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Cobalt in PDB 1iwb: Crystal Structure of Diol Dehydratase

Enzymatic activity of Crystal Structure of Diol Dehydratase

All present enzymatic activity of Crystal Structure of Diol Dehydratase:
4.2.1.28;

Protein crystallography data

The structure of Crystal Structure of Diol Dehydratase, PDB code: 1iwb was solved by N.Shibata, J.Masuda, Y.Morimoto, N.Yasuoka, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.790, 122.400, 207.590, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 25.6

Other elements in 1iwb:

The structure of Crystal Structure of Diol Dehydratase also contains other interesting chemical elements:

Potassium (K) 6 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Diol Dehydratase (pdb code 1iwb). 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 Diol Dehydratase, PDB code: 1iwb:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1iwb

Go back to Cobalt Binding Sites List in 1iwb
Cobalt binding site 1 out of 2 in the Crystal Structure of Diol Dehydratase


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 Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1601

b:16.7
occ:1.00
CO B:B121601 0.0 16.7 1.0
N21 B:B121601 1.9 14.7 1.0
N24 B:B121601 1.9 13.9 1.0
N23 B:B121601 1.9 16.9 1.0
N22 B:B121601 1.9 12.3 1.0
N3B B:B121601 2.3 17.5 1.0
C19 B:B121601 2.8 9.8 1.0
C9 B:B121601 2.9 11.8 1.0
C4 B:B121601 2.9 14.6 1.0
C11 B:B121601 2.9 21.0 1.0
C1 B:B121601 2.9 16.6 1.0
C14 B:B121601 2.9 15.7 1.0
C16 B:B121601 2.9 16.4 1.0
C6 B:B121601 3.0 16.3 1.0
C2B B:B121601 3.2 17.5 1.0
C10 B:B121601 3.2 14.9 1.0
C5 B:B121601 3.3 16.2 1.0
C9B B:B121601 3.4 15.1 1.0
C15 B:B121601 3.4 15.9 1.0
C20 B:B121601 3.5 15.6 1.0
C4B B:B121601 3.9 6.3 1.0
C18 B:B121601 4.1 11.2 1.0
C2 B:B121601 4.2 15.3 1.0
C3 B:B121601 4.2 15.9 1.0
C12 B:B121601 4.2 25.8 1.0
C17 B:B121601 4.2 17.2 1.0
C13 B:B121601 4.2 14.2 1.0
C8 B:B121601 4.2 19.9 1.0
C7 B:B121601 4.3 17.5 1.0
N1B B:B121601 4.4 18.3 1.0
C26 B:B121601 4.5 28.5 1.0
C8B B:B121601 4.5 12.2 1.0
C49 B:B121601 4.7 14.7 1.0
C46 B:B121601 4.7 16.7 1.0
C54 B:B121601 4.7 10.1 1.0
C35 B:B121601 4.8 14.4 1.0
C41 B:B121601 4.8 20.6 1.0
C53 B:B121601 4.9 7.1 1.0

Cobalt binding site 2 out of 2 in 1iwb

Go back to Cobalt Binding Sites List in 1iwb
Cobalt binding site 2 out of 2 in the Crystal Structure of Diol Dehydratase


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 Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1602

b:21.6
occ:1.00
CO E:B121602 0.0 21.6 1.0
N21 E:B121602 1.9 20.9 1.0
N24 E:B121602 1.9 15.8 1.0
N23 E:B121602 1.9 18.7 1.0
N22 E:B121602 1.9 16.6 1.0
N3B E:B121602 2.2 25.1 1.0
C9 E:B121602 2.9 22.4 1.0
C19 E:B121602 2.9 16.3 1.0
C4 E:B121602 2.9 19.8 1.0
C1 E:B121602 2.9 16.6 1.0
C11 E:B121602 2.9 16.3 1.0
C14 E:B121602 2.9 18.2 1.0
C16 E:B121602 2.9 14.4 1.0
C6 E:B121602 3.0 15.0 1.0
C2B E:B121602 3.2 35.2 1.0
C10 E:B121602 3.3 14.6 1.0
C9B E:B121602 3.3 27.1 1.0
C5 E:B121602 3.3 19.1 1.0
C15 E:B121602 3.4 18.3 1.0
C20 E:B121602 3.6 14.5 1.0
O28 E:B121602 3.7 29.6 1.0
C4B E:B121602 3.8 24.5 1.0
C18 E:B121602 4.1 13.3 1.0
C2 E:B121602 4.2 21.7 1.0
C3 E:B121602 4.2 23.4 1.0
C8 E:B121602 4.2 24.1 1.0
C12 E:B121602 4.2 18.5 1.0
C17 E:B121602 4.2 18.6 1.0
C13 E:B121602 4.2 15.0 1.0
C7 E:B121602 4.3 20.9 1.0
C27 E:B121602 4.4 27.5 1.0
N1B E:B121602 4.4 32.4 1.0
C8B E:B121602 4.5 25.0 1.0
O E:HOH1641 4.7 53.1 1.0
C46 E:B121602 4.7 12.5 1.0
C26 E:B121602 4.7 18.9 1.0
C49 E:B121602 4.7 32.4 1.0
C54 E:B121602 4.8 23.9 1.0
C41 E:B121602 4.8 21.6 1.0
C35 E:B121602 4.8 17.4 1.0
C53 E:B121602 4.9 14.2 1.0

Reference:

N.Shibata, J.Masuda, Y.Morimoto, N.Yasuoka, T.Toraya. Substrate-Induced Conformational Change of A Coenzyme B12-Dependent Enzyme: Crystal Structure of the Substrate-Free Form of Diol Dehydratase Biochemistry V. 41 12607 2002.
ISSN: ISSN 0006-2960
PubMed: 12379103
DOI: 10.1021/BI026104Z
Page generated: Sun Dec 13 10:35:14 2020

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