Cobalt in PDB 7xrm: Ethanolamine Ammonia-Lyase Complexed with Adomecbl

All present enzymatic activity of Ethanolamine Ammonia-Lyase Complexed with Adomecbl:
4.3.1.7;

The structure of Ethanolamine Ammonia-Lyase Complexed with Adomecbl, PDB code: 7xrm 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)	46.42 / 2.13
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	242.885, 242.885, 76.638, 90, 90, 120
R / Rfree (%)	19.4 / 22

The binding sites of Cobalt atom in the Ethanolamine Ammonia-Lyase Complexed with Adomecbl (pdb code 7xrm). 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, PDB code: 7xrm:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Ethanolamine Ammonia-Lyase 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 Ethanolamine Ammonia-Lyase Complexed with Adomecbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:41.5 occ:1.00 CO B:B12301 0.0 41.5 1.0 N24 B:B12301 1.8 39.3 1.0 N21 B:B12301 1.8 41.4 1.0 N23 B:B12301 1.8 37.8 1.0 N22 B:B12301 1.9 41.0 1.0 N3B B:B12301 2.3 37.7 1.0 C6' A:FWK506 2.6 42.4 1.0 C19 B:B12301 2.8 43.9 1.0 C4 B:B12301 2.8 39.8 1.0 C14 B:B12301 2.8 37.1 1.0 C9 B:B12301 2.8 40.0 1.0 C1 B:B12301 2.8 42.2 1.0 C11 B:B12301 2.9 36.0 1.0 C6 B:B12301 3.0 38.0 1.0 C16 B:B12301 3.0 37.0 1.0 C9B B:B12301 3.2 40.0 1.0 C5' A:FWK506 3.3 39.7 1.0 C10 B:B12301 3.3 36.2 1.0 C5 B:B12301 3.3 40.5 1.0 C2B B:B12301 3.3 39.7 1.0 C15 B:B12301 3.3 36.8 1.0 C20 B:B12301 3.6 44.1 1.0 C4B B:B12301 3.7 43.4 1.0 C2 B:B12301 4.0 42.4 1.0 C18 B:B12301 4.0 41.3 1.0 C3 B:B12301 4.1 38.2 1.0 C13 B:B12301 4.1 40.1 1.0 C8 B:B12301 4.1 38.1 1.0 C17 B:B12301 4.2 38.4 1.0 C12 B:B12301 4.2 34.6 1.0 C7 B:B12301 4.2 39.3 1.0 C26 B:B12301 4.4 38.7 1.0 C8B B:B12301 4.5 39.2 1.0 N1B B:B12301 4.5 39.0 1.0 C4' A:FWK506 4.6 32.3 1.0 C35 B:B12301 4.7 41.9 1.0 C53 B:B12301 4.8 40.4 1.0 C41 B:B12301 4.8 45.4 1.0 C42 B:B12301 4.9 42.3 1.0 C48 B:B12301 4.9 36.1 1.0 C3' A:FWK506 5.0 37.0 1.0 C54 B:B12301 5.0 37.1 1.0 O28 B:B12301 5.0 42.5 1.0

Cobalt binding site 2 out of 2 in the Ethanolamine Ammonia-Lyase 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 Ethanolamine Ammonia-Lyase Complexed with Adomecbl within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:65.0 occ:1.00 CO D:B12301 0.0 65.0 1.0 N24 D:B12301 1.8 63.0 1.0 N21 D:B12301 1.8 65.5 1.0 N23 D:B12301 1.8 63.6 1.0 N22 D:B12301 1.8 68.3 1.0 N3B D:B12301 2.3 61.5 1.0 C6' C:FWK509 2.7 59.5 1.0 C19 D:B12301 2.8 64.3 1.0 C9 D:B12301 2.8 66.7 1.0 C4 D:B12301 2.8 65.8 1.0 C14 D:B12301 2.8 55.8 1.0 C1 D:B12301 2.8 64.9 1.0 C11 D:B12301 2.9 64.8 1.0 C6 D:B12301 3.0 69.8 1.0 C16 D:B12301 3.0 56.7 1.0 C9B D:B12301 3.2 70.0 1.0 C10 D:B12301 3.3 64.4 1.0 C5 D:B12301 3.3 69.4 1.0 C2B D:B12301 3.3 61.8 1.0 C15 D:B12301 3.3 54.7 1.0 C5' C:FWK509 3.3 55.3 1.0 C20 D:B12301 3.6 62.8 1.0 C4B D:B12301 3.6 67.0 1.0 C18 D:B12301 4.0 58.3 1.0 C2 D:B12301 4.0 64.7 1.0 C8 D:B12301 4.1 67.6 1.0 C3 D:B12301 4.1 62.8 1.0 C13 D:B12301 4.1 51.0 1.0 C17 D:B12301 4.2 56.9 1.0 C12 D:B12301 4.2 55.0 1.0 C7 D:B12301 4.2 70.3 1.0 C8B D:B12301 4.5 69.1 1.0 N1B D:B12301 4.5 66.9 1.0 C26 D:B12301 4.5 59.8 1.0 C41 D:B12301 4.6 66.9 1.0 C35 D:B12301 4.7 66.0 1.0 C4' C:FWK509 4.7 49.0 1.0 C53 D:B12301 4.8 51.6 1.0 C48 D:B12301 4.9 55.9 1.0 C54 D:B12301 4.9 52.1 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