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Cobalt in PDB 1eex: Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca

Enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca

All present enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca:
4.2.1.28;

Protein crystallography data

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca, PDB code: 1eex was solved by N.Shibata, J.Masuda, 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.380, 121.400, 207.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 22.6

Other elements in 1eex:

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca also contains other interesting chemical elements:

Potassium (K) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca (pdb code 1eex). 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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca, PDB code: 1eex:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1eex

Go back to Cobalt Binding Sites List in 1eex
Cobalt binding site 1 out of 2 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co601

b:11.4
occ:1.00
CO A:COY601 0.0 11.4 1.0
N24 A:COY601 1.9 8.9 1.0
N23 A:COY601 1.9 11.3 1.0
N21 A:COY601 1.9 12.2 1.0
N22 A:COY601 1.9 10.7 1.0
C75 A:COY601 2.1 11.7 1.0
N3B A:COY601 2.2 9.9 1.0
C9 A:COY601 2.8 9.1 1.0
C19 A:COY601 2.9 6.5 1.0
C4 A:COY601 2.9 10.5 1.0
C14 A:COY601 2.9 10.2 1.0
C11 A:COY601 2.9 12.9 1.0
C1 A:COY601 2.9 11.6 1.0
C16 A:COY601 2.9 7.5 1.0
C6 A:COY601 3.0 7.4 1.0
C74 A:COY601 3.2 13.9 1.0
C2B A:COY601 3.2 8.5 1.0
C10 A:COY601 3.2 11.8 1.0
C9B A:COY601 3.3 9.9 1.0
C15 A:COY601 3.3 9.4 1.0
C5 A:COY601 3.3 11.6 1.0
C20 A:COY601 3.5 8.9 1.0
C4B A:COY601 3.8 11.3 1.0
C18 A:COY601 4.1 12.4 1.0
C3 A:COY601 4.2 13.1 1.0
C2 A:COY601 4.2 13.1 1.0
C8 A:COY601 4.2 10.4 1.0
C12 A:COY601 4.2 15.1 1.0
C13 A:COY601 4.2 13.7 1.0
C17 A:COY601 4.2 16.4 1.0
C7 A:COY601 4.3 13.1 1.0
N1B A:COY601 4.4 12.4 1.0
C73 A:COY601 4.4 14.1 1.0
C8B A:COY601 4.5 14.2 1.0
C26 A:COY601 4.6 12.5 1.0
C46 A:COY601 4.7 9.8 1.0
C41 A:COY601 4.7 13.1 1.0
C49 A:COY601 4.7 11.1 1.0
C54 A:COY601 4.8 10.9 1.0
C35 A:COY601 4.8 9.7 1.0
C53 A:COY601 4.8 7.4 1.0
C37 A:COY601 4.9 10.2 1.0
C48 A:COY601 4.9 10.8 1.0

Cobalt binding site 2 out of 2 in 1eex

Go back to Cobalt Binding Sites List in 1eex
Cobalt binding site 2 out of 2 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co601

b:19.7
occ:1.00
CO L:COY601 0.0 19.7 1.0
N21 L:COY601 1.9 24.4 1.0
N24 L:COY601 1.9 16.1 1.0
N22 L:COY601 1.9 16.4 1.0
C75 L:COY601 1.9 23.6 1.0
N23 L:COY601 1.9 18.2 1.0
N3B L:COY601 2.1 26.8 1.0
C19 L:COY601 2.8 21.0 1.0
C9 L:COY601 2.8 18.2 1.0
C4 L:COY601 2.8 24.7 1.0
C1 L:COY601 2.9 27.0 1.0
C11 L:COY601 2.9 20.6 1.0
C14 L:COY601 2.9 14.0 1.0
C16 L:COY601 3.0 13.6 1.0
C6 L:COY601 3.0 19.6 1.0
C2B L:COY601 3.1 31.2 1.0
C74 L:COY601 3.2 24.2 1.0
C10 L:COY601 3.2 19.3 1.0
C9B L:COY601 3.3 23.3 1.0
C5 L:COY601 3.3 21.1 1.0
C15 L:COY601 3.4 17.9 1.0
C20 L:COY601 3.6 18.5 1.0
C4B L:COY601 3.8 26.7 1.0
C18 L:COY601 4.1 17.6 1.0
C2 L:COY601 4.1 20.1 1.0
C3 L:COY601 4.2 22.3 1.0
C8 L:COY601 4.2 19.2 1.0
C12 L:COY601 4.2 18.7 1.0
C17 L:COY601 4.2 14.3 1.0
C13 L:COY601 4.2 14.5 1.0
C7 L:COY601 4.3 16.5 1.0
N1B L:COY601 4.3 25.1 1.0
C73 L:COY601 4.4 26.6 1.0
C8B L:COY601 4.4 29.1 1.0
C26 L:COY601 4.5 15.8 1.0
C46 L:COY601 4.7 14.5 1.0
C54 L:COY601 4.7 16.7 1.0
C49 L:COY601 4.7 26.0 1.0
C35 L:COY601 4.8 25.8 1.0
C41 L:COY601 4.8 23.7 1.0
C53 L:COY601 4.9 16.2 1.0
C37 L:COY601 4.9 19.9 1.0
C48 L:COY601 5.0 20.9 1.0

Reference:

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
Page generated: Sun Dec 13 10:34:38 2020

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