Potassium in PDB 7xrk: Diol Dehydratase Complexed with Adomecbl

Enzymatic activity of Diol Dehydratase Complexed with Adomecbl

All present enzymatic activity of Diol Dehydratase Complexed with Adomecbl:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase Complexed with Adomecbl, PDB code: 7xrk 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) 45.07 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.313, 111.564, 197.058, 90, 90, 90
R / Rfree (%) 16.5 / 22.5

Other elements in 7xrk:

The structure of Diol Dehydratase Complexed with Adomecbl also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Calcium (Ca) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Diol Dehydratase Complexed with Adomecbl (pdb code 7xrk). 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 Complexed with Adomecbl, PDB code: 7xrk:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7xrk

Go back to Potassium Binding Sites List in 7xrk
Potassium binding site 1 out of 2 in the Diol Dehydratase Complexed with Adomecbl


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Diol Dehydratase Complexed with Adomecbl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:23.5
occ:1.00
OE2 A:GLU265 2.7 20.2 1.0
OE1 A:GLU280 2.8 21.6 1.0
O A:GLY261 2.8 22.8 1.0
O A:HOH761 2.8 17.6 1.0
SG A:CYS283 2.9 17.6 1.0
OG A:SER264 3.0 19.3 1.0
O A:HOH709 3.0 17.2 1.0
OE1 A:GLU265 3.3 19.9 1.0
CD A:GLU265 3.3 21.5 1.0
C A:GLY261 3.5 24.3 1.0
N A:GLY261 3.9 23.8 1.0
CA A:GLU280 4.0 14.9 1.0
CD A:GLU280 4.0 25.5 1.0
CB A:CYS283 4.2 15.8 1.0
N A:SER262 4.2 23.5 1.0
CB A:GLU280 4.3 14.2 1.0
CA A:GLY261 4.3 21.2 1.0
N A:GLU280 4.3 15.5 1.0
CA A:SER262 4.3 21.4 1.0
CB A:SER264 4.3 20.9 1.0
O A:LEU279 4.4 20.3 1.0
C A:LEU279 4.5 17.6 1.0
N A:GLY227 4.6 13.7 1.0
CB A:SER260 4.7 15.8 1.0
N A:SER264 4.7 22.9 1.0
CG A:GLU280 4.8 20.0 1.0
CG A:GLU265 4.8 16.9 1.0
N A:GLY263 4.9 18.7 1.0
C A:SER262 4.9 19.8 1.0
OE2 A:GLU280 4.9 21.9 1.0
C A:SER260 5.0 21.1 1.0

Potassium binding site 2 out of 2 in 7xrk

Go back to Potassium Binding Sites List in 7xrk
Potassium binding site 2 out of 2 in the Diol Dehydratase Complexed with Adomecbl


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Diol Dehydratase Complexed with Adomecbl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:22.7
occ:1.00
O D:GLY261 2.7 16.9 1.0
OE2 D:GLU265 2.8 23.8 1.0
OE1 D:GLU280 2.8 27.3 1.0
OG D:SER264 2.8 21.6 1.0
O D:HOH721 2.8 17.0 1.0
O D:HOH742 2.8 16.6 1.0
OE1 D:GLU265 3.1 19.2 1.0
CD D:GLU265 3.3 28.6 1.0
C D:GLY261 3.4 24.4 1.0
SG D:CYS283 3.6 18.2 1.0
N D:GLY261 3.8 26.9 1.0
CB D:SER264 4.0 20.3 1.0
CD D:GLU280 4.0 23.4 1.0
N D:SER262 4.1 21.1 1.0
CA D:GLU280 4.1 16.8 1.0
CA D:SER262 4.2 24.3 1.0
CA D:GLY261 4.2 21.7 1.0
N D:SER264 4.3 22.4 1.0
CB D:GLU280 4.4 13.2 1.0
N D:GLU280 4.5 14.4 1.0
O D:LEU279 4.5 19.5 1.0
N D:GLY263 4.5 18.0 1.0
C D:SER262 4.6 23.0 1.0
C D:LEU279 4.7 17.7 1.0
CB D:SER260 4.7 20.0 1.0
CB D:CYS283 4.7 16.6 1.0
CA D:SER264 4.8 19.8 1.0
CG D:GLU265 4.8 18.7 1.0
CG D:GLU280 4.8 19.7 1.0
N D:GLY227 4.8 22.9 1.0
C D:SER260 4.9 22.4 1.0
OE2 D:GLU280 4.9 18.0 1.0
N D:GLU265 5.0 18.2 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 14:47:52 2023

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