Cobalt in PDB 7xrk: Diol Dehydratase Complexed with Adomecbl

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

The structure of Diol Dehydratase Complexed with Adomecbl, PDB code: 7xrk was solved by N.Shibata, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.07 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.313, 111.564, 197.058, 90, 90, 90
R / Rfree (%)	16.5 / 22.5

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

Calcium	(Ca)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Cobalt atom in the Diol Dehydratase Complexed with Adomecbl (pdb code 7xrk). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Diol Dehydratase Complexed with Adomecbl, PDB code: 7xrk:
Jump to Cobalt binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Diol Dehydratase Complexed with Adomecbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:18.8 occ:1.00 CO B:B12301 0.0 18.8 1.0 N24 B:B12301 1.8 20.8 1.0 N21 B:B12301 1.8 18.9 1.0 N23 B:B12301 1.8 19.1 1.0 N22 B:B12301 1.8 22.4 1.0 C6' A:FWK603 2.2 17.4 1.0 N3B B:B12301 2.3 19.5 1.0 C19 B:B12301 2.8 17.2 1.0 C4 B:B12301 2.8 18.8 1.0 C9 B:B12301 2.8 22.0 1.0 C14 B:B12301 2.8 20.7 1.0 C1 B:B12301 2.8 19.0 1.0 C11 B:B12301 2.9 19.9 1.0 C6 B:B12301 3.0 17.2 1.0 C16 B:B12301 3.0 20.9 1.0 C5' A:FWK603 3.1 18.7 1.0 C9B B:B12301 3.2 21.5 1.0 C2B B:B12301 3.3 22.0 1.0 C5 B:B12301 3.3 20.5 1.0 C10 B:B12301 3.3 20.0 1.0 C15 B:B12301 3.3 23.4 1.0 C20 B:B12301 3.6 16.2 1.0 C4B B:B12301 3.7 21.1 1.0 C18 B:B12301 4.0 18.9 1.0 C2 B:B12301 4.1 21.0 1.0 C3 B:B12301 4.1 22.3 1.0 C8 B:B12301 4.1 21.8 1.0 C13 B:B12301 4.2 21.5 1.0 C17 B:B12301 4.2 24.9 1.0 C12 B:B12301 4.2 24.2 1.0 C7 B:B12301 4.2 26.3 1.0 N1B B:B12301 4.4 24.8 1.0 C4' A:FWK603 4.5 22.8 1.0 C8B B:B12301 4.5 21.3 1.0 C26 B:B12301 4.5 20.5 1.0 C49 B:B12301 4.6 21.3 1.0 C37 B:B12301 4.7 25.1 1.0 C35 B:B12301 4.8 20.5 1.0 C41 B:B12301 4.8 23.3 1.0 C46 B:B12301 4.8 19.4 1.0 C53 B:B12301 4.8 25.9 1.0 C54 B:B12301 4.9 17.2 1.0 C48 B:B12301 5.0 21.3 1.0 O4' A:FWK603 5.0 21.9 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Diol Dehydratase Complexed with Adomecbl within 5.0Å range: probe atom residue distance (Å) B Occ E:Co301 b:22.9 occ:1.00 CO E:B12301 0.0 22.9 1.0 N24 E:B12301 1.8 29.1 1.0 N21 E:B12301 1.8 28.4 1.0 N23 E:B12301 1.8 27.7 1.0 N22 E:B12301 1.8 28.2 1.0 C6' D:FWK603 2.2 24.3 1.0 N3B E:B12301 2.3 27.9 1.0 C19 E:B12301 2.8 25.6 1.0 C9 E:B12301 2.8 24.7 1.0 C4 E:B12301 2.8 24.6 1.0 C14 E:B12301 2.8 24.7 1.0 C1 E:B12301 2.8 27.6 1.0 C11 E:B12301 2.9 26.5 1.0 C6 E:B12301 3.0 23.9 1.0 C16 E:B12301 3.0 21.4 1.0 C5' D:FWK603 3.1 25.0 1.0 C9B E:B12301 3.2 29.1 1.0 C10 E:B12301 3.3 21.5 1.0 C2B E:B12301 3.3 28.9 1.0 C5 E:B12301 3.3 30.3 1.0 C15 E:B12301 3.3 25.0 1.0 C20 E:B12301 3.6 24.7 1.0 C4B E:B12301 3.7 25.0 1.0 C18 E:B12301 4.0 24.6 1.0 C2 E:B12301 4.0 29.6 1.0 C3 E:B12301 4.1 22.5 1.0 C8 E:B12301 4.1 24.6 1.0 C13 E:B12301 4.2 25.7 1.0 C17 E:B12301 4.2 29.8 1.0 C12 E:B12301 4.2 26.1 1.0 C7 E:B12301 4.2 27.7 1.0 N1B E:B12301 4.4 33.1 1.0 C4' D:FWK603 4.5 32.6 1.0 C26 E:B12301 4.5 33.6 1.0 C8B E:B12301 4.5 28.7 1.0 C49 E:B12301 4.6 29.7 1.0 C35 E:B12301 4.8 21.9 1.0 C37 E:B12301 4.8 27.3 1.0 C46 E:B12301 4.8 24.4 1.0 C41 E:B12301 4.8 24.7 1.0 C53 E:B12301 4.8 24.4 1.0 C54 E:B12301 4.9 26.3 1.0 C48 E:B12301 5.0 27.4 1.0 O4' D:FWK603 5.0 25.4 1.0

N.Shibata, Y.Higuchi, B.Krautler, T.Toraya. Structural Insights Into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry V. 28 02196 2022.
ISSN: ISSN 0947-6539
PubMed: 35974426
DOI: 10.1002/CHEM.202202196