Potassium in PDB 1dio: Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca

All present enzymatic activity of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca:
4.2.1.28;

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

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.200, 122.300, 209.600, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.6

The structure of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

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

Potassium binding site 1 out of 2 in the Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:18.4 occ:1.00 OE1 A:GLN141 2.2 13.4 1.0 OE1 A:GLU170 2.3 19.5 1.0 OE1 A:GLN296 2.4 21.7 1.0 O1 A:PGO602 2.4 23.4 1.0 O A:SER362 2.4 21.9 1.0 O2 A:PGO602 2.4 24.7 1.0 OE1 A:GLU221 2.5 19.4 1.0 CD A:GLU170 3.2 19.5 1.0 C2 A:PGO602 3.3 24.9 1.0 CD A:GLU221 3.3 22.6 1.0 C1 A:PGO602 3.4 23.6 1.0 CD A:GLN141 3.4 14.8 1.0 CD A:GLN296 3.4 23.3 1.0 C A:SER362 3.5 21.1 1.0 OE2 A:GLU170 3.5 18.6 1.0 OE2 A:GLU221 3.7 24.1 1.0 NE2 A:GLN296 3.9 20.6 1.0 NE2 A:HIS143 3.9 16.7 1.0 NE2 A:GLN141 4.0 15.1 1.0 CB A:SER362 4.0 16.1 1.0 NE2 A:GLN200 4.1 16.7 1.0 OG A:SER362 4.2 15.4 1.0 CA A:SER362 4.2 19.6 1.0 OD2 A:ASP335 4.4 22.8 1.0 N A:GLY363 4.4 21.3 1.0 CD2 A:HIS143 4.5 16.3 1.0 CG A:GLU170 4.5 15.8 1.0 CG A:GLU221 4.6 22.4 1.0 CG A:GLN141 4.6 14.9 1.0 CA A:GLY363 4.6 23.7 1.0 C3 A:PGO602 4.7 25.1 1.0 CB A:GLU170 4.7 17.3 1.0 CG A:GLN296 4.8 21.6 1.0

Potassium binding site 2 out of 2 in the Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Diol Dehydratase-Cyanocobalamin Complex From Klebsiella Oxytoca within 5.0Å range: probe atom residue distance (Å) B Occ L:K603 b:19.9 occ:1.00 OE1 L:GLN141 2.2 19.0 1.0 OE1 L:GLN296 2.2 24.1 1.0 OE1 L:GLU170 2.3 25.9 1.0 O1 L:PGO602 2.4 25.2 1.0 O2 L:PGO602 2.4 25.3 1.0 OE1 L:GLU221 2.4 28.6 1.0 O L:SER362 2.6 21.5 1.0 CD L:GLU170 3.4 25.1 1.0 C2 L:PGO602 3.4 24.9 1.0 C1 L:PGO602 3.4 23.5 1.0 CD L:GLN296 3.4 25.6 1.0 CD L:GLN141 3.5 17.4 1.0 C L:SER362 3.5 20.9 1.0 CD L:GLU221 3.5 27.9 1.0 OE2 L:GLU170 3.7 26.3 1.0 CB L:SER362 4.0 17.6 1.0 NE2 L:GLN296 4.0 25.2 1.0 NE2 L:GLN141 4.1 19.2 1.0 NE2 L:GLN200 4.1 26.1 1.0 NE2 L:HIS143 4.2 19.3 1.0 OD2 L:ASP335 4.2 25.6 1.0 OG L:SER362 4.2 18.8 1.0 OE2 L:GLU221 4.2 29.0 1.0 CA L:SER362 4.2 21.0 1.0 N L:GLY363 4.3 21.6 1.0 CD2 L:HIS143 4.4 18.1 1.0 CA L:GLY363 4.5 23.6 1.0 CG L:GLN141 4.6 18.2 1.0 CG L:GLU170 4.6 24.2 1.0 CG L:GLU221 4.6 24.3 1.0 CG L:GLN296 4.7 24.8 1.0 CB L:GLU170 4.7 21.9 1.0 C3 L:PGO602 4.8 21.9 1.0

N.Shibata, J.Masuda, T.Tobimatsu, T.Toraya, K.Suto, Y.Morimoto, N.Yasuoka. A New Mode of B12 Binding and the Direct Participation of A Potassium Ion in Enzyme Catalysis: X-Ray Structure of Diol Dehydratase. Structure Fold.Des. V. 7 997 1999.
ISSN: ISSN 0969-2126
PubMed: 10467140
DOI: 10.1016/S0969-2126(99)80126-9