Sodium in PDB 6ejj: Structure of A Glycosyltransferase / State 2

The structure of Structure of A Glycosyltransferase / State 2, PDB code: 6ejj 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)	29.81 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.510, 125.780, 71.010, 90.00, 90.28, 90.00
R / Rfree (%)	20.6 / 24.4

The structure of Structure of A Glycosyltransferase / State 2 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of A Glycosyltransferase / State 2 (pdb code 6ejj). 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 / State 2, PDB code: 6ejj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of A Glycosyltransferase / State 2


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 / State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:59.4 occ:1.00 O A:HOH513 2.4 68.7 1.0 O36 A:BUE408 2.6 75.0 1.0 O37 A:BUE408 2.6 78.2 1.0 P35 A:BUE408 3.3 75.4 1.0 O38 A:BUE408 4.3 75.8 1.0 NH1 A:ARG72 4.6 77.0 1.0 O34 A:BUE408 4.6 73.0 1.0 O40 A:BUE408 4.9 74.1 1.0 C1 A:NDG407 5.0 70.8 1.0

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


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 / State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:58.4 occ:1.00 OE2 A:GLU267 2.7 54.3 1.0 CL A:CL404 3.2 82.4 1.0 O3A A:UDP401 3.3 45.3 1.0 O3B A:UDP401 3.4 46.1 1.0 CD A:GLU267 3.9 55.7 1.0 PB A:UDP401 4.0 46.5 1.0 CA A:PRO270 4.0 43.4 1.0 N A:GLY268 4.0 55.5 1.0 N A:LEU269 4.1 58.6 1.0 O A:HIS118 4.1 59.3 1.0 N A:PRO270 4.2 45.0 1.0 C A:LEU269 4.2 49.0 1.0 O A:LEU269 4.3 46.0 1.0 O2A A:UDP401 4.3 43.9 1.0 PA A:UDP401 4.5 45.3 1.0 CA A:GLY268 4.6 55.4 1.0 OE1 A:GLU267 4.6 62.8 1.0 CB A:PRO270 4.7 40.0 1.0 C A:GLY268 4.8 56.8 1.0 CA A:LEU269 4.8 51.9 1.0 CB A:GLU267 4.8 50.2 1.0 CG A:PRO270 4.8 45.0 1.0 O2B A:UDP401 4.9 47.4 1.0 CD A:PRO270 5.0 46.7 1.0 CG A:GLU267 5.0 51.4 1.0 CA A:GLU267 5.0 50.4 1.0

Sodium binding site 3 out of 4 in the Structure of A Glycosyltransferase / State 2


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 / State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:53.5 occ:1.00 O2A B:UDP401 2.4 50.0 1.0 NZ B:LYS196 2.8 50.4 1.0 CA B:GLY190 3.0 45.8 1.0 O B:ILE189 3.1 48.4 1.0 CE B:LYS196 3.2 46.9 1.0 O2B B:UDP401 3.3 50.3 1.0 PA B:UDP401 3.8 49.6 1.0 C B:ILE189 3.8 43.6 1.0 CD B:LYS196 3.9 47.2 1.0 N B:GLY190 3.9 46.0 1.0 C5' B:UDP401 3.9 49.2 1.0 CG1 B:VAL272 4.1 32.2 1.0 N B:ARG191 4.2 43.5 1.0 C B:GLY190 4.2 48.2 1.0 CG2 B:VAL272 4.3 39.2 1.0 O5' B:UDP401 4.3 49.2 1.0 O3A B:UDP401 4.3 49.9 1.0 PB B:UDP401 4.4 50.1 1.0 CD1 B:LEU262 4.6 42.0 1.0 OE1 B:GLU267 4.8 57.0 1.0 O1A B:UDP401 4.8 49.5 1.0 CB B:VAL272 4.9 36.9 1.0 CG B:LYS196 4.9 53.9 1.0

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


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 / State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:71.5 occ:1.00 O37 B:BUE407 2.4 80.9 1.0 O34 B:BUE407 2.8 76.2 1.0 P35 B:BUE407 3.2 77.0 1.0 CE2 B:PHE62 3.7 87.3 1.0 O38 B:BUE407 3.8 77.3 1.0 CD2 B:PHE62 4.0 92.0 1.0 O41 B:BUE407 4.1 75.7 1.0 CZ B:PHE62 4.2 83.3 1.0 P39 B:BUE407 4.4 75.6 1.0 O40 B:BUE407 4.4 78.0 1.0 NH2 B:ARG72 4.4 0.0 1.0 CG B:PHE62 4.6 94.7 1.0 O36 B:BUE407 4.7 74.5 1.0 CE1 B:PHE62 4.8 82.7 1.0 CD1 B:PHE62 5.0 89.4 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