Iodine in PDB 6eyt: Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese

The structure of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese, PDB code: 6eyt was solved by D.Esposito, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.970, 85.940, 96.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.1

The structure of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese (pdb code 6eyt). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese, PDB code: 6eyt:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:34.2 occ:0.82 NE A:ARG189 3.5 44.7 1.0 N A:GLY186 3.6 44.7 1.0 NH2 A:ARG189 3.8 32.8 1.0 CB A:PHE53 3.9 27.6 1.0 CA A:LEU185 4.1 49.4 1.0 CD2 A:PHE53 4.1 23.1 1.0 CZ A:ARG189 4.2 34.7 1.0 O A:GLY186 4.2 32.5 1.0 CB A:LEU185 4.4 49.2 1.0 C A:LEU185 4.4 41.4 1.0 CD2 A:LEU185 4.4 45.5 1.0 CB A:ARG189 4.4 33.4 1.0 CD2 A:PHE190 4.5 27.9 1.0 CG A:PHE53 4.5 24.6 1.0 CB A:ARG55 4.5 35.6 1.0 CA A:GLY186 4.5 39.5 1.0 CD A:ARG189 4.6 38.0 1.0 CD A:ARG55 4.7 39.2 1.0 O A:PHE53 4.7 22.6 1.0 C A:GLY186 4.8 34.8 1.0 C A:PHE53 4.8 23.8 1.0 CG A:ARG189 4.9 37.7 1.0 N A:PHE190 4.9 26.7 1.0 CG A:ARG55 4.9 40.1 1.0 CA A:PHE53 5.0 23.8 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:46.3 occ:0.57 NZ A:LYS105 3.5 55.3 1.0 CE A:LYS105 3.8 52.0 1.0 CD A:LYS105 4.0 43.9 1.0 CG A:LYS105 4.8 39.2 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:I401 b:28.1 occ:0.78 CG B:ARG55 3.7 42.9 1.0 NH1 B:ARG189 3.7 32.2 1.0 N B:GLY186 3.7 35.2 1.0 CD B:ARG55 3.9 46.5 1.0 CD B:ARG189 3.9 35.7 1.0 CB B:PHE53 3.9 26.3 1.0 NH1 B:ARG55 4.0 36.0 1.0 CD2 B:PHE53 4.1 26.8 1.0 CA B:LEU185 4.2 43.4 1.0 CB B:ARG189 4.2 30.0 1.0 O B:GLY186 4.2 33.6 1.0 CB B:LEU185 4.4 45.3 1.0 CG B:ARG189 4.4 32.5 1.0 CD2 B:PHE190 4.5 30.5 1.0 CD2 B:LEU185 4.5 49.9 1.0 CG B:PHE53 4.5 24.9 1.0 C B:LEU185 4.5 38.6 1.0 CZ B:ARG189 4.6 31.2 1.0 CA B:GLY186 4.6 36.0 1.0 NE B:ARG189 4.7 34.5 1.0 C B:GLY186 4.8 31.0 1.0 NE B:ARG55 4.8 45.3 1.0 N B:PHE190 4.9 25.8 1.0 CZ B:ARG55 4.9 49.6 1.0 O B:PHE53 4.9 28.0 1.0 C B:PHE53 5.0 26.3 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:I402 b:75.1 occ:0.39 CE B:LYS210 3.5 32.4 1.0 NZ B:LYS118 3.7 36.6 1.0 CD B:LYS118 3.8 27.7 1.0 OE2 B:GLU111 3.9 40.5 1.0 NZ B:LYS210 3.9 32.6 1.0 N B:HIS211 4.1 25.4 1.0 O B:HIS211 4.1 29.5 1.0 CA B:LYS210 4.3 30.9 1.0 CE B:LYS118 4.3 34.6 1.0 CB B:LYS210 4.4 28.6 1.0 CD B:LYS210 4.5 28.8 1.0 CD B:GLU111 4.5 41.2 1.0 C B:LYS210 4.6 26.5 1.0

D.Esposito, R.A.Gunster, L.Martino, K.El Omari, A.Wagner, T.L.M.Thurston, K.Rittinger. Structural Basis For the Glycosyltransferase Activity of Thesalmonellaeffector SSEK3. J. Biol. Chem. V. 293 5064 2018.
ISSN: ESSN 1083-351X
PubMed: 29449376
DOI: 10.1074/JBC.RA118.001796