Potassium in PDB 8dcl: Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

Enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

All present enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36:
5.1.3.13;

Protein crystallography data

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36, PDB code: 8dcl was solved by J.B.Thoden, M.K.Ghosh, D.F.Xiang, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.75 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.84, 44.766, 57.428, 83.25, 79.35, 65.08
R / Rfree (%) 16.5 / 20

Other elements in 8dcl:

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 (pdb code 8dcl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36, PDB code: 8dcl:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 8dcl

Go back to Potassium Binding Sites List in 8dcl
Potassium binding site 1 out of 2 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:16.0
occ:1.00
 O A:HOH472 2.6 21.4 1.0
O A:LEU48 2.6 11.7 1.0
O A:ASP41 2.7 12.2 1.0
O A:PRO45 3.0 19.6 1.0
O A:HOH468 3.0 28.6 1.0
O A:HOH444 3.0 17.7 1.0
O A:LEU44 3.2 15.8 1.0
C A:PRO45 3.7 22.1 1.0
C A:LEU44 3.7 17.4 1.0
C A:ASP41 3.7 13.1 1.0
C A:LEU48 3.8 13.3 1.0
CB A:LEU44 3.8 13.2 1.0
N A:LEU48 4.1 16.1 1.0
N A:ASN46 4.2 23.7 1.0
CA A:LEU44 4.2 14.3 1.0
CA A:ASN46 4.2 24.8 1.0
NA A:NA204 4.2 30.1 1.0
N A:GLY47 4.2 19.0 1.0
N A:LEU44 4.4 13.1 1.0
N A:PRO45 4.5 18.5 1.0
CA A:LEU48 4.5 14.4 1.0
C A:ASN46 4.5 22.6 1.0
N A:LYS42 4.5 14.2 1.0
CA A:LYS42 4.6 16.4 1.0
CA A:PRO45 4.6 19.7 1.0
CA A:ASP41 4.7 11.8 1.0
CB A:ASP41 4.7 13.1 1.0
C A:LYS42 4.8 15.8 1.0
CG A:LYS49 4.8 14.3 1.0
N A:LYS49 4.9 11.9 1.0
O A:LYS42 4.9 15.9 1.0
CB A:LEU48 4.9 16.0 1.0
CG A:LEU44 4.9 13.9 1.0

Potassium binding site 2 out of 2 in 8dcl

Go back to Potassium Binding Sites List in 8dcl
Potassium binding site 2 out of 2 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K202

b:19.9
occ:1.00
 O B:HOH446 2.6 30.4 1.0
O B:ASP41 2.8 14.3 1.0
O B:LEU48 2.8 13.9 1.0
O B:PRO45 2.9 14.5 1.0
O B:HOH460 3.0 30.2 1.0
O B:LEU44 3.0 15.3 1.0
C B:LEU44 3.6 17.3 1.0
CB B:LEU44 3.7 14.8 1.0
C B:ASP41 3.8 13.9 1.0
C B:PRO45 3.8 17.3 1.0
C B:LEU48 4.0 13.7 1.0
CA B:LEU44 4.0 15.0 1.0
N B:LEU48 4.2 15.6 1.0
N B:LEU44 4.2 14.7 1.0
N B:PRO45 4.3 18.0 1.0
O B:HOH330 4.3 32.1 1.0
NA B:NA203 4.4 30.9 1.0
CA B:LYS42 4.4 17.6 1.0
N B:LYS42 4.5 14.9 1.0
C B:LYS42 4.5 18.5 1.0
N B:ASN46 4.5 17.7 1.0
CA B:LEU48 4.6 16.2 1.0
O B:LYS42 4.6 16.7 1.0
N B:GLY47 4.6 16.6 1.0
CA B:PRO45 4.7 17.9 1.0
CA B:ASN46 4.7 19.5 1.0
CA B:ASP41 4.8 12.7 1.0
CB B:ASP41 4.8 11.9 1.0
C B:ASN46 4.9 18.9 1.0
CB B:LEU48 4.9 17.2 1.0
CG B:LEU44 4.9 16.5 1.0

Reference:

M.K.Ghosh, D.F.Xiang, J.B.Thoden, H.M.Holden, F.M.Raushel. C3- and C3/C5-Epimerases Required For the Biosynthesis of the Capsular Polysaccharides From Campylobacter Jejuni . Biochemistry V. 61 2036 2022.
ISSN: ISSN 0006-2960
PubMed: 36093987
DOI: 10.1021/ACS.BIOCHEM.2C00364
Page generated: Wed Apr 5 10:42:50 2023

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