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Cobalt in PDB 5ysh: Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.330, 110.490, 115.480, 92.69, 95.97, 105.44
R / Rfree (%) 16.4 / 19.1

Other elements in 5ysh:

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal also contains other interesting chemical elements:

Potassium (K) 8 atoms
Calcium (Ca) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal (pdb code 5ysh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5ysh

Go back to Cobalt Binding Sites List in 5ysh
Cobalt binding site 1 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1601

b:39.3
occ:1.00
CO B:B121601 0.0 39.3 1.0
N21 B:B121601 1.8 40.5 1.0
N23 B:B121601 1.9 38.2 1.0
N22 B:B121601 1.9 40.0 1.0
N24 B:B121601 1.9 38.8 1.0
N3B B:B121601 2.3 42.7 1.0
C19 B:B121601 2.7 39.1 1.0
C1 B:B121601 2.8 40.8 1.0
C9 B:B121601 2.8 39.4 1.0
C4 B:B121601 2.8 41.0 1.0
C14 B:B121601 2.8 37.9 1.0
C11 B:B121601 2.9 37.6 1.0
C6 B:B121601 3.0 40.3 1.0
C16 B:B121601 3.0 38.1 1.0
C2B B:B121601 3.2 45.6 1.0
C9B B:B121601 3.3 44.6 1.0
C10 B:B121601 3.3 38.1 1.0
C5 B:B121601 3.3 40.8 1.0
C15 B:B121601 3.4 37.8 1.0
C20 B:B121601 3.6 43.0 1.0
C4B B:B121601 3.8 45.2 1.0
C2 B:B121601 4.0 40.7 1.0
C18 B:B121601 4.0 39.4 1.0
C3 B:B121601 4.1 41.6 1.0
C8 B:B121601 4.1 40.3 1.0
C13 B:B121601 4.2 37.2 1.0
C12 B:B121601 4.2 36.4 1.0
C17 B:B121601 4.2 39.3 1.0
C7 B:B121601 4.2 40.2 1.0
C26 B:B121601 4.4 38.3 1.0
N1B B:B121601 4.4 45.4 1.0
C8B B:B121601 4.5 46.4 1.0
C46 B:B121601 4.7 34.0 1.0
C41 B:B121601 4.7 42.6 1.0
C49 B:B121601 4.7 45.3 1.0
C35 B:B121601 4.8 41.1 1.0
C54 B:B121601 4.8 35.5 1.0
C53 B:B121601 4.9 37.2 1.0
C37 B:B121601 4.9 38.0 1.0

Cobalt binding site 2 out of 4 in 5ysh

Go back to Cobalt Binding Sites List in 5ysh
Cobalt binding site 2 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1601

b:31.1
occ:1.00
CO E:B121601 0.0 31.1 1.0
N21 E:B121601 1.9 25.9 1.0
N23 E:B121601 1.9 26.4 1.0
N22 E:B121601 1.9 30.0 1.0
N24 E:B121601 1.9 21.5 1.0
N3B E:B121601 2.3 23.6 1.0
C19 E:B121601 2.8 21.6 1.0
C1 E:B121601 2.8 24.6 1.0
C9 E:B121601 2.8 22.9 1.0
C14 E:B121601 2.8 21.4 1.0
C4 E:B121601 2.8 27.6 1.0
C11 E:B121601 2.9 21.2 1.0
C6 E:B121601 3.0 23.7 1.0
C16 E:B121601 3.0 19.5 1.0
C9B E:B121601 3.3 30.8 1.0
C2B E:B121601 3.3 29.2 1.0
C10 E:B121601 3.3 24.0 1.0
C5 E:B121601 3.3 29.6 1.0
C15 E:B121601 3.3 24.0 1.0
C20 E:B121601 3.5 23.4 1.0
C4B E:B121601 3.8 29.9 1.0
C2 E:B121601 4.1 26.4 1.0
C18 E:B121601 4.1 21.7 1.0
C3 E:B121601 4.1 24.0 1.0
C8 E:B121601 4.2 22.8 1.0
C13 E:B121601 4.2 20.1 1.0
C12 E:B121601 4.2 22.3 1.0
C17 E:B121601 4.2 20.3 1.0
C7 E:B121601 4.3 22.9 1.0
N1B E:B121601 4.4 30.9 1.0
C8B E:B121601 4.5 30.6 1.0
C26 E:B121601 4.6 20.9 1.0
C49 E:B121601 4.7 23.3 1.0
C46 E:B121601 4.7 21.1 1.0
C41 E:B121601 4.8 25.8 1.0
C35 E:B121601 4.8 23.1 1.0
C53 E:B121601 4.8 18.7 1.0
C54 E:B121601 4.9 19.2 1.0
C37 E:B121601 4.9 21.4 1.0
C48 E:B121601 5.0 20.9 1.0

Cobalt binding site 3 out of 4 in 5ysh

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Cobalt binding site 3 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co1601

b:35.0
occ:1.00
CO H:B121601 0.0 35.0 1.0
N21 H:B121601 1.8 35.1 1.0
N22 H:B121601 1.8 37.0 1.0
N24 H:B121601 1.8 32.7 1.0
N23 H:B121601 1.9 35.7 1.0
N3B H:B121601 2.3 35.1 1.0
C19 H:B121601 2.7 36.2 1.0
C9 H:B121601 2.8 38.9 1.0
C1 H:B121601 2.8 37.0 1.0
C4 H:B121601 2.8 36.3 1.0
C14 H:B121601 2.8 32.2 1.0
C11 H:B121601 2.9 35.3 1.0
C6 H:B121601 2.9 36.5 1.0
C16 H:B121601 3.0 31.4 1.0
C9B H:B121601 3.2 37.8 1.0
C2B H:B121601 3.2 37.2 1.0
C5 H:B121601 3.3 40.8 1.0
C10 H:B121601 3.3 36.2 1.0
C15 H:B121601 3.3 31.9 1.0
C20 H:B121601 3.6 35.6 1.0
C4B H:B121601 3.7 38.1 1.0
C2 H:B121601 4.0 37.0 1.0
C18 H:B121601 4.1 36.3 1.0
C8 H:B121601 4.1 38.0 1.0
C3 H:B121601 4.1 37.0 1.0
C13 H:B121601 4.2 33.5 1.0
C12 H:B121601 4.2 31.2 1.0
C17 H:B121601 4.2 32.6 1.0
C7 H:B121601 4.2 39.1 1.0
N1B H:B121601 4.4 35.8 1.0
C8B H:B121601 4.5 37.1 1.0
C26 H:B121601 4.5 38.2 1.0
C46 H:B121601 4.7 33.8 1.0
C49 H:B121601 4.7 37.0 1.0
C41 H:B121601 4.7 41.3 1.0
C54 H:B121601 4.8 29.7 1.0
C35 H:B121601 4.8 38.3 1.0
C53 H:B121601 4.8 30.6 1.0
C37 H:B121601 4.9 36.7 1.0

Cobalt binding site 4 out of 4 in 5ysh

Go back to Cobalt Binding Sites List in 5ysh
Cobalt binding site 4 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Co1601

b:68.1
occ:1.00
CO K:B121601 0.0 68.1 1.0
N21 K:B121601 1.8 68.8 1.0
N24 K:B121601 1.8 66.3 1.0
N23 K:B121601 1.9 67.3 1.0
N22 K:B121601 1.9 69.8 1.0
N3B K:B121601 2.3 70.7 1.0
C19 K:B121601 2.7 66.2 1.0
C1 K:B121601 2.8 68.1 1.0
C4 K:B121601 2.8 69.7 1.0
C9 K:B121601 2.8 70.2 1.0
C14 K:B121601 2.8 66.3 1.0
C11 K:B121601 2.9 67.8 1.0
C6 K:B121601 3.0 70.7 1.0
C16 K:B121601 3.0 65.1 1.0
C9B K:B121601 3.2 72.6 1.0
C2B K:B121601 3.3 70.5 1.0
C10 K:B121601 3.3 69.2 1.0
C5 K:B121601 3.3 70.5 1.0
C15 K:B121601 3.3 65.1 1.0
C20 K:B121601 3.5 69.6 1.0
C4B K:B121601 3.7 73.8 1.0
C2 K:B121601 4.0 68.1 1.0
C18 K:B121601 4.0 65.2 1.0
C3 K:B121601 4.1 69.7 1.0
C8 K:B121601 4.1 72.0 1.0
C13 K:B121601 4.2 66.3 1.0
C12 K:B121601 4.2 66.6 1.0
C17 K:B121601 4.2 64.0 1.0
C7 K:B121601 4.2 71.9 1.0
C26 K:B121601 4.4 66.0 1.0
N1B K:B121601 4.4 72.3 1.0
C8B K:B121601 4.5 73.8 1.0
C46 K:B121601 4.7 64.5 1.0
C49 K:B121601 4.8 70.1 1.0
C41 K:B121601 4.8 74.1 1.0
C35 K:B121601 4.8 71.1 1.0
C53 K:B121601 4.8 64.0 1.0
C54 K:B121601 4.9 61.9 1.0
C37 K:B121601 4.9 70.5 1.0
C30 K:B121601 5.0 71.9 1.0

Reference:

N.Shibata, Y.Sueyoshi, Y.Higuchi, T.Toraya. Direct Participation of A Peripheral Side Chain of A Corrin Ring in Coenzyme B12CATALYSIS. Angew. Chem. Int. Ed. Engl. V. 57 7830 2018.
ISSN: ESSN 1521-3773
PubMed: 29797764
DOI: 10.1002/ANIE.201803591
Page generated: Sun Dec 13 10:49:20 2020

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