Sodium in PDB 5hut: Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose

All present enzymatic activity of Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose:
2.4.1.15;

The structure of Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose, PDB code: 5hut was solved by Y.Miao, R.G.Brennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.29 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	98.714, 98.714, 187.653, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.6

The binding sites of Sodium atom in the Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose (pdb code 5hut). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose, PDB code: 5hut:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-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 Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:41.7 occ:1.00 O A:HOH732 2.3 41.5 1.0 O A:VAL272 2.4 36.0 1.0 O A:PHE269 2.4 34.8 1.0 O A:HOH699 2.5 45.1 1.0 O A:HOH793 2.5 53.7 1.0 HB3 A:PHE269 3.0 44.8 1.0 C A:PHE269 3.4 42.3 1.0 H A:VAL272 3.5 43.7 1.0 HB2 A:PHE269 3.5 44.8 1.0 HG23 A:VAL274 3.6 32.9 1.0 C A:VAL272 3.6 26.9 1.0 CB A:PHE269 3.7 37.3 1.0 HA A:LYS270 3.9 50.3 1.0 HA A:LYS273 3.9 32.3 1.0 CA A:PHE269 4.2 34.8 1.0 HG22 A:VAL272 4.2 47.7 1.0 N A:VAL272 4.2 36.4 1.0 N A:LYS270 4.3 41.5 1.0 O1 A:SO4505 4.3 49.1 1.0 HH12 A:ARG395 4.3 46.9 1.0 HG23 A:VAL272 4.3 47.7 1.0 C A:LYS270 4.3 39.4 1.0 CA A:LYS270 4.3 41.9 1.0 O A:LYS270 4.4 40.5 1.0 O A:HOH719 4.4 42.5 1.0 CG2 A:VAL274 4.5 27.4 1.0 OD2 A:ASP370 4.5 33.6 1.0 HG21 A:VAL274 4.5 32.9 1.0 N A:LYS273 4.5 29.1 1.0 CA A:VAL272 4.5 28.4 1.0 CA A:LYS273 4.6 26.9 1.0 CG2 A:VAL272 4.7 39.7 1.0 HA A:PHE269 4.7 41.7 1.0 N A:ASP271 4.9 41.6 1.0 H A:VAL274 4.9 29.1 1.0 O A:LYS266 4.9 38.8 1.0 HA A:LYS266 4.9 46.4 1.0 NH1 A:ARG395 4.9 39.1 1.0 C A:LYS273 5.0 27.9 1.0 CG A:PHE269 5.0 37.9 1.0 HD3 A:LYS273 5.0 46.5 1.0

Sodium binding site 2 out of 2 in the Structure of Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-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 Candida Albicans Trehalose-6-Phosphate Synthase in Complex with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:41.0 occ:1.00 O B:HOH686 2.3 37.4 1.0 O B:VAL272 2.3 34.4 1.0 O B:PHE269 2.4 32.1 1.0 O B:HOH730 2.5 57.3 1.0 O B:HOH656 2.6 42.9 1.0 HB3 B:PHE269 3.0 42.3 1.0 C B:PHE269 3.4 35.9 1.0 HB2 B:PHE269 3.5 42.3 1.0 HG23 B:VAL274 3.6 33.8 1.0 C B:VAL272 3.6 35.0 1.0 CB B:PHE269 3.6 35.2 1.0 H B:VAL272 3.7 42.4 1.0 HA B:LYS273 3.8 31.9 1.0 HA B:LYS270 3.9 44.4 1.0 O3 B:SO4505 4.1 55.8 1.0 HG22 B:VAL272 4.1 39.6 1.0 CA B:PHE269 4.2 34.3 1.0 HG23 B:VAL272 4.2 39.6 1.0 HH12 B:ARG395 4.3 46.8 1.0 H162 B:1PE506 4.3 59.4 1.0 N B:LYS270 4.3 34.5 1.0 N B:VAL272 4.3 35.4 1.0 OD2 B:ASP370 4.4 34.2 1.0 CA B:LYS270 4.4 37.0 1.0 CG2 B:VAL274 4.4 28.1 1.0 N B:LYS273 4.5 27.5 1.0 C B:LYS270 4.5 31.3 1.0 CA B:LYS273 4.5 26.6 1.0 O B:LYS270 4.5 37.3 1.0 HG21 B:VAL274 4.5 33.8 1.0 O B:HOH613 4.5 37.7 1.0 CA B:VAL272 4.5 27.6 1.0 O1 B:SO4505 4.6 72.5 1.0 CG2 B:VAL272 4.6 33.0 1.0 HA B:PHE269 4.7 41.2 1.0 H B:VAL274 4.7 32.2 1.0 C B:LYS273 4.9 31.1 1.0 NH1 B:ARG395 4.9 39.0 1.0 N B:VAL274 4.9 26.9 1.0 HA B:LYS266 4.9 37.8 1.0 CG B:PHE269 4.9 34.9 1.0 S B:SO4505 5.0 80.7 1.0

Y.Miao, J.L.Tenor, D.L.Toffaletti, S.A.Maskarinec, J.Liu, R.E.Lee, J.R.Perfect, R.G.Brennan. Structural and in Vivo Studies on Trehalose-6-Phosphate Synthase From Pathogenic Fungi Provide Insights Into Its Catalytic Mechanism, Biological Necessity, and Potential For Novel Antifungal Drug Design. Mbio V. 8 2017.
ISSN: ESSN 2150-7511
PubMed: 28743811
DOI: 10.1128/MBIO.00643-17