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Sodium in PDB 1uda: Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose

Enzymatic activity of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose

All present enzymatic activity of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose:
5.1.3.2;

Protein crystallography data

The structure of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose, PDB code: 1uda was solved by J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.500, 83.500, 108.900, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1uda:

The structure of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose also contains other interesting chemical elements:

Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose (pdb code 1uda). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose, PDB code: 1uda:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1uda

Go back to Sodium Binding Sites List in 1uda
Sodium binding site 1 out of 3 in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na420

b:6.8
occ:1.00
 OE1 A:GLN91 2.1 23.3 1.0
O A:HOH956 2.3 29.4 1.0
O A:HOH647 2.6 19.0 1.0
CD A:GLN91 3.1 22.7 1.0
NE2 A:GLN91 3.6 15.2 1.0
O A:HOH806 4.2 29.5 1.0
CA A:GLN91 4.3 25.0 1.0
CG A:GLN91 4.4 9.2 1.0
CB A:GLN91 4.6 30.1 1.0
O A:VAL90 4.7 13.7 1.0
O A:GLN91 4.8 15.6 1.0
O A:HOH820 4.9 61.5 1.0
O A:HOH979 5.0 46.6 1.0

Sodium binding site 2 out of 3 in 1uda

Go back to Sodium Binding Sites List in 1uda
Sodium binding site 2 out of 3 in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na421

b:16.2
occ:1.00
 O A:GLN194 2.3 26.4 1.0
O A:HOH551 2.4 14.7 1.0
O A:HOH898 2.4 21.3 1.0
O A:HOH959 2.4 54.8 1.0
O A:HOH986 2.6 47.9 1.0
C A:GLN194 3.5 18.4 1.0
N A:GLN194 3.8 13.1 1.0
CA A:GLN194 4.0 28.1 1.0
CB A:GLN194 4.2 14.7 1.0
O A:HOH714 4.4 30.4 1.0
O A:HOH756 4.6 16.9 1.0
N A:GLY195 4.6 26.6 1.0
O A:HOH932 4.7 33.7 1.0
OD1 A:ASN35 4.7 20.9 1.0
C A:PRO193 4.8 17.8 1.0
O A:ILE196 4.8 14.3 1.0
O A:HOH801 4.9 16.6 1.0
O A:HOH918 4.9 55.1 1.0
CA A:GLY195 4.9 18.5 1.0
O A:HOH1057 5.0 57.0 1.0

Sodium binding site 3 out of 3 in 1uda

Go back to Sodium Binding Sites List in 1uda
Sodium binding site 3 out of 3 in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na422

b:8.9
occ:1.00
 O A:HOH948 2.1 36.9 1.0
O A:GLN334 2.2 31.9 1.0
O A:HOH864 2.5 55.5 1.0
O A:HOH799 2.5 30.3 1.0
O A:HOH624 2.7 24.2 1.0
O A:HOH916 3.1 57.9 1.0
O A:HOH861 3.2 65.9 1.0
C A:GLN334 3.3 33.2 1.0
O A:TYR336 3.9 28.8 1.0
CA A:GLN334 4.1 21.8 1.0
N A:GLY335 4.2 37.1 1.0
CB A:GLN334 4.3 31.0 1.0
CA A:GLY335 4.4 17.2 1.0
NZ A:LYS37 4.4 33.8 1.0
NE2 A:GLN334 4.5 0.0 1.0
OE1 A:GLN194 4.6 31.0 1.0
OD2 A:ASP192 4.6 12.1 1.0
NE2 A:GLN194 4.6 26.9 1.0
N A:TYR336 4.7 26.0 1.0
OD1 A:ASP338 4.7 0.0 1.0
C A:GLY335 4.7 16.2 1.0
OD1 A:ASP192 4.7 14.8 1.0
O A:HOH814 4.8 33.8 1.0
C A:TYR336 4.9 16.0 1.0

Reference:

J.B.Thoden, A.D.Hegeman, G.Wesenberg, M.C.Chapeau, P.A.Frey, H.M.Holden. Structural Analysis of Udp-Sugar Binding to Udp-Galactose 4-Epimerase From Escherichia Coli. Biochemistry V. 36 6294 1997.
ISSN: ISSN 0006-2960
PubMed: 9174344
DOI: 10.1021/BI970025J
Page generated: Sun Oct 6 22:45:04 2024

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