Sodium in PDB 1kvu: Udp-Galactose 4-Epimerase Complexed with Udp-Phenol

All present enzymatic activity of Udp-Galactose 4-Epimerase Complexed with Udp-Phenol:
5.1.3.2;

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

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.500, 83.500, 108.400, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

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

Sodium binding site 1 out of 3 in the Udp-Galactose 4-Epimerase Complexed with Udp-Phenol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Udp-Galactose 4-Epimerase Complexed with Udp-Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:50.5 occ:1.00 O A:HOH580 2.3 35.7 1.0 OE1 A:GLN91 2.3 32.9 1.0 O A:HOH492 2.7 31.2 1.0 O A:HOH796 3.1 60.4 1.0 CD A:GLN91 3.3 21.0 1.0 NE2 A:GLN91 3.6 40.5 1.0 CA A:GLN91 4.5 29.7 1.0 CG A:GLN91 4.6 31.3 1.0 CB A:GLN91 4.7 23.4 1.0 O A:VAL90 4.8 16.6 1.0

Sodium binding site 2 out of 3 in the Udp-Galactose 4-Epimerase Complexed with Udp-Phenol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Udp-Galactose 4-Epimerase Complexed with Udp-Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:33.4 occ:1.00 O A:HOH679 2.3 42.2 1.0 O A:GLN194 2.3 30.7 1.0 O A:HOH650 2.4 24.7 1.0 O A:HOH630 2.5 22.7 1.0 O A:HOH708 2.6 25.9 1.0 O A:HOH892 2.8 62.5 1.0 C A:GLN194 3.4 26.4 1.0 N A:GLN194 3.7 15.3 1.0 O A:HOH792 3.8 48.6 1.0 CA A:GLN194 3.9 26.2 1.0 CB A:GLN194 4.0 16.7 1.0 O A:HOH535 4.2 24.9 1.0 O A:HOH611 4.5 36.0 1.0 O A:HOH707 4.5 19.3 1.0 N A:GLY195 4.5 23.2 1.0 O A:ILE196 4.6 22.1 1.0 OD1 A:ASN35 4.7 22.8 1.0 C A:PRO193 4.7 24.9 1.0 O A:HOH539 4.8 29.0 1.0 O A:HOH810 4.8 46.9 1.0 CA A:GLY195 4.8 24.9 1.0 CB A:PRO193 5.0 20.3 1.0

Sodium binding site 3 out of 3 in the Udp-Galactose 4-Epimerase Complexed with Udp-Phenol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Udp-Galactose 4-Epimerase Complexed with Udp-Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:38.7 occ:1.00 O A:GLN334 2.2 52.3 1.0 O A:HOH641 2.4 38.1 1.0 O A:HOH593 2.5 30.3 1.0 O A:HOH451 2.7 25.5 1.0 O A:HOH723 2.8 39.9 1.0 C A:GLN334 3.4 33.2 1.0 O A:HOH858 3.9 75.9 1.0 O A:HOH871 3.9 0.0 1.0 O A:TYR336 4.0 28.3 1.0 CA A:GLN334 4.1 33.9 1.0 N A:GLY335 4.3 30.0 1.0 CB A:GLN334 4.5 36.6 1.0 NZ A:LYS37 4.5 32.4 1.0 CA A:GLY335 4.5 15.5 1.0 NE2 A:GLN334 4.5 0.0 1.0 OD1 A:ASP338 4.6 0.0 1.0 OD1 A:ASP192 4.6 28.0 1.0 OD2 A:ASP192 4.6 19.4 1.0 NE2 A:GLN194 4.7 26.5 1.0 O A:HOH768 4.7 38.6 1.0 C A:GLY335 4.7 16.2 1.0 OE1 A:GLN194 4.7 40.2 1.0 N A:TYR336 4.7 33.7 1.0 C A:TYR336 4.9 22.1 1.0

Y.Liu, J.B.Thoden, J.Kim, E.Berger, A.M.Gulick, F.J.Ruzicka, H.M.Holden, P.A.Frey. Mechanistic Roles of Tyrosine 149 and Serine 124 in Udp-Galactose 4-Epimerase From Escherichia Coli. Biochemistry V. 36 10675 1997.
ISSN: ISSN 0006-2960
PubMed: 9271498
DOI: 10.1021/BI970430A