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

Sodium binding site 1 out of 4 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:Na412 b:28.4 occ:1.00 OE1 A:GLN91 2.2 21.3 1.0 O A:HOH553 2.4 19.4 1.0 O A:HOH817 2.4 37.4 1.0 O A:HOH552 2.5 19.3 1.0 CD A:GLN91 3.2 23.1 1.0 NE2 A:GLN91 3.6 19.3 1.0 O A:HOH551 4.1 34.7 1.0 CA A:GLN91 4.3 20.8 1.0 CG A:GLN91 4.5 11.6 1.0 CB A:GLN91 4.6 18.3 1.0 O A:VAL90 4.7 15.9 1.0 O A:GLN91 4.8 18.7 1.0

Sodium binding site 2 out of 4 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:Na413 b:35.6 occ:1.00 O A:HOH668 2.1 24.2 1.0 O A:GLN194 2.3 23.4 1.0 O A:HOH467 2.4 17.5 1.0 O A:HOH833 2.5 39.1 1.0 O A:HOH471 2.7 25.2 1.0 O A:HOH672 3.1 45.5 1.0 C A:GLN194 3.4 24.1 1.0 N A:GLN194 3.5 13.7 1.0 CA A:GLN194 3.9 14.4 1.0 O A:HOH468 4.0 21.6 1.0 CB A:GLN194 4.2 15.2 1.0 O A:HOH544 4.3 31.1 1.0 O A:ILE196 4.4 19.2 1.0 O A:HOH529 4.5 18.6 1.0 N A:GLY195 4.5 22.4 1.0 O A:HOH473 4.5 15.3 1.0 C A:PRO193 4.5 23.4 1.0 OD1 A:ASN35 4.7 17.1 1.0 CB A:PRO193 4.8 17.4 1.0 O A:HOH803 4.8 40.1 1.0 CA A:GLY195 4.8 16.0 1.0 O A:HOH834 4.9 39.4 1.0 CA A:PRO193 4.9 12.3 1.0 C A:GLY195 4.9 15.6 1.0

Sodium binding site 3 out of 4 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:Na414 b:34.0 occ:1.00 O A:GLN334 2.1 36.7 1.0 O A:HOH793 2.5 40.0 1.0 O A:HOH794 2.5 28.5 1.0 O A:HOH795 2.6 26.4 1.0 O A:HOH866 2.6 39.5 1.0 C A:GLN334 3.1 33.3 1.0 O A:TYR336 4.0 24.3 1.0 CA A:GLN334 4.0 28.9 1.0 N A:GLY335 4.1 38.8 1.0 CB A:GLN334 4.1 23.6 1.0 CA A:GLY335 4.2 20.3 1.0 C A:GLY335 4.5 31.9 1.0 NZ A:LYS37 4.5 31.5 1.0 OE1 A:GLN194 4.6 33.4 1.0 OD1 A:ASP192 4.6 23.4 1.0 OD2 A:ASP192 4.6 19.9 1.0 NE2 A:GLN194 4.6 26.8 1.0 N A:TYR336 4.6 29.7 1.0 NE2 A:GLN334 4.7 0.0 1.0 C A:TYR336 4.9 22.5 1.0

Sodium binding site 4 out of 4 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 4 of Udp-Galactose 4-Epimerase Complexed with Udp-Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na415 b:32.1 occ:0.50 O A:HOH518 2.1 24.7 1.0 O A:HOH519 2.2 28.9 1.0 O A:HOH820 2.6 67.2 1.0 O A:ASN115 2.7 22.0 1.0 O A:HOH821 2.8 47.6 1.0 O A:HOH871 3.1 57.4 1.0 C A:ASN115 3.6 31.5 1.0 O A:HOH520 3.8 40.8 1.0 O A:HOH521 4.1 18.7 1.0 O A:HOH426 4.3 38.3 1.0 O A:ALA114 4.3 28.5 1.0 CA A:VAL116 4.3 24.8 1.0 N A:VAL116 4.3 14.4 1.0 CG2 A:VAL116 4.4 15.2 1.0 CB A:ASN115 4.5 26.4 1.0 O A:HOH937 4.5 70.8 1.0 O A:ILE74 4.5 19.5 1.0 CA A:ASN115 4.5 21.6 1.0 O A:HOH522 4.7 29.1 1.0 O A:HOH580 4.9 37.9 1.0 CB A:VAL116 5.0 18.3 1.0

J.B.Thoden, A.M.Gulick, H.M.Holden. Molecular Structures of the S124A, S124T, and S124V Site-Directed Mutants of Udp-Galactose 4-Epimerase From Escherichia Coli. Biochemistry V. 36 10685 1997.
ISSN: ISSN 0006-2960
PubMed: 9271499
DOI: 10.1021/BI9704313