Atomistry » Cobalt » PDB 7vo8-7ygp » 7xrl
Atomistry »
  Cobalt »
    PDB 7vo8-7ygp »
      7xrl »

Cobalt in PDB 7xrl: Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol

Enzymatic activity of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol

All present enzymatic activity of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl was solved by N.Shibata, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.718, 117.246, 201.55, 90, 90, 90
R / Rfree (%) 16.7 / 20.6

Other elements in 7xrl:

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol also contains other interesting chemical elements:

Potassium (K) 2 atoms
Calcium (Ca) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol (pdb code 7xrl). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 7xrl

Go back to Cobalt Binding Sites List in 7xrl
Cobalt binding site 1 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:13.7
occ:1.00
CO B:B12301 0.0 13.7 1.0
N24 B:B12301 1.8 16.2 1.0
N21 B:B12301 1.8 14.8 1.0
N23 B:B12301 1.8 16.5 1.0
N22 B:B12301 1.9 13.6 1.0
C6' A:FWK605 2.2 15.2 1.0
N3B B:B12301 2.3 15.7 1.0
C19 B:B12301 2.8 19.7 1.0
C4 B:B12301 2.8 15.4 1.0
C14 B:B12301 2.8 22.5 1.0
C1 B:B12301 2.8 16.5 1.0
C9 B:B12301 2.8 14.5 1.0
C11 B:B12301 2.9 15.9 1.0
C6 B:B12301 3.0 14.0 1.0
C16 B:B12301 3.0 18.3 1.0
C5' A:FWK605 3.1 14.7 1.0
C2B B:B12301 3.2 12.5 1.0
C9B B:B12301 3.3 12.5 1.0
C5 B:B12301 3.3 15.0 1.0
C10 B:B12301 3.3 16.9 1.0
C15 B:B12301 3.3 23.6 1.0
C20 B:B12301 3.6 18.9 1.0
C4B B:B12301 3.8 12.8 1.0
C18 B:B12301 4.0 21.5 1.0
C2 B:B12301 4.1 22.0 1.0
C3 B:B12301 4.1 14.2 1.0
C8 B:B12301 4.2 16.4 1.0
C13 B:B12301 4.2 19.9 1.0
C17 B:B12301 4.2 26.9 1.0
C12 B:B12301 4.2 19.4 1.0
C7 B:B12301 4.2 18.1 1.0
N1B B:B12301 4.4 16.9 1.0
C4' A:FWK605 4.4 15.5 1.0
C8B B:B12301 4.5 13.4 1.0
C26 B:B12301 4.5 19.5 1.0
C49 B:B12301 4.7 27.1 1.0
C46 B:B12301 4.8 14.3 1.0
C35 B:B12301 4.8 18.0 1.0
C41 B:B12301 4.8 13.4 1.0
C53 B:B12301 4.8 23.6 1.0
C54 B:B12301 4.8 29.3 1.0
C37 B:B12301 4.8 15.0 1.0
O4' A:FWK605 4.9 15.6 1.0
C48 B:B12301 5.0 19.7 1.0

Cobalt binding site 2 out of 2 in 7xrl

Go back to Cobalt Binding Sites List in 7xrl
Cobalt binding site 2 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co301

b:32.2
occ:1.00
CO E:B12301 0.0 32.2 1.0
N21 E:B12301 1.8 34.4 1.0
N24 E:B12301 1.8 32.0 1.0
N23 E:B12301 1.8 30.1 1.0
N22 E:B12301 1.9 32.7 1.0
C6' D:FWK605 2.2 30.2 1.0
N3B E:B12301 2.3 34.6 1.0
C19 E:B12301 2.8 33.1 1.0
C4 E:B12301 2.8 35.3 1.0
C9 E:B12301 2.8 32.0 1.0
C1 E:B12301 2.8 35.1 1.0
C14 E:B12301 2.8 32.7 1.0
C11 E:B12301 2.9 29.3 1.0
C6 E:B12301 2.9 34.0 1.0
C16 E:B12301 3.0 31.3 1.0
C5' D:FWK605 3.1 28.8 1.0
C9B E:B12301 3.2 36.5 1.0
C5 E:B12301 3.3 35.0 1.0
C2B E:B12301 3.3 34.5 1.0
C10 E:B12301 3.3 30.1 1.0
C15 E:B12301 3.4 29.4 1.0
C20 E:B12301 3.6 36.7 1.0
C4B E:B12301 3.7 37.6 1.0
C18 E:B12301 4.0 34.1 1.0
C2 E:B12301 4.0 36.1 1.0
C3 E:B12301 4.1 36.8 1.0
C8 E:B12301 4.1 33.1 1.0
C13 E:B12301 4.2 31.0 1.0
C12 E:B12301 4.2 30.0 1.0
C17 E:B12301 4.2 41.7 1.0
C7 E:B12301 4.2 33.9 1.0
N1B E:B12301 4.4 37.5 1.0
C26 E:B12301 4.5 46.7 1.0
C4' D:FWK605 4.5 28.6 1.0
C8B E:B12301 4.5 37.6 1.0
C49 E:B12301 4.6 35.1 1.0
C41 E:B12301 4.7 34.9 1.0
C35 E:B12301 4.7 35.9 1.0
C46 E:B12301 4.7 25.7 1.0
C37 E:B12301 4.8 32.2 1.0
C53 E:B12301 4.9 35.0 1.0
C54 E:B12301 4.9 34.7 1.0
C48 E:B12301 4.9 30.7 1.0
O4' D:FWK605 5.0 26.2 1.0

Reference:

N.Shibata, Y.Higuchi, B.Krautler, T.Toraya. Structural Insights Into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry V. 28 02196 2022.
ISSN: ISSN 0947-6539
PubMed: 35974426
DOI: 10.1002/CHEM.202202196
Page generated: Tue Apr 11 13:31:12 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy