Cobalt in PDB 5ysn: Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free

All present enzymatic activity of Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free:
4.3.1.7;

The structure of Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free, PDB code: 5ysn was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	242.723, 242.723, 76.573, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 19.2

The binding sites of Cobalt atom in the Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free (pdb code 5ysn). 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, Adocbl/Substrate-Free, PDB code: 5ysn:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free


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, Adocbl/Substrate-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:Co601 b:26.8 occ:1.00 CO B:B12601 0.0 26.8 1.0 N21 B:B12601 1.8 29.6 1.0 N23 B:B12601 1.8 29.0 1.0 N22 B:B12601 1.9 27.4 1.0 N24 B:B12601 1.9 29.2 1.0 N3B B:B12601 2.3 28.6 1.0 C19 B:B12601 2.7 30.4 1.0 C1 B:B12601 2.8 31.6 1.0 C9 B:B12601 2.8 25.6 1.0 C14 B:B12601 2.8 27.6 1.0 C4 B:B12601 2.8 27.7 1.0 C11 B:B12601 2.9 27.1 1.0 C5' A:5AD501 3.0 28.3 1.0 C6 B:B12601 3.0 24.2 1.0 C16 B:B12601 3.0 27.6 1.0 C9B B:B12601 3.2 29.3 1.0 C10 B:B12601 3.3 25.0 1.0 C2B B:B12601 3.3 26.9 1.0 C5 B:B12601 3.4 25.0 1.0 C15 B:B12601 3.4 26.6 1.0 C20 B:B12601 3.5 31.6 1.0 C4B B:B12601 3.7 26.9 1.0 C2 B:B12601 4.0 29.9 1.0 C18 B:B12601 4.1 29.1 1.0 C3 B:B12601 4.1 27.1 1.0 C13 B:B12601 4.1 26.5 1.0 C8 B:B12601 4.2 24.4 1.0 C12 B:B12601 4.2 26.2 1.0 C17 B:B12601 4.3 28.1 1.0 C7 B:B12601 4.3 24.8 1.0 C4' A:5AD501 4.4 29.3 1.0 C26 B:B12601 4.4 32.0 1.0 N1B B:B12601 4.5 27.9 1.0 C8B B:B12601 4.5 28.5 1.0 C42 B:B12601 4.8 25.2 1.0 C35 B:B12601 4.9 24.6 1.0 C48 B:B12601 4.9 27.6 1.0 C53 B:B12601 4.9 25.4 1.0 C46 B:B12601 4.9 22.3 1.0 C3' A:5AD501 5.0 32.1 1.0 C30 B:B12601 5.0 28.2 1.0

Cobalt binding site 2 out of 2 in the Ethanolamine Ammonia-Lyase, Adocbl/Substrate-Free


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, Adocbl/Substrate-Free within 5.0Å range: probe atom residue distance (Å) B Occ D:Co601 b:38.9 occ:1.00 CO D:B12601 0.0 38.9 1.0 N21 D:B12601 1.8 40.6 1.0 N23 D:B12601 1.8 39.5 1.0 N22 D:B12601 1.9 42.0 1.0 N24 D:B12601 1.9 36.4 1.0 N3B D:B12601 2.3 34.9 1.0 C19 D:B12601 2.7 36.5 1.0 C1 D:B12601 2.8 38.6 1.0 C9 D:B12601 2.8 41.9 1.0 C4 D:B12601 2.8 41.5 1.0 C14 D:B12601 2.9 36.2 1.0 C11 D:B12601 2.9 39.0 1.0 C6 D:B12601 3.0 40.9 1.0 C16 D:B12601 3.0 34.2 1.0 C5' C:5AD501 3.1 38.7 1.0 C9B D:B12601 3.2 36.2 1.0 C10 D:B12601 3.3 40.5 1.0 C2B D:B12601 3.3 35.0 1.0 C5 D:B12601 3.3 40.5 1.0 C15 D:B12601 3.4 33.9 1.0 C20 D:B12601 3.6 38.2 1.0 C4B D:B12601 3.7 34.7 1.0 C2 D:B12601 4.0 39.2 1.0 C3 D:B12601 4.1 41.2 1.0 C18 D:B12601 4.1 35.3 1.0 C8 D:B12601 4.1 41.7 1.0 C13 D:B12601 4.2 33.7 1.0 C12 D:B12601 4.2 34.3 1.0 C26 D:B12601 4.3 38.3 1.0 C17 D:B12601 4.3 33.8 1.0 C7 D:B12601 4.3 40.7 1.0 C4' C:5AD501 4.4 39.1 1.0 N1B D:B12601 4.5 36.0 1.0 C8B D:B12601 4.5 37.0 1.0 C41 D:B12601 4.8 42.7 1.0 C35 D:B12601 4.8 39.0 1.0 C53 D:B12601 4.9 32.0 1.0 C46 D:B12601 4.9 30.6 1.0 C54 D:B12601 5.0 32.9 1.0 C30 D:B12601 5.0 42.1 1.0

N.Shibata, Y.Sueyoshi, Y.Higuchi, T.Toraya. Direct Participation of A Peripheral Side Chain of A Corrin Ring in Coenzyme B12CATALYSIS. Angew. Chem. Int. Ed. Engl. V. 57 7830 2018.
ISSN: ESSN 1521-3773
PubMed: 29797764
DOI: 10.1002/ANIE.201803591