Cobalt in PDB 1uc5: Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol

All present enzymatic activity of Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol:
4.2.1.28;

The structure of Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol, PDB code: 1uc5 was solved by N.Shibata, Y.Nakanishi, M.Fukuoka, M.Yamanishi, N.Yasuoka, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.85 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.640, 122.270, 207.430, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.5

The structure of Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Cobalt atom in the Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol (pdb code 1uc5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol, PDB code: 1uc5:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1601 b:31.6 occ:1.00 CO B:CNC1601 0.0 31.6 1.0 N21 B:CNC1601 1.9 30.4 1.0 N24 B:CNC1601 1.9 29.8 1.0 N22 B:CNC1601 1.9 30.5 1.0 N23 B:CNC1601 1.9 29.2 1.0 N3B B:CNC1601 2.3 25.8 1.0 C9 B:CNC1601 2.9 30.1 1.0 C19 B:CNC1601 2.9 30.4 1.0 C4 B:CNC1601 2.9 31.6 1.0 C1 B:CNC1601 2.9 31.3 1.0 C11 B:CNC1601 2.9 29.1 1.0 C16 B:CNC1601 3.0 30.5 1.0 C14 B:CNC1601 3.0 29.0 1.0 C6 B:CNC1601 3.0 30.5 1.0 C2B B:CNC1601 3.2 25.6 1.0 C10 B:CNC1601 3.2 29.4 1.0 C5 B:CNC1601 3.4 31.6 1.0 C15 B:CNC1601 3.4 30.0 1.0 C9B B:CNC1601 3.5 27.1 1.0 C20 B:CNC1601 3.6 30.8 1.0 C4B B:CNC1601 4.0 26.1 1.0 C2 B:CNC1601 4.1 33.1 1.0 C18 B:CNC1601 4.2 30.3 1.0 C3 B:CNC1601 4.2 33.3 1.0 C8 B:CNC1601 4.2 30.3 1.0 C17 B:CNC1601 4.3 29.4 1.0 C12 B:CNC1601 4.3 29.8 1.0 C13 B:CNC1601 4.3 28.5 1.0 C7 B:CNC1601 4.3 31.0 1.0 N1B B:CNC1601 4.4 28.8 1.0 C26 B:CNC1601 4.5 36.0 1.0 C8B B:CNC1601 4.6 28.0 1.0 C49 B:CNC1601 4.8 29.5 1.0 C41 B:CNC1601 4.8 31.3 1.0 C35 B:CNC1601 4.9 29.1 1.0 C53 B:CNC1601 5.0 29.3 1.0 C46 B:CNC1601 5.0 27.6 1.0

Cobalt binding site 2 out of 2 in the Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Diol Dehydratase Complexed with (R)-1,2- Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ E:Co2601 b:39.5 occ:1.00 CO E:CNC2601 0.0 39.5 1.0 N21 E:CNC2601 1.9 40.7 1.0 N24 E:CNC2601 1.9 38.9 1.0 N22 E:CNC2601 1.9 39.7 1.0 N23 E:CNC2601 1.9 41.0 1.0 N3B E:CNC2601 2.3 40.1 1.0 C9 E:CNC2601 2.9 40.7 1.0 C19 E:CNC2601 2.9 38.2 1.0 C4 E:CNC2601 2.9 40.7 1.0 C1 E:CNC2601 2.9 39.4 1.0 C11 E:CNC2601 3.0 40.9 1.0 C16 E:CNC2601 3.0 37.2 1.0 C6 E:CNC2601 3.0 39.8 1.0 C14 E:CNC2601 3.0 39.5 1.0 C2B E:CNC2601 3.2 42.5 1.0 C10 E:CNC2601 3.2 40.6 1.0 C5 E:CNC2601 3.4 40.2 1.0 C15 E:CNC2601 3.5 38.5 1.0 C9B E:CNC2601 3.5 41.9 1.0 C20 E:CNC2601 3.6 38.1 1.0 O28 E:CNC2601 3.9 39.8 1.0 C4B E:CNC2601 4.1 40.7 1.0 C2 E:CNC2601 4.2 40.1 1.0 C18 E:CNC2601 4.2 37.2 1.0 C3 E:CNC2601 4.2 39.9 1.0 C8 E:CNC2601 4.2 39.9 1.0 C17 E:CNC2601 4.3 36.0 1.0 C7 E:CNC2601 4.3 39.4 1.0 C12 E:CNC2601 4.3 40.2 1.0 C13 E:CNC2601 4.4 39.7 1.0 C27 E:CNC2601 4.4 41.2 1.0 N1B E:CNC2601 4.5 42.7 1.0 C8B E:CNC2601 4.7 42.7 1.0 C26 E:CNC2601 4.7 40.8 1.0 C41 E:CNC2601 4.8 39.3 1.0 C35 E:CNC2601 4.9 41.3 1.0 C49 E:CNC2601 4.9 37.8 1.0 C53 E:CNC2601 5.0 39.8 1.0

N.Shibata, Y.Nakanishi, M.Fukuoka, M.Yamanishi, N.Yasuoka, T.Toraya. Structural Rationalization For the Lack of Stereospecificity in Coenzyme B12-Dependent Diol Dehydratase J.Biol.Chem. V. 278 22717 2003.
ISSN: ISSN 0021-9258
PubMed: 12684496
DOI: 10.1074/JBC.M301513200