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

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

All present enzymatic activity of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Glucose:
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-Glucose, PDB code: 1udb 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 / 1.65
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 1udb:

The structure of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-4-Deoxy-4- Fluoro-Alpha-D-Glucose 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-Glucose (pdb code 1udb). 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-Glucose, PDB code: 1udb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1udb

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


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-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:13.8
occ:1.00
 OE1 A:GLN91 2.1 30.1 1.0
O A:HOH723 2.3 50.2 1.0
O A:HOH564 2.4 29.3 1.0
O A:HOH656 2.5 47.3 1.0
CD A:GLN91 3.1 25.5 1.0
NE2 A:GLN91 3.5 29.5 1.0
O A:HOH811 4.0 40.2 1.0
CA A:GLN91 4.3 23.1 1.0
CG A:GLN91 4.4 18.6 1.0
CB A:GLN91 4.6 27.1 1.0
O A:VAL90 4.8 25.8 1.0
O A:GLN91 4.8 22.7 1.0

Sodium binding site 2 out of 3 in 1udb

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


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-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:20.0
occ:1.00
 O A:HOH679 2.3 29.6 1.0
O A:GLN194 2.4 32.2 1.0
O A:HOH985 2.5 51.8 1.0
O A:HOH551 2.5 23.9 1.0
O A:HOH793 2.5 33.5 1.0
C A:GLN194 3.5 37.4 1.0
N A:GLN194 3.8 21.0 1.0
CA A:GLN194 4.0 25.3 1.0
O A:HOH597 4.2 30.8 1.0
CB A:GLN194 4.3 21.8 1.0
O A:HOH827 4.3 42.6 1.0
O A:HOH1050 4.4 57.3 1.0
O A:ILE196 4.6 24.1 1.0
O A:HOH788 4.6 23.8 1.0
N A:GLY195 4.6 29.6 1.0
O A:HOH598 4.7 29.8 1.0
C A:PRO193 4.8 24.4 1.0
OD1 A:ASN35 4.8 27.1 1.0
O A:HOH785 4.8 68.8 1.0
O A:HOH766 4.8 46.8 1.0
CA A:GLY195 4.9 23.8 1.0
CB A:PRO193 5.0 22.1 1.0

Sodium binding site 3 out of 3 in 1udb

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


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-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:15.2
occ:1.00
 O A:GLN334 2.2 37.4 1.0
O A:HOH640 2.3 39.9 1.0
O A:HOH961 2.3 59.4 1.0
O A:HOH889 2.4 49.3 1.0
O A:HOH632 2.5 34.1 1.0
O A:HOH1016 2.7 45.1 1.0
O A:HOH838 3.0 51.0 1.0
C A:GLN334 3.3 30.2 1.0
O A:TYR336 3.9 28.9 1.0
O A:HOH944 3.9 73.8 1.0
CA A:GLN334 4.1 33.4 1.0
NZ A:LYS37 4.1 46.5 1.0
N A:GLY335 4.2 40.5 1.0
CB A:GLN334 4.4 33.0 1.0
CA A:GLY335 4.4 25.8 1.0
NE2 A:GLN334 4.5 0.0 1.0
OD1 A:ASP192 4.5 29.7 1.0
NE2 A:GLN194 4.5 31.6 1.0
OD2 A:ASP192 4.6 24.8 1.0
OE1 A:GLN194 4.6 36.9 1.0
C A:GLY335 4.6 27.4 1.0
N A:TYR336 4.7 36.7 1.0
O A:HOH844 4.7 44.4 1.0
OD1 A:ASP338 4.7 0.0 1.0
O A:HOH923 4.8 66.2 1.0
C A:TYR336 4.9 25.9 1.0
CE A:LYS37 4.9 97.7 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: Tue Dec 15 05:36:57 2020

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