Chlorine 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
Sodium	(Na)	4 atoms

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

Chlorine binding site 1 out of 3 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:67.7 occ:1.00 N A:TYR66 3.4 47.7 1.0 ND2 B:ASN50 3.6 41.0 1.0 CB A:TYR66 3.7 44.8 1.0 N A:LEU65 3.8 54.4 1.0 CB A:THR64 3.8 41.9 1.0 OG1 A:THR64 4.0 46.5 1.0 OD1 B:ASN50 4.1 39.8 1.0 CA A:TYR66 4.2 46.6 1.0 CB A:LEU65 4.2 56.2 1.0 CA A:LEU65 4.3 55.7 1.0 C A:LEU65 4.3 51.7 1.0 CG B:ASN50 4.3 39.0 1.0 C A:THR64 4.5 52.8 1.0 CA A:THR64 4.7 49.0 1.0 CG2 A:THR64 4.8 42.1 1.0

Chlorine binding site 2 out of 3 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:79.2 occ:1.00 O A:HOH566 3.0 42.5 1.0 O A:HOH567 3.1 33.8 1.0 K A:K402 3.5 44.9 1.0 O A:SER14 3.6 47.0 1.0 OG A:SER14 3.7 45.7 1.0 CA A:GLY15 3.8 35.0 1.0 C5B A:UD2401 3.8 30.7 1.0 C A:SER14 3.9 40.3 1.0 NH2 A:ARG191 3.9 40.8 1.0 N A:GLY15 4.0 32.8 1.0 O3A A:UD2401 4.2 35.0 1.0 O4B A:UD2401 4.3 39.0 1.0 O A:HOH536 4.3 45.3 1.0 CB A:ARG191 4.5 32.8 1.0 N A:ARG191 4.5 36.6 1.0 NE A:ARG191 4.5 43.1 1.0 CB A:SER14 4.5 42.1 1.0 C4B A:UD2401 4.6 35.9 1.0 CZ A:ARG191 4.6 38.8 1.0 C A:GLY15 4.6 35.1 1.0 C6 A:UD2401 4.8 34.8 1.0 N A:GLY16 4.8 36.2 1.0 CA A:ARG191 4.8 37.5 1.0 CA A:SER14 4.9 40.4 1.0 O2B A:UD2401 4.9 37.9 1.0 O5B A:UD2401 5.0 41.0 1.0

Chlorine binding site 3 out of 3 in the Structure of A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:72.4 occ:1.00 O B:HOH576 3.1 37.8 1.0 K B:K402 3.3 34.2 1.0 NA B:NA405 3.4 38.6 1.0 N B:GLY15 3.7 35.1 1.0 OG B:SER14 3.7 36.7 1.0 CA B:GLY15 3.7 33.6 1.0 C5B B:UD2401 3.9 32.2 1.0 C B:SER14 3.9 38.6 1.0 CB B:SER14 4.0 32.7 1.0 O B:SER14 4.1 50.1 1.0 O4B B:UD2401 4.2 37.7 1.0 NH2 B:ARG191 4.2 32.1 1.0 O3A B:UD2401 4.3 30.0 1.0 C6 B:UD2401 4.5 32.4 1.0 C4B B:UD2401 4.5 31.3 1.0 CA B:SER14 4.6 37.3 1.0 N B:ARG191 4.6 39.5 1.0 CB B:ARG191 4.6 30.4 1.0 NE B:ARG191 4.7 41.6 1.0 C B:GLY15 4.7 31.5 1.0 CZ B:ARG191 4.8 33.4 1.0 N1 B:UD2401 4.9 33.5 1.0 C1B B:UD2401 4.9 31.0 1.0 CA B:ARG191 5.0 35.7 1.0 O5B B:UD2401 5.0 36.6 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