Sodium in PDB 1udc: Structure of Udp-Galactose-4-Epimerase Complexed with Udp-Mannose

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

The structure of Structure of Udp-Galactose-4-Epimerase Complexed with Udp-Mannose, PDB code: 1udc 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

The binding sites of Sodium atom in the Structure of Udp-Galactose-4-Epimerase Complexed with Udp-Mannose (pdb code 1udc). 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-Mannose, PDB code: 1udc:
Jump to Sodium binding site number: 1; 2; 3;

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


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-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na350 b:11.7 occ:1.00 O A:HOH629 2.3 30.5 1.0 OE1 A:GLN91 2.4 23.1 1.0 O A:HOH933 2.4 34.9 1.0 O A:HOH626 2.5 20.4 1.0 O A:HOH928 2.5 19.2 1.0 O A:HOH932 2.5 15.5 1.0 CD A:GLN91 3.3 19.0 1.0 NE2 A:GLN91 3.6 21.7 1.0 O A:HOH630 4.0 33.8 1.0 O A:HOH935 4.1 30.0 1.0 O A:HOH934 4.2 46.8 1.0 CA A:GLN91 4.4 15.8 1.0 O A:HOH931 4.4 51.2 1.0 CG A:GLN91 4.6 13.2 1.0 CB A:GLN91 4.7 13.7 1.0 O A:VAL90 4.8 13.6 1.0 O A:GLN91 4.9 15.6 1.0

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


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-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na351 b:9.2 occ:1.00 O A:HOH740 2.2 31.9 1.0 O A:GLN194 2.3 21.5 1.0 O A:HOH736 2.3 21.4 1.0 O A:HOH974 2.3 40.5 1.0 O A:HOH549 2.5 15.2 1.0 O A:HOH547 2.6 23.9 1.0 C A:GLN194 3.5 20.5 1.0 N A:GLN194 3.8 14.6 1.0 CA A:GLN194 4.0 12.9 1.0 CB A:GLN194 4.2 13.0 1.0 O A:HOH548 4.2 17.1 1.0 O A:HOH622 4.3 24.5 1.0 O A:HOH747 4.5 45.7 1.0 O A:ILE196 4.6 17.7 1.0 N A:GLY195 4.6 19.1 1.0 O A:HOH546 4.6 12.3 1.0 OD1 A:ASN35 4.7 17.8 1.0 O A:HOH550 4.7 31.7 1.0 O A:HOH925 4.8 46.4 1.0 O A:HOH741 4.8 49.0 1.0 C A:PRO193 4.8 21.9 1.0 O A:HOH614 4.8 18.4 1.0 CA A:GLY195 4.9 15.7 1.0 CB A:PRO193 5.0 19.9 1.0

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


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-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na352 b:10.6 occ:1.00 O A:GLN334 2.3 34.7 1.0 O A:HOH744 2.3 30.9 1.0 O A:HOH746 2.4 27.7 1.0 O A:HOH609 2.5 40.7 1.0 O A:HOH745 2.6 24.6 1.0 C A:GLN334 3.3 31.3 1.0 O A:HOH1038 3.4 51.4 1.0 O A:TYR336 3.9 21.8 1.0 CA A:GLN334 4.1 26.8 1.0 CB A:GLN334 4.3 25.8 1.0 N A:GLY335 4.3 27.5 1.0 NZ A:LYS37 4.4 26.4 1.0 NE2 A:GLN334 4.4 0.0 1.0 CA A:GLY335 4.5 13.7 1.0 OE1 A:GLN194 4.5 26.9 1.0 NE2 A:GLN194 4.6 22.5 1.0 OD1 A:ASP192 4.6 15.6 1.0 OD2 A:ASP192 4.6 17.1 1.0 C A:GLY335 4.7 26.0 1.0 N A:TYR336 4.8 18.2 1.0 OD1 A:ASP338 4.9 78.1 1.0 C A:TYR336 5.0 19.1 1.0

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