Cobalt in PDB 1eex: Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca

All present enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca:
4.2.1.28;

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

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.380, 121.400, 207.600, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 22.6

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Cobalt atom in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca (pdb code 1eex). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca, PDB code: 1eex:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin 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 Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ A:Co601 b:11.4 occ:1.00 CO A:COY601 0.0 11.4 1.0 N24 A:COY601 1.9 8.9 1.0 N23 A:COY601 1.9 11.3 1.0 N21 A:COY601 1.9 12.2 1.0 N22 A:COY601 1.9 10.7 1.0 C75 A:COY601 2.1 11.7 1.0 N3B A:COY601 2.2 9.9 1.0 C9 A:COY601 2.8 9.1 1.0 C19 A:COY601 2.9 6.5 1.0 C4 A:COY601 2.9 10.5 1.0 C14 A:COY601 2.9 10.2 1.0 C11 A:COY601 2.9 12.9 1.0 C1 A:COY601 2.9 11.6 1.0 C16 A:COY601 2.9 7.5 1.0 C6 A:COY601 3.0 7.4 1.0 C74 A:COY601 3.2 13.9 1.0 C2B A:COY601 3.2 8.5 1.0 C10 A:COY601 3.2 11.8 1.0 C9B A:COY601 3.3 9.9 1.0 C15 A:COY601 3.3 9.4 1.0 C5 A:COY601 3.3 11.6 1.0 C20 A:COY601 3.5 8.9 1.0 C4B A:COY601 3.8 11.3 1.0 C18 A:COY601 4.1 12.4 1.0 C3 A:COY601 4.2 13.1 1.0 C2 A:COY601 4.2 13.1 1.0 C8 A:COY601 4.2 10.4 1.0 C12 A:COY601 4.2 15.1 1.0 C13 A:COY601 4.2 13.7 1.0 C17 A:COY601 4.2 16.4 1.0 C7 A:COY601 4.3 13.1 1.0 N1B A:COY601 4.4 12.4 1.0 C73 A:COY601 4.4 14.1 1.0 C8B A:COY601 4.5 14.2 1.0 C26 A:COY601 4.6 12.5 1.0 C46 A:COY601 4.7 9.8 1.0 C41 A:COY601 4.7 13.1 1.0 C49 A:COY601 4.7 11.1 1.0 C54 A:COY601 4.8 10.9 1.0 C35 A:COY601 4.8 9.7 1.0 C53 A:COY601 4.8 7.4 1.0 C37 A:COY601 4.9 10.2 1.0 C48 A:COY601 4.9 10.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin 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 Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ L:Co601 b:19.7 occ:1.00 CO L:COY601 0.0 19.7 1.0 N21 L:COY601 1.9 24.4 1.0 N24 L:COY601 1.9 16.1 1.0 N22 L:COY601 1.9 16.4 1.0 C75 L:COY601 1.9 23.6 1.0 N23 L:COY601 1.9 18.2 1.0 N3B L:COY601 2.1 26.8 1.0 C19 L:COY601 2.8 21.0 1.0 C9 L:COY601 2.8 18.2 1.0 C4 L:COY601 2.8 24.7 1.0 C1 L:COY601 2.9 27.0 1.0 C11 L:COY601 2.9 20.6 1.0 C14 L:COY601 2.9 14.0 1.0 C16 L:COY601 3.0 13.6 1.0 C6 L:COY601 3.0 19.6 1.0 C2B L:COY601 3.1 31.2 1.0 C74 L:COY601 3.2 24.2 1.0 C10 L:COY601 3.2 19.3 1.0 C9B L:COY601 3.3 23.3 1.0 C5 L:COY601 3.3 21.1 1.0 C15 L:COY601 3.4 17.9 1.0 C20 L:COY601 3.6 18.5 1.0 C4B L:COY601 3.8 26.7 1.0 C18 L:COY601 4.1 17.6 1.0 C2 L:COY601 4.1 20.1 1.0 C3 L:COY601 4.2 22.3 1.0 C8 L:COY601 4.2 19.2 1.0 C12 L:COY601 4.2 18.7 1.0 C17 L:COY601 4.2 14.3 1.0 C13 L:COY601 4.2 14.5 1.0 C7 L:COY601 4.3 16.5 1.0 N1B L:COY601 4.3 25.1 1.0 C73 L:COY601 4.4 26.6 1.0 C8B L:COY601 4.4 29.1 1.0 C26 L:COY601 4.5 15.8 1.0 C46 L:COY601 4.7 14.5 1.0 C54 L:COY601 4.7 16.7 1.0 C49 L:COY601 4.7 26.0 1.0 C35 L:COY601 4.8 25.8 1.0 C41 L:COY601 4.8 23.7 1.0 C53 L:COY601 4.9 16.2 1.0 C37 L:COY601 4.9 19.9 1.0 C48 L:COY601 5.0 20.9 1.0

J.Masuda, N.Shibata, Y.Morimoto, T.Toraya, N.Yasuoka. How A Protein Generates A Catalytic Radical From Coenzyme B(12): X-Ray Structure of A Diol-Dehydratase-Adeninylpentylcobalamin Complex. Structure Fold.Des. V. 8 775 2000.
ISSN: ISSN 0969-2126
PubMed: 10903944
DOI: 10.1016/S0969-2126(00)00164-7