Atomistry » Sodium » PDB 1ubs-1v54 » 1uda
Atomistry »
  Sodium »
    PDB 1ubs-1v54 »
      1uda »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy