Cobalt in PDB 7xrl: Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol

All present enzymatic activity of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol:
4.2.1.28;

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl 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)	45.72 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.718, 117.246, 201.55, 90, 90, 90
R / Rfree (%)	16.7 / 20.6

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol also contains other interesting chemical elements:

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

The binding sites of Cobalt atom in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol (pdb code 7xrl). 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 and 1,2-Propanediol, PDB code: 7xrl:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


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 and 1,2-Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:13.7 occ:1.00 CO B:B12301 0.0 13.7 1.0 N24 B:B12301 1.8 16.2 1.0 N21 B:B12301 1.8 14.8 1.0 N23 B:B12301 1.8 16.5 1.0 N22 B:B12301 1.9 13.6 1.0 C6' A:FWK605 2.2 15.2 1.0 N3B B:B12301 2.3 15.7 1.0 C19 B:B12301 2.8 19.7 1.0 C4 B:B12301 2.8 15.4 1.0 C14 B:B12301 2.8 22.5 1.0 C1 B:B12301 2.8 16.5 1.0 C9 B:B12301 2.8 14.5 1.0 C11 B:B12301 2.9 15.9 1.0 C6 B:B12301 3.0 14.0 1.0 C16 B:B12301 3.0 18.3 1.0 C5' A:FWK605 3.1 14.7 1.0 C2B B:B12301 3.2 12.5 1.0 C9B B:B12301 3.3 12.5 1.0 C5 B:B12301 3.3 15.0 1.0 C10 B:B12301 3.3 16.9 1.0 C15 B:B12301 3.3 23.6 1.0 C20 B:B12301 3.6 18.9 1.0 C4B B:B12301 3.8 12.8 1.0 C18 B:B12301 4.0 21.5 1.0 C2 B:B12301 4.1 22.0 1.0 C3 B:B12301 4.1 14.2 1.0 C8 B:B12301 4.2 16.4 1.0 C13 B:B12301 4.2 19.9 1.0 C17 B:B12301 4.2 26.9 1.0 C12 B:B12301 4.2 19.4 1.0 C7 B:B12301 4.2 18.1 1.0 N1B B:B12301 4.4 16.9 1.0 C4' A:FWK605 4.4 15.5 1.0 C8B B:B12301 4.5 13.4 1.0 C26 B:B12301 4.5 19.5 1.0 C49 B:B12301 4.7 27.1 1.0 C46 B:B12301 4.8 14.3 1.0 C35 B:B12301 4.8 18.0 1.0 C41 B:B12301 4.8 13.4 1.0 C53 B:B12301 4.8 23.6 1.0 C54 B:B12301 4.8 29.3 1.0 C37 B:B12301 4.8 15.0 1.0 O4' A:FWK605 4.9 15.6 1.0 C48 B:B12301 5.0 19.7 1.0

Cobalt binding site 2 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


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 and 1,2-Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ E:Co301 b:32.2 occ:1.00 CO E:B12301 0.0 32.2 1.0 N21 E:B12301 1.8 34.4 1.0 N24 E:B12301 1.8 32.0 1.0 N23 E:B12301 1.8 30.1 1.0 N22 E:B12301 1.9 32.7 1.0 C6' D:FWK605 2.2 30.2 1.0 N3B E:B12301 2.3 34.6 1.0 C19 E:B12301 2.8 33.1 1.0 C4 E:B12301 2.8 35.3 1.0 C9 E:B12301 2.8 32.0 1.0 C1 E:B12301 2.8 35.1 1.0 C14 E:B12301 2.8 32.7 1.0 C11 E:B12301 2.9 29.3 1.0 C6 E:B12301 2.9 34.0 1.0 C16 E:B12301 3.0 31.3 1.0 C5' D:FWK605 3.1 28.8 1.0 C9B E:B12301 3.2 36.5 1.0 C5 E:B12301 3.3 35.0 1.0 C2B E:B12301 3.3 34.5 1.0 C10 E:B12301 3.3 30.1 1.0 C15 E:B12301 3.4 29.4 1.0 C20 E:B12301 3.6 36.7 1.0 C4B E:B12301 3.7 37.6 1.0 C18 E:B12301 4.0 34.1 1.0 C2 E:B12301 4.0 36.1 1.0 C3 E:B12301 4.1 36.8 1.0 C8 E:B12301 4.1 33.1 1.0 C13 E:B12301 4.2 31.0 1.0 C12 E:B12301 4.2 30.0 1.0 C17 E:B12301 4.2 41.7 1.0 C7 E:B12301 4.2 33.9 1.0 N1B E:B12301 4.4 37.5 1.0 C26 E:B12301 4.5 46.7 1.0 C4' D:FWK605 4.5 28.6 1.0 C8B E:B12301 4.5 37.6 1.0 C49 E:B12301 4.6 35.1 1.0 C41 E:B12301 4.7 34.9 1.0 C35 E:B12301 4.7 35.9 1.0 C46 E:B12301 4.7 25.7 1.0 C37 E:B12301 4.8 32.2 1.0 C53 E:B12301 4.9 35.0 1.0 C54 E:B12301 4.9 34.7 1.0 C48 E:B12301 4.9 30.7 1.0 O4' D:FWK605 5.0 26.2 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