Sodium in PDB 6eji: Structure of A Glycosyltransferase

The structure of Structure of A Glycosyltransferase, PDB code: 6eji was solved by A.S.Ramirez, J.Boilevin, A.R.Mehdipour, G.Hummer, T.Darbre, J.L.Reymond, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.620, 127.030, 71.580, 90.00, 90.13, 90.00
R / Rfree (%)	19.6 / 22.3

The structure of Structure of A Glycosyltransferase also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Structure of A Glycosyltransferase (pdb code 6eji). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Glycosyltransferase, PDB code: 6eji:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:40.9 occ:1.00 O2A A:UD2401 2.6 30.7 1.0 O A:HOH554 2.9 30.0 1.0 N A:THR271 3.0 26.3 1.0 O1A A:UD2401 3.1 35.2 1.0 N A:VAL272 3.1 22.4 1.0 CG2 A:VAL272 3.3 24.1 1.0 C A:PRO270 3.4 28.3 1.0 CB A:PRO270 3.4 27.1 1.0 PA A:UD2401 3.4 34.0 1.0 CA A:PRO270 3.5 28.5 1.0 CG1 A:VAL272 3.6 27.4 1.0 CB A:VAL272 3.8 29.2 1.0 CA A:THR271 3.9 22.4 1.0 NZ A:LYS196 4.0 35.5 1.0 C A:THR271 4.0 25.7 1.0 CA A:VAL272 4.1 24.5 1.0 CD1 A:LEU262 4.2 29.0 1.0 CB A:THR271 4.2 33.4 1.0 O5B A:UD2401 4.2 41.0 1.0 O A:PRO270 4.3 27.8 1.0 OG1 A:THR271 4.6 32.9 1.0 OE1 A:GLU267 4.7 31.3 1.0 N A:LEU273 4.9 26.9 1.0 CG A:PRO270 4.9 27.4 1.0 O3A A:UD2401 4.9 35.0 1.0 N A:PRO270 5.0 29.4 1.0 OE2 A:GLU267 5.0 35.4 1.0 C A:VAL272 5.0 26.5 1.0

Sodium binding site 2 out of 4 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:43.0 occ:1.00 O2B A:UD2401 2.7 37.9 1.0 O A:HOH588 2.8 48.8 1.0 N A:ALA17 3.1 28.1 1.0 N A:GLY16 3.3 36.2 1.0 CB A:ALA17 3.5 27.8 1.0 OE1 A:GLU18 3.6 43.3 1.0 C A:GLY15 3.8 35.1 1.0 PB A:UD2401 3.8 30.1 1.0 C1' A:UD2401 3.9 28.7 1.0 CA A:GLY15 3.9 35.0 1.0 CA A:ALA17 3.9 33.2 1.0 CA A:GLY16 4.0 31.5 1.0 C A:GLY16 4.0 34.0 1.0 O1' A:UD2401 4.0 37.3 1.0 O5' A:UD2401 4.0 28.8 1.0 NH2 A:ARG191 4.4 40.8 1.0 CD2 A:LEU95 4.5 39.1 1.0 CD1 A:LEU95 4.6 45.4 1.0 CD A:GLU18 4.6 41.2 1.0 O A:GLY15 4.7 33.4 1.0 N A:GLU18 4.7 28.5 1.0 O3A A:UD2401 4.8 35.0 1.0 O1B A:UD2401 4.8 31.2 1.0 C A:ALA17 4.9 31.9 1.0 OE2 A:GLU18 4.9 48.0 1.0

Sodium binding site 3 out of 4 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:44.2 occ:1.00 O1B B:UD2401 2.8 27.1 1.0 N B:ALA17 3.0 24.4 1.0 N B:GLY16 3.2 30.8 1.0 CB B:ALA17 3.6 26.1 1.0 OE2 B:GLU18 3.6 42.9 1.0 C1' B:UD2401 3.7 23.2 1.0 CA B:GLY16 3.8 28.0 1.0 PB B:UD2401 3.9 24.6 1.0 C B:GLY15 3.9 31.5 1.0 O5' B:UD2401 3.9 24.9 1.0 C B:GLY16 3.9 26.7 1.0 CA B:ALA17 3.9 28.5 1.0 O1' B:UD2401 4.0 31.0 1.0 CA B:GLY15 4.1 33.6 1.0 NH2 B:ARG191 4.5 32.1 1.0 CD B:GLU18 4.6 36.9 1.0 CD1 B:LEU95 4.6 45.2 1.0 CD2 B:LEU95 4.6 32.9 1.0 OE1 B:GLU18 4.7 44.6 1.0 N B:GLU18 4.7 28.1 1.0 O B:GLY15 4.7 28.7 1.0 O3A B:UD2401 4.8 30.0 1.0 O2B B:UD2401 4.9 24.0 1.0 C B:ALA17 4.9 28.2 1.0

Sodium binding site 4 out of 4 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:38.6 occ:1.00 O1A B:UD2401 2.8 30.6 1.0 O3A B:UD2401 3.0 30.0 1.0 N B:ARG191 3.1 39.5 1.0 PA B:UD2401 3.4 27.8 1.0 CL B:CL406 3.4 72.4 1.0 CA B:GLY190 3.5 34.8 1.0 CE B:LYS196 3.6 25.9 1.0 NZ B:LYS196 3.6 23.4 1.0 C5B B:UD2401 3.7 32.2 1.0 O2B B:UD2401 3.8 24.0 1.0 NH2 B:ARG191 3.8 32.1 1.0 C B:GLY190 3.8 35.4 1.0 CB B:ARG191 3.8 30.4 1.0 PB B:UD2401 4.0 24.6 1.0 O B:HOH575 4.1 23.9 1.0 CA B:ARG191 4.1 35.7 1.0 CZ B:ARG191 4.1 33.4 1.0 O5B B:UD2401 4.1 36.6 1.0 CD B:LYS196 4.5 32.1 1.0 O1B B:UD2401 4.5 27.1 1.0 NE B:ARG191 4.6 41.6 1.0 NH1 B:ARG191 4.6 25.1 1.0 O2A B:UD2401 4.6 27.5 1.0 N B:GLY190 4.8 28.7 1.0

A.S.Ramirez, J.Boilevin, A.R.Mehdipour, G.Hummer, T.Darbre, J.L.Reymond, K.P.Locher. Structural Basis of the Molecular Ruler Mechanism of A Bacterial Glycosyltransferase. Nat Commun V. 9 445 2018.
ISSN: ESSN 2041-1723
PubMed: 29386647
DOI: 10.1038/S41467-018-02880-2