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

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy