1 A:2FO204 2.4 34.5 0.8 OE1 A:GLU57 2.4 23.4 1.0 CD A:GLU57 2.7 25.4 1.0 CE1 A:HIS95 3.1 22.4 1.0 CE1 A:HIS51 3.1 24.6 1.0 CD2 A:HIS95 3.2 22.5 1.0 CG A:HIS51 3.3 22.6 1.0 OE1 A:GLU110 3.6 42.6 1.0 CB A:HIS51 3.7 22.0 1.0 C A:2FO204 3.7 30.7 0.8 N A:2FO204 3.8 31.2 0.8 CG A:GLU57 4.2 25.8 1.0 ND1 A:HIS95 4.2 20.5 1.0 NE2 A:HIS51 4.3 22.4 1.0 CG A:HIS95 4.3 17.9 1.0 CD2 A:HIS51 4.4 23.8 1.0 OD2 A:ASP53 4.4 22.2 1.0 CB A:ASP53 4.6 22.6 1.0 CD A:GLU110 4.6 32.5 1.0 O2 A:2FO204 4.7 24.2 0.5 OE2 A:GLU110 5.0 28.6 1.0

Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - Enol Tautomers of Acms Bidentately 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 - Enol Tautomers of Acms Bidentately Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:34.0 occ:1.00 SG A:CYS125 2.3 36.7 1.0 SG A:CYS162 2.3 35.1 1.0 SG A:CYS128 2.3 42.5 1.0 SG A:CYS165 2.3 40.0 1.0 CB A:CYS125 3.0 31.9 1.0 CB A:CYS162 3.2 33.4 1.0 CB A:CYS128 3.3 42.5 1.0 CB A:CYS165 3.3 43.7 1.0 N A:CYS128 3.7 40.7 1.0 N A:CYS165 3.8 45.4 1.0 CA A:CYS128 4.0 42.6 1.0 CA A:CYS165 4.1 45.2 1.0 CB A:HIS164 4.5 45.4 1.0 CA A:CYS125 4.5 25.6 1.0 CB A:ALA127 4.5 42.9 1.0 CA A:CYS162 4.6 30.4 1.0 C A:CYS128 4.6 43.7 1.0 C A:CYS165 4.7 38.9 1.0 N A:GLY129 4.7 37.7 1.0 O A:HOH394 4.8 33.3 1.0 CB A:HIS130 4.8 39.4 1.0 CB A:GLN167 4.8 34.7 1.0 C A:ALA127 4.8 44.0 1.0 C A:HIS164 4.8 49.4 1.0 N A:GLY166 4.9 37.7 1.0 N A:HIS130 4.9 39.7 1.0 N A:GLN167 4.9 33.7 1.0 N A:HIS164 5.0 44.2 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