Cobalt in PDB 1egm: Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K.

All present enzymatic activity of Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K.:
4.2.1.28;

The structure of Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K., PDB code: 1egm was solved by J.Masuda, N.Shibata, 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 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.000, 121.600, 207.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24.9

The structure of Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K. also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K. (pdb code 1egm). 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 Diol Dehydratase-Cyanocobalamin Complex at 100K., PDB code: 1egm:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K.


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 Diol Dehydratase-Cyanocobalamin Complex at 100K. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co601 b:12.3 occ:1.00 CO A:CNC601 0.0 12.3 1.0 N21 A:CNC601 1.8 13.7 1.0 N24 A:CNC601 1.9 16.4 1.0 N23 A:CNC601 1.9 16.5 1.0 N22 A:CNC601 1.9 18.7 1.0 N3B A:CNC601 2.2 14.6 1.0 C9 A:CNC601 2.8 14.7 1.0 C19 A:CNC601 2.8 17.7 1.0 C4 A:CNC601 2.9 16.7 1.0 C1 A:CNC601 2.9 16.1 1.0 C11 A:CNC601 2.9 16.7 1.0 C14 A:CNC601 2.9 17.9 1.0 C16 A:CNC601 2.9 15.4 1.0 C6 A:CNC601 3.0 15.4 1.0 C2B A:CNC601 3.2 15.3 1.0 C10 A:CNC601 3.2 14.9 1.0 C9B A:CNC601 3.3 10.7 1.0 C5 A:CNC601 3.3 17.2 1.0 C15 A:CNC601 3.4 18.3 1.0 C20 A:CNC601 3.5 13.1 1.0 C4B A:CNC601 3.8 14.9 1.0 C18 A:CNC601 4.1 20.2 1.0 C2 A:CNC601 4.1 18.5 1.0 C3 A:CNC601 4.2 18.0 1.0 C8 A:CNC601 4.2 13.1 1.0 C12 A:CNC601 4.2 20.3 1.0 C17 A:CNC601 4.2 20.0 1.0 C13 A:CNC601 4.2 19.3 1.0 C7 A:CNC601 4.3 13.6 1.0 N1B A:CNC601 4.4 15.6 1.0 C8B A:CNC601 4.4 11.7 1.0 C26 A:CNC601 4.5 15.4 1.0 C49 A:CNC601 4.7 21.3 1.0 C46 A:CNC601 4.7 9.3 1.0 C54 A:CNC601 4.8 9.2 1.0 C35 A:CNC601 4.8 11.6 1.0 C41 A:CNC601 4.8 20.1 1.0 C53 A:CNC601 4.9 12.4 1.0 C37 A:CNC601 4.9 17.6 1.0 C48 A:CNC601 4.9 14.7 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Diol Dehydratase-Cyanocobalamin Complex at 100K.


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 Diol Dehydratase-Cyanocobalamin Complex at 100K. within 5.0Å range: probe atom residue distance (Å) B Occ L:Co601 b:23.7 occ:1.00 CO L:CNC601 0.0 23.7 1.0 N21 L:CNC601 1.8 35.6 1.0 N24 L:CNC601 1.9 27.3 1.0 N22 L:CNC601 1.9 26.6 1.0 N23 L:CNC601 1.9 33.0 1.0 N3B L:CNC601 2.3 22.1 1.0 C9 L:CNC601 2.8 31.5 1.0 C19 L:CNC601 2.9 25.4 1.0 C1 L:CNC601 2.9 27.8 1.0 C4 L:CNC601 2.9 30.7 1.0 C16 L:CNC601 2.9 24.3 1.0 C11 L:CNC601 2.9 30.0 1.0 C14 L:CNC601 3.0 30.4 1.0 C6 L:CNC601 3.0 35.6 1.0 C10 L:CNC601 3.2 27.7 1.0 C2B L:CNC601 3.3 28.7 1.0 C5 L:CNC601 3.3 34.1 1.0 C9B L:CNC601 3.4 29.5 1.0 C15 L:CNC601 3.4 26.1 1.0 C20 L:CNC601 3.5 29.4 1.0 C4B L:CNC601 3.9 41.5 1.0 C18 L:CNC601 4.1 23.8 1.0 C2 L:CNC601 4.1 26.4 1.0 C3 L:CNC601 4.2 34.1 1.0 C8 L:CNC601 4.2 28.1 1.0 C17 L:CNC601 4.2 20.2 1.0 C12 L:CNC601 4.3 27.6 1.0 C7 L:CNC601 4.3 29.6 1.0 C13 L:CNC601 4.3 25.5 1.0 N1B L:CNC601 4.5 26.7 1.0 C8B L:CNC601 4.6 27.2 1.0 C26 L:CNC601 4.6 28.4 1.0 C49 L:CNC601 4.7 29.6 1.0 C41 L:CNC601 4.7 19.0 1.0 O28 L:CNC601 4.8 59.2 1.0 C54 L:CNC601 4.8 18.4 1.0 C46 L:CNC601 4.8 21.4 1.0 C35 L:CNC601 4.8 25.1 1.0 C53 L:CNC601 4.9 24.2 1.0 C37 L:CNC601 4.9 25.7 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