Cobalt in PDB 1iwb: Crystal Structure of Diol Dehydratase

All present enzymatic activity of Crystal Structure of Diol Dehydratase:
4.2.1.28;

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

Resolution Low / High (Å)	10.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.790, 122.400, 207.590, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 25.6

The structure of Crystal Structure of Diol Dehydratase also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Cobalt atom in the Crystal Structure of Diol Dehydratase (pdb code 1iwb). 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, PDB code: 1iwb:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Diol Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1601 b:16.7 occ:1.00 CO B:B121601 0.0 16.7 1.0 N21 B:B121601 1.9 14.7 1.0 N24 B:B121601 1.9 13.9 1.0 N23 B:B121601 1.9 16.9 1.0 N22 B:B121601 1.9 12.3 1.0 N3B B:B121601 2.3 17.5 1.0 C19 B:B121601 2.8 9.8 1.0 C9 B:B121601 2.9 11.8 1.0 C4 B:B121601 2.9 14.6 1.0 C11 B:B121601 2.9 21.0 1.0 C1 B:B121601 2.9 16.6 1.0 C14 B:B121601 2.9 15.7 1.0 C16 B:B121601 2.9 16.4 1.0 C6 B:B121601 3.0 16.3 1.0 C2B B:B121601 3.2 17.5 1.0 C10 B:B121601 3.2 14.9 1.0 C5 B:B121601 3.3 16.2 1.0 C9B B:B121601 3.4 15.1 1.0 C15 B:B121601 3.4 15.9 1.0 C20 B:B121601 3.5 15.6 1.0 C4B B:B121601 3.9 6.3 1.0 C18 B:B121601 4.1 11.2 1.0 C2 B:B121601 4.2 15.3 1.0 C3 B:B121601 4.2 15.9 1.0 C12 B:B121601 4.2 25.8 1.0 C17 B:B121601 4.2 17.2 1.0 C13 B:B121601 4.2 14.2 1.0 C8 B:B121601 4.2 19.9 1.0 C7 B:B121601 4.3 17.5 1.0 N1B B:B121601 4.4 18.3 1.0 C26 B:B121601 4.5 28.5 1.0 C8B B:B121601 4.5 12.2 1.0 C49 B:B121601 4.7 14.7 1.0 C46 B:B121601 4.7 16.7 1.0 C54 B:B121601 4.7 10.1 1.0 C35 B:B121601 4.8 14.4 1.0 C41 B:B121601 4.8 20.6 1.0 C53 B:B121601 4.9 7.1 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Diol Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Co1602 b:21.6 occ:1.00 CO E:B121602 0.0 21.6 1.0 N21 E:B121602 1.9 20.9 1.0 N24 E:B121602 1.9 15.8 1.0 N23 E:B121602 1.9 18.7 1.0 N22 E:B121602 1.9 16.6 1.0 N3B E:B121602 2.2 25.1 1.0 C9 E:B121602 2.9 22.4 1.0 C19 E:B121602 2.9 16.3 1.0 C4 E:B121602 2.9 19.8 1.0 C1 E:B121602 2.9 16.6 1.0 C11 E:B121602 2.9 16.3 1.0 C14 E:B121602 2.9 18.2 1.0 C16 E:B121602 2.9 14.4 1.0 C6 E:B121602 3.0 15.0 1.0 C2B E:B121602 3.2 35.2 1.0 C10 E:B121602 3.3 14.6 1.0 C9B E:B121602 3.3 27.1 1.0 C5 E:B121602 3.3 19.1 1.0 C15 E:B121602 3.4 18.3 1.0 C20 E:B121602 3.6 14.5 1.0 O28 E:B121602 3.7 29.6 1.0 C4B E:B121602 3.8 24.5 1.0 C18 E:B121602 4.1 13.3 1.0 C2 E:B121602 4.2 21.7 1.0 C3 E:B121602 4.2 23.4 1.0 C8 E:B121602 4.2 24.1 1.0 C12 E:B121602 4.2 18.5 1.0 C17 E:B121602 4.2 18.6 1.0 C13 E:B121602 4.2 15.0 1.0 C7 E:B121602 4.3 20.9 1.0 C27 E:B121602 4.4 27.5 1.0 N1B E:B121602 4.4 32.4 1.0 C8B E:B121602 4.5 25.0 1.0 O E:HOH1641 4.7 53.1 1.0 C46 E:B121602 4.7 12.5 1.0 C26 E:B121602 4.7 18.9 1.0 C49 E:B121602 4.7 32.4 1.0 C54 E:B121602 4.8 23.9 1.0 C41 E:B121602 4.8 21.6 1.0 C35 E:B121602 4.8 17.4 1.0 C53 E:B121602 4.9 14.2 1.0

N.Shibata, J.Masuda, Y.Morimoto, N.Yasuoka, T.Toraya. Substrate-Induced Conformational Change of A Coenzyme B12-Dependent Enzyme: Crystal Structure of the Substrate-Free Form of Diol Dehydratase Biochemistry V. 41 12607 2002.
ISSN: ISSN 0006-2960
PubMed: 12379103
DOI: 10.1021/BI026104Z