Cobalt in PDB 5ysr: Ethanolamine Ammonia-Lyase, Adocbl/2-Amino-1-Propanol

All present enzymatic activity of Ethanolamine Ammonia-Lyase, Adocbl/2-Amino-1-Propanol:
4.3.1.7;

The structure of Ethanolamine Ammonia-Lyase, Adocbl/2-Amino-1-Propanol, PDB code: 5ysr 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 / 2.05
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	242.500, 242.500, 77.020, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 25.7

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

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


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/2-Amino-1-Propanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co601 b:28.5 occ:1.00 CO B:B12601 0.0 28.5 1.0 N21 B:B12601 1.8 20.4 1.0 N24 B:B12601 1.8 26.3 1.0 N23 B:B12601 1.8 19.5 1.0 N22 B:B12601 1.9 26.9 1.0 N3B B:B12601 2.3 26.7 1.0 C19 B:B12601 2.7 28.2 1.0 C1 B:B12601 2.8 28.8 1.0 C4 B:B12601 2.8 23.4 1.0 C14 B:B12601 2.8 22.4 1.0 C9 B:B12601 2.8 24.8 1.0 C11 B:B12601 2.9 19.1 1.0 C16 B:B12601 3.0 23.0 1.0 C6 B:B12601 3.0 23.1 1.0 C9B B:B12601 3.2 23.1 1.0 C10 B:B12601 3.3 18.9 1.0 C5 B:B12601 3.3 22.9 1.0 C15 B:B12601 3.3 20.0 1.0 C2B B:B12601 3.3 23.7 1.0 C20 B:B12601 3.5 28.7 1.0 C4B B:B12601 3.6 21.5 1.0 O28 B:B12601 3.7 25.9 1.0 C2 B:B12601 4.0 24.6 1.0 C18 B:B12601 4.0 21.1 1.0 C3 B:B12601 4.1 21.0 1.0 C13 B:B12601 4.1 20.6 1.0 C8 B:B12601 4.2 19.0 1.0 C17 B:B12601 4.2 23.2 1.0 C12 B:B12601 4.2 19.6 1.0 C7 B:B12601 4.3 20.9 1.0 C27 B:B12601 4.4 20.3 1.0 C26 B:B12601 4.5 20.3 1.0 C8B B:B12601 4.5 25.6 1.0 N1B B:B12601 4.5 24.9 1.0 O3' A:5AD501 4.6 48.4 1.0 C42 B:B12601 4.7 22.6 1.0 C3' A:5AD501 4.7 44.5 1.0 C35 B:B12601 4.8 22.5 1.0 C54 B:B12601 4.8 21.8 1.0 C53 B:B12601 4.8 20.1 1.0 C46 B:B12601 4.9 18.1 1.0 C48 B:B12601 4.9 21.0 1.0 C2' A:5AD501 4.9 45.2 1.0 C30 B:B12601 5.0 23.8 1.0

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


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/2-Amino-1-Propanol within 5.0Å range: probe atom residue distance (Å) B Occ D:Co601 b:30.7 occ:1.00 CO D:B12601 0.0 30.7 1.0 N21 D:B12601 1.8 29.7 1.0 N23 D:B12601 1.8 26.3 1.0 N24 D:B12601 1.8 24.0 1.0 N22 D:B12601 1.9 23.3 1.0 N3B D:B12601 2.3 30.5 1.0 C19 D:B12601 2.7 23.6 1.0 C1 D:B12601 2.8 28.4 1.0 C14 D:B12601 2.8 24.7 1.0 C4 D:B12601 2.8 28.0 1.0 C9 D:B12601 2.8 22.6 1.0 C11 D:B12601 2.9 25.1 1.0 C16 D:B12601 3.0 22.5 1.0 C6 D:B12601 3.0 18.0 1.0 C9B D:B12601 3.2 28.6 1.0 C10 D:B12601 3.3 24.0 1.0 C5 D:B12601 3.3 18.1 1.0 C15 D:B12601 3.3 25.1 1.0 C2B D:B12601 3.4 26.3 1.0 C20 D:B12601 3.6 34.7 1.0 O28 D:B12601 3.6 18.8 1.0 C4B D:B12601 3.6 25.5 1.0 C2 D:B12601 4.0 27.1 1.0 C18 D:B12601 4.0 24.4 1.0 C3 D:B12601 4.1 23.7 1.0 C13 D:B12601 4.1 23.3 1.0 C8 D:B12601 4.2 23.5 1.0 C12 D:B12601 4.2 18.0 1.0 O3' C:5AD501 4.2 42.1 1.0 C17 D:B12601 4.2 25.0 1.0 C27 D:B12601 4.3 19.4 1.0 C7 D:B12601 4.3 21.9 1.0 O2' C:5AD501 4.3 40.7 1.0 C26 D:B12601 4.4 24.5 1.0 C8B D:B12601 4.5 31.8 1.0 N1B D:B12601 4.5 29.3 1.0 C2' C:5AD501 4.5 37.5 1.0 C3' C:5AD501 4.6 35.6 1.0 C42 D:B12601 4.7 26.0 1.0 C35 D:B12601 4.8 18.0 1.0 C53 D:B12601 4.8 24.7 1.0 C46 D:B12601 4.8 29.1 1.0 C48 D:B12601 5.0 23.4 1.0 C54 D:B12601 5.0 28.9 1.0 C5B D:B12601 5.0 20.6 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