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Sodium 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:

Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8dcl

Go back to Sodium Binding Sites List in 8dcl
Sodium 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 Sodium with other atoms in the Na 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:Na204

b:30.1
occ:1.00
 O A:HOH467 2.4 29.2 1.0
O A:LEU44 2.4 15.8 1.0
O A:HOH472 2.6 21.4 1.0
O A:HOH497 2.8 23.7 1.0
O A:LYS42 2.9 15.9 1.0
C A:LEU44 3.6 17.4 1.0
N A:ASN46 3.7 23.7 1.0
C A:LYS42 3.9 15.8 1.0
OD1 A:ASN46 3.9 44.6 1.0
C A:PRO45 4.0 22.1 1.0
K A:K202 4.2 16.0 1.0
CA A:PRO45 4.2 19.7 1.0
N A:PRO45 4.3 18.5 1.0
CA A:ASN46 4.4 24.8 1.0
N A:LEU44 4.5 13.1 1.0
O A:HOH409 4.5 35.7 1.0
CA A:LYS42 4.5 16.4 1.0
O A:PRO45 4.7 19.6 1.0
C A:LEU43 4.7 13.8 1.0
CA A:LEU44 4.7 14.3 1.0
N A:LEU43 4.9 13.6 1.0
CG A:ASN46 4.9 37.7 1.0
O A:ASP41 4.9 12.2 1.0

Sodium binding site 2 out of 2 in 8dcl

Go back to Sodium Binding Sites List in 8dcl
Sodium 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 Sodium with other atoms in the Na 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:Na203

b:30.9
occ:1.00
 O B:HOH441 1.8 30.3 1.0
O B:LYS42 2.4 16.7 1.0
O B:LEU44 2.5 15.3 1.0
O B:HOH357 2.7 18.8 1.0
O B:HOH446 2.9 30.4 1.0
C B:LYS42 3.5 18.5 1.0
C B:LEU44 3.6 17.3 1.0
O B:HOH471 3.8 39.4 1.0
C B:LEU43 4.1 15.2 1.0
O B:HOH330 4.2 32.1 1.0
N B:LEU44 4.2 14.7 1.0
N B:LEU43 4.3 15.9 1.0
K B:K202 4.4 19.9 1.0
O B:LEU43 4.4 16.0 1.0
CA B:LYS42 4.4 17.6 1.0
ND2 B:ASN46 4.4 21.0 1.0
N B:PRO45 4.4 18.0 1.0
CA B:PRO45 4.4 17.9 1.0
CA B:LEU43 4.5 15.3 1.0
C B:PRO45 4.5 17.3 1.0
CA B:LEU44 4.5 15.0 1.0
N B:ASN46 4.7 17.7 1.0
O B:HOH467 4.7 22.2 1.0
O B:PRO45 4.8 14.5 1.0
O B:ASP41 4.9 14.3 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 Oct 9 11:27:41 2024

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