Cobalt in PDB 1dio: Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca

All present enzymatic activity of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca:
4.2.1.28;

The structure of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca, PDB code: 1dio was solved by N.Shibata, J.Masuda, T.Tobimatsu, T.Toraya, K.Suto, Y.Morimoto, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.200, 122.300, 209.600, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.6

The structure of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Cobalt atom in the Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca (pdb code 1dio). 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-Cyanocobalamin Complex From Klebsiella Oxytoca, PDB code: 1dio:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ B:Co601 b:22.4 occ:1.00 CO B:B12601 0.0 22.4 1.0 N24 B:B12601 1.8 24.4 1.0 N23 B:B12601 1.8 23.9 1.0 N21 B:B12601 1.9 25.0 1.0 N22 B:B12601 2.0 25.3 1.0 N3B B:B12601 2.5 24.4 1.0 C19 B:B12601 2.8 24.2 1.0 C14 B:B12601 2.8 22.2 1.0 C16 B:B12601 2.8 21.7 1.0 C1 B:B12601 2.9 24.8 1.0 C11 B:B12601 2.9 24.2 1.0 C4 B:B12601 2.9 24.7 1.0 C9 B:B12601 3.0 24.7 1.0 C6 B:B12601 3.1 23.1 1.0 C15 B:B12601 3.2 22.4 1.0 C10 B:B12601 3.3 23.9 1.0 C2B B:B12601 3.4 24.8 1.0 C5 B:B12601 3.4 24.0 1.0 C20 B:B12601 3.6 21.4 1.0 C9B B:B12601 3.6 25.8 1.0 C4B B:B12601 4.0 26.1 1.0 O28 B:B12601 4.1 40.0 1.0 C18 B:B12601 4.1 23.0 1.0 C13 B:B12601 4.1 20.4 1.0 C17 B:B12601 4.1 24.1 1.0 C2 B:B12601 4.2 27.3 1.0 C12 B:B12601 4.2 22.8 1.0 C3 B:B12601 4.2 26.6 1.0 C8 B:B12601 4.4 24.8 1.0 C7 B:B12601 4.4 25.4 1.0 N1B B:B12601 4.6 25.8 1.0 C46 B:B12601 4.6 20.0 1.0 C27 B:B12601 4.6 37.3 1.0 C49 B:B12601 4.7 21.1 1.0 C54 B:B12601 4.7 21.1 1.0 C8B B:B12601 4.7 26.6 1.0 C53 B:B12601 4.7 22.3 1.0 C26 B:B12601 4.7 31.6 1.0 C48 B:B12601 4.8 20.7 1.0 C35 B:B12601 4.9 18.5 1.0

Cobalt binding site 2 out of 2 in the Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ E:Co601 b:27.6 occ:1.00 CO E:B12601 0.0 27.6 1.0 N21 E:B12601 1.8 28.1 1.0 N24 E:B12601 1.9 28.1 1.0 N23 E:B12601 1.9 26.4 1.0 N22 E:B12601 1.9 28.8 1.0 N3B E:B12601 2.5 29.4 1.0 C4 E:B12601 2.8 28.5 1.0 C19 E:B12601 2.8 26.9 1.0 C1 E:B12601 2.9 27.9 1.0 C9 E:B12601 2.9 26.9 1.0 C14 E:B12601 2.9 26.3 1.0 C11 E:B12601 2.9 26.8 1.0 C6 E:B12601 3.0 27.1 1.0 C16 E:B12601 3.0 25.9 1.0 C5 E:B12601 3.2 28.3 1.0 C10 E:B12601 3.3 27.0 1.0 C15 E:B12601 3.4 25.1 1.0 C2B E:B12601 3.5 29.8 1.0 C20 E:B12601 3.5 27.7 1.0 C9B E:B12601 3.5 30.8 1.0 O28 E:B12601 3.7 38.2 1.0 C4B E:B12601 4.0 30.1 1.0 C3 E:B12601 4.1 30.0 1.0 C2 E:B12601 4.1 29.2 1.0 C18 E:B12601 4.1 25.4 1.0 C12 E:B12601 4.2 25.2 1.0 C13 E:B12601 4.2 25.5 1.0 C17 E:B12601 4.3 27.2 1.0 C8 E:B12601 4.3 27.2 1.0 C7 E:B12601 4.3 27.9 1.0 C27 E:B12601 4.4 35.8 1.0 N1B E:B12601 4.6 31.1 1.0 C46 E:B12601 4.6 22.5 1.0 C49 E:B12601 4.6 27.7 1.0 C26 E:B12601 4.7 32.2 1.0 C8B E:B12601 4.7 31.5 1.0 C35 E:B12601 4.7 29.1 1.0 C54 E:B12601 4.9 26.3 1.0 C53 E:B12601 4.9 23.6 1.0 C41 E:B12601 4.9 25.5 1.0 C37 E:B12601 4.9 27.9 1.0 C48 E:B12601 4.9 27.3 1.0

N.Shibata, J.Masuda, T.Tobimatsu, T.Toraya, K.Suto, Y.Morimoto, N.Yasuoka. A New Mode of B12 Binding and the Direct Participation of A Potassium Ion in Enzyme Catalysis: X-Ray Structure of Diol Dehydratase. Structure Fold.Des. V. 7 997 1999.
ISSN: ISSN 0969-2126
PubMed: 10467140
DOI: 10.1016/S0969-2126(99)80126-9