Cobalt in PDB 3auj: Structure of Diol Dehydratase Complexed with Glycerol

All present enzymatic activity of Structure of Diol Dehydratase Complexed with Glycerol:
4.2.1.28;

The structure of Structure of Diol Dehydratase Complexed with Glycerol, PDB code: 3auj was solved by M.Yamanishi, K.Kinoshita, M.Fukuoka, T.Shibata, T.Tobimatsu, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.34 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	190.610, 196.800, 77.360, 90.00, 95.03, 90.00
R / Rfree (%)	18.6 / 19.1

The structure of Structure of Diol Dehydratase Complexed with Glycerol also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Cobalt atom in the Structure of Diol Dehydratase Complexed with Glycerol (pdb code 3auj). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Diol Dehydratase Complexed with Glycerol, PDB code: 3auj:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Diol Dehydratase Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Diol Dehydratase Complexed with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1601 b:20.9 occ:1.00 CO B:B121601 0.0 20.9 1.0 N24 B:B121601 1.9 18.2 1.0 N21 B:B121601 1.9 18.8 1.0 N22 B:B121601 1.9 17.5 1.0 N23 B:B121601 1.9 18.6 1.0 N3B B:B121601 2.3 23.3 1.0 C9 B:B121601 2.9 20.7 1.0 C19 B:B121601 2.9 19.6 1.0 C1 B:B121601 2.9 19.2 1.0 C4 B:B121601 2.9 19.3 1.0 C11 B:B121601 2.9 17.5 1.0 C16 B:B121601 3.0 19.3 1.0 C6 B:B121601 3.0 20.2 1.0 C14 B:B121601 3.0 17.0 1.0 C2B B:B121601 3.2 21.2 1.0 C10 B:B121601 3.2 18.3 1.0 C5 B:B121601 3.4 19.0 1.0 C9B B:B121601 3.4 23.5 1.0 C15 B:B121601 3.5 18.7 1.0 C20 B:B121601 3.6 17.7 1.0 O28 B:B121601 3.7 20.5 1.0 C4B B:B121601 4.0 23.8 1.0 C18 B:B121601 4.2 18.9 1.0 C2 B:B121601 4.2 19.4 1.0 C8 B:B121601 4.2 20.0 1.0 C3 B:B121601 4.3 19.3 1.0 C17 B:B121601 4.3 20.1 1.0 C27 B:B121601 4.3 22.2 1.0 C7 B:B121601 4.3 21.0 1.0 C12 B:B121601 4.3 19.1 1.0 C13 B:B121601 4.3 18.6 1.0 N1B B:B121601 4.5 22.9 1.0 C8B B:B121601 4.6 22.7 1.0 C26 B:B121601 4.7 19.9 1.0 C41 B:B121601 4.8 20.9 1.0 C49 B:B121601 4.8 23.2 1.0 C35 B:B121601 4.9 18.8 1.0 C46 B:B121601 5.0 20.1 1.0 C53 B:B121601 5.0 19.4 1.0

Cobalt binding site 2 out of 2 in the Structure of Diol Dehydratase Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Diol Dehydratase Complexed with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ E:Co2601 b:20.4 occ:1.00 CO E:B122601 0.0 20.4 1.0 N24 E:B122601 1.9 20.2 1.0 N21 E:B122601 1.9 20.5 1.0 N22 E:B122601 1.9 19.5 1.0 N23 E:B122601 1.9 21.6 1.0 N3B E:B122601 2.3 24.8 1.0 C9 E:B122601 2.9 20.9 1.0 C19 E:B122601 2.9 19.4 1.0 C4 E:B122601 2.9 19.8 1.0 C1 E:B122601 2.9 20.7 1.0 C11 E:B122601 2.9 21.4 1.0 C16 E:B122601 3.0 21.2 1.0 C6 E:B122601 3.0 19.7 1.0 C14 E:B122601 3.0 20.9 1.0 C2B E:B122601 3.2 23.9 1.0 C10 E:B122601 3.2 21.2 1.0 C5 E:B122601 3.4 18.9 1.0 C15 E:B122601 3.4 21.1 1.0 C9B E:B122601 3.5 23.7 1.0 C20 E:B122601 3.6 18.1 1.0 O28 E:B122601 3.8 19.7 1.0 C4B E:B122601 4.1 23.1 1.0 C18 E:B122601 4.2 18.6 1.0 C2 E:B122601 4.2 19.7 1.0 C8 E:B122601 4.2 20.8 1.0 C3 E:B122601 4.2 19.5 1.0 C17 E:B122601 4.3 19.3 1.0 C27 E:B122601 4.3 21.9 1.0 C12 E:B122601 4.3 21.5 1.0 C7 E:B122601 4.3 19.7 1.0 C13 E:B122601 4.3 20.4 1.0 N1B E:B122601 4.5 25.5 1.0 C8B E:B122601 4.6 23.4 1.0 C26 E:B122601 4.7 19.6 1.0 C41 E:B122601 4.8 21.1 1.0 C49 E:B122601 4.8 22.2 1.0 C35 E:B122601 4.9 19.8 1.0 C53 E:B122601 5.0 21.1 1.0 C46 E:B122601 5.0 21.6 1.0

M.Yamanishi, K.Kinoshita, M.Fukuoka, T.Saito, A.Tanokuchi, Y.Ikeda, H.Obayashi, K.Mori, N.Shibata, T.Tobimatsu, T.Toraya. Redesign of Coenzyme B(12) Dependent Diol Dehydratase to Be Resistant to the Mechanism-Based Inactivation By Glycerol and Act on Longer Chain 1,2-Diols Febs J. V. 279 793 2012.
ISSN: ISSN 1742-464X
PubMed: 22221669
DOI: 10.1111/J.1742-4658.2012.08470.X