Cobalt in PDB 7xrn: Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate

All present enzymatic activity of Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate:
4.3.1.7;

The structure of Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate, PDB code: 7xrn 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)	48.16 / 2.07
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	242.383, 242.383, 76.586, 90, 90, 120
R / Rfree (%)	21.4 / 24.1

The binding sites of Cobalt atom in the Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate (pdb code 7xrn). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate, PDB code: 7xrn:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co601 b:33.6 occ:1.00 CO B:B12601 0.0 33.6 1.0 N24 B:B12601 1.8 32.9 1.0 N21 B:B12601 1.8 30.9 1.0 N23 B:B12601 1.8 32.2 1.0 N22 B:B12601 1.9 29.3 1.0 N3B B:B12601 2.3 32.4 1.0 C19 B:B12601 2.8 34.3 1.0 C4 B:B12601 2.8 32.5 1.0 C14 B:B12601 2.8 33.6 1.0 C9 B:B12601 2.8 29.0 1.0 C1 B:B12601 2.8 36.1 1.0 C11 B:B12601 2.9 29.8 1.0 C6 B:B12601 3.0 29.6 1.0 C16 B:B12601 3.0 30.8 1.0 C9B B:B12601 3.2 32.7 1.0 C5' A:FWK501 3.2 32.5 0.5 C10 B:B12601 3.3 30.8 1.0 C5 B:B12601 3.3 30.2 1.0 C2B B:B12601 3.3 32.8 1.0 C15 B:B12601 3.3 30.1 1.0 C20 B:B12601 3.6 33.5 1.0 C4B B:B12601 3.6 32.9 1.0 O28 B:B12601 3.6 31.9 0.6 O3' A:FWK501 3.8 34.6 0.6 C18 B:B12601 4.0 34.1 1.0 C2 B:B12601 4.0 34.5 1.0 C3 B:B12601 4.1 32.1 1.0 O28 B:B12601 4.1 31.3 0.5 C13 B:B12601 4.1 34.0 1.0 C8 B:B12601 4.2 29.1 1.0 C17 B:B12601 4.2 31.9 1.0 C12 B:B12601 4.2 28.8 1.0 C7 B:B12601 4.3 29.4 1.0 C27 B:B12601 4.3 31.3 0.6 C3' A:FWK501 4.4 31.7 0.6 C8B B:B12601 4.5 34.1 1.0 N1B B:B12601 4.5 33.8 1.0 C26 B:B12601 4.5 31.9 0.5 C26 B:B12601 4.5 31.7 0.6 C27 B:B12601 4.7 31.8 0.5 C4' A:FWK501 4.7 32.2 0.5 C42 B:B12601 4.7 31.3 1.0 C35 B:B12601 4.7 30.4 1.0 C53 B:B12601 4.8 30.4 1.0 C48 B:B12601 4.8 30.5 1.0 C2' A:FWK501 4.9 31.7 0.6 C46 B:B12601 4.9 30.5 1.0 C54 B:B12601 5.0 31.2 1.0

Cobalt binding site 2 out of 2 in the Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Ethanolamine Ammonia-Lyase Complexed with Adomecbl in the Presence of Substrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Co601 b:37.5 occ:1.00 CO D:B12601 0.0 37.5 1.0 N24 D:B12601 1.8 35.7 1.0 N21 D:B12601 1.8 33.1 1.0 N23 D:B12601 1.8 39.1 1.0 N22 D:B12601 1.9 33.1 1.0 N3B D:B12601 2.3 35.6 1.0 C19 D:B12601 2.8 33.5 1.0 C4 D:B12601 2.8 33.1 1.0 C9 D:B12601 2.8 34.8 1.0 C14 D:B12601 2.8 35.5 1.0 C1 D:B12601 2.8 35.6 1.0 C11 D:B12601 2.9 37.2 1.0 C6 D:B12601 3.0 33.1 1.0 C16 D:B12601 3.0 33.5 1.0 C5' C:FWK501 3.2 39.9 1.0 C9B D:B12601 3.2 36.8 1.0 C5 D:B12601 3.3 33.1 1.0 C10 D:B12601 3.3 35.3 1.0 C2B D:B12601 3.3 35.6 1.0 C15 D:B12601 3.3 34.2 1.0 C20 D:B12601 3.6 34.0 1.0 C4B D:B12601 3.6 37.8 1.0 O28 D:B12601 3.9 33.3 1.0 C18 D:B12601 4.0 33.5 1.0 C2 D:B12601 4.0 33.6 1.0 C3 D:B12601 4.1 33.2 1.0 C13 D:B12601 4.1 34.5 1.0 C8 D:B12601 4.2 35.1 1.0 C17 D:B12601 4.2 34.4 1.0 C12 D:B12601 4.2 33.4 1.0 C7 D:B12601 4.3 33.2 1.0 C8B D:B12601 4.5 41.9 1.0 N1B D:B12601 4.5 39.6 1.0 C4' C:FWK501 4.5 37.2 1.0 C26 D:B12601 4.5 33.3 1.0 C27 D:B12601 4.6 33.3 1.0 C35 D:B12601 4.7 33.2 1.0 C42 D:B12601 4.7 33.5 1.0 C3' C:FWK501 4.8 35.9 1.0 C53 D:B12601 4.8 34.7 1.0 C48 D:B12601 4.9 34.9 1.0 C46 D:B12601 4.9 33.5 1.0 C54 D:B12601 5.0 33.6 1.0 C30 D:B12601 5.0 35.9 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