Cobalt in PDB 1iwp: Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae

All present enzymatic activity of Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae:
4.2.1.30;

The structure of Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae, PDB code: 1iwp was solved by M.Yamanishi, M.Yunoki, T.Tobimatsu, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.380, 108.223, 113.141, 90.00, 96.75, 90.00
R / Rfree (%)	20.9 / 24.7

The structure of Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Cobalt atom in the Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae (pdb code 1iwp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae, PDB code: 1iwp:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1601 b:1.0 occ:1.00 CO B:B121601 0.0 1.0 1.0 N24 B:B121601 1.8 14.6 1.0 N23 B:B121601 1.8 16.4 1.0 N21 B:B121601 1.9 15.0 1.0 N22 B:B121601 2.0 16.7 1.0 N3B B:B121601 2.5 18.5 1.0 C19 B:B121601 2.8 14.5 1.0 C14 B:B121601 2.9 12.6 1.0 C16 B:B121601 2.9 13.3 1.0 C11 B:B121601 2.9 14.8 1.0 C1 B:B121601 2.9 14.0 1.0 C9 B:B121601 3.0 17.1 1.0 C4 B:B121601 3.0 13.1 1.0 C6 B:B121601 3.1 13.8 1.0 C15 B:B121601 3.3 13.3 1.0 C10 B:B121601 3.3 17.4 1.0 C2B B:B121601 3.3 17.6 1.0 C5 B:B121601 3.5 14.8 1.0 C9B B:B121601 3.6 19.5 1.0 C20 B:B121601 3.6 16.9 1.0 O28 B:B121601 3.7 19.4 1.0 C4B B:B121601 4.1 18.3 1.0 C18 B:B121601 4.1 16.2 1.0 C2 B:B121601 4.2 15.9 1.0 C17 B:B121601 4.2 16.1 1.0 C13 B:B121601 4.2 17.1 1.0 C12 B:B121601 4.2 17.4 1.0 C3 B:B121601 4.3 16.0 1.0 C27 B:B121601 4.3 19.0 1.0 O A:HOH1723 4.3 24.0 1.0 C8 B:B121601 4.3 19.4 1.0 C7 B:B121601 4.4 20.8 1.0 N1B B:B121601 4.5 22.1 1.0 C26 B:B121601 4.7 18.2 1.0 C46 B:B121601 4.7 18.8 1.0 C8B B:B121601 4.7 19.0 1.0 C53 B:B121601 4.8 14.9 1.0 C54 B:B121601 4.9 15.3 1.0 C49 B:B121601 4.9 20.3 1.0 C48 B:B121601 5.0 17.5 1.0

Cobalt binding site 2 out of 2 in the Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Glycerol Dehydratase-Cyanocobalamin Complex of Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Co2601 b:1.0 occ:1.00 CO E:B122601 0.0 1.0 1.0 N24 E:B122601 1.8 18.3 1.0 N23 E:B122601 1.8 16.0 1.0 N21 E:B122601 1.9 17.9 1.0 N22 E:B122601 2.0 18.9 1.0 N3B E:B122601 2.5 27.2 1.0 C19 E:B122601 2.9 16.8 1.0 C14 E:B122601 2.9 15.2 1.0 C16 E:B122601 2.9 14.0 1.0 C11 E:B122601 2.9 16.1 1.0 C1 E:B122601 2.9 17.6 1.0 C4 E:B122601 3.0 17.0 1.0 C9 E:B122601 3.0 16.9 1.0 C6 E:B122601 3.1 17.6 1.0 C15 E:B122601 3.3 15.3 1.0 C10 E:B122601 3.3 16.6 1.0 C2B E:B122601 3.3 25.1 1.0 C5 E:B122601 3.5 20.8 1.0 C9B E:B122601 3.6 24.9 1.0 C20 E:B122601 3.6 17.5 1.0 O28 E:B122601 3.7 26.3 1.0 C4B E:B122601 4.1 25.4 1.0 C18 E:B122601 4.1 17.7 1.0 C2 E:B122601 4.2 19.5 1.0 C17 E:B122601 4.2 18.4 1.0 C13 E:B122601 4.2 17.0 1.0 C12 E:B122601 4.2 18.2 1.0 C3 E:B122601 4.3 20.4 1.0 C27 E:B122601 4.3 26.8 1.0 C8 E:B122601 4.4 20.9 1.0 C7 E:B122601 4.4 21.8 1.0 N1B E:B122601 4.5 26.2 1.0 C26 E:B122601 4.6 23.2 1.0 O L:HOH2754 4.6 50.3 1.0 C46 E:B122601 4.7 17.5 1.0 C8B E:B122601 4.7 27.0 1.0 C53 E:B122601 4.8 16.0 1.0 C54 E:B122601 4.9 15.9 1.0

M.Yamanishi, M.Yunoki, T.Tobimatsu, H.Sato, J.Matsui, A.Dokiya, Y.Iuchi, K.Oe, K.Suto, N.Shibata, Y.Morimoto, N.Yasuoka, T.Toraya. The Crystal Structure of Coenzyme B12-Dependent Glycerol Dehydratase in Complex with Cobalamin and Propane-1,2-Diol. Eur.J.Biochem. V. 269 4484 2002.
ISSN: ISSN 0014-2956
PubMed: 12230560
DOI: 10.1046/J.1432-1033.2002.03151.X