Manganese 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:

Iodine

(I)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Salmonella Effector SSEK3 in Complex with Udp-Glcnac and Manganese, PDB code: 6eyt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn403 b:30.1 occ:1.00 O1B A:UDP404 2.0 33.5 1.0 O1A A:UDP404 2.0 27.6 1.0 OD1 A:ASP325 2.1 35.3 1.0 OG A:SER327 2.1 34.4 1.0 OD2 A:ASP228 2.1 29.0 1.0 O A:HOH551 2.3 32.8 1.0 CG A:ASP228 3.2 27.9 1.0 CB A:SER327 3.2 34.2 1.0 PB A:UDP404 3.2 35.1 1.0 CG A:ASP325 3.3 35.9 1.0 PA A:UDP404 3.3 29.8 1.0 OD1 A:ASP228 3.6 28.7 1.0 O3A A:UDP404 3.7 35.3 1.0 O A:HOH531 3.8 37.8 1.0 H8C1 A:NDG405 3.8 41.2 1.0 HA A:NDG405 3.8 54.5 1.0 H8C3 A:NDG405 4.0 41.2 1.0 O3B A:UDP404 4.0 36.2 1.0 OD2 A:ASP325 4.1 39.0 1.0 N A:SER327 4.1 32.7 1.0 O A:HOH534 4.2 28.7 1.0 O2A A:UDP404 4.2 34.2 1.0 CA A:ASP325 4.2 32.4 1.0 CA A:SER327 4.2 34.1 1.0 CB A:ASP325 4.2 35.5 1.0 CB A:ASP228 4.4 27.7 1.0 C8 A:NDG405 4.4 34.4 1.0 OD2 A:ASP226 4.4 27.3 1.0 O5' A:UDP404 4.4 28.2 1.0 O2B A:UDP404 4.4 39.3 1.0 C A:ASP325 4.5 32.2 1.0 N A:SER328 4.6 35.3 1.0 C5' A:UDP404 4.7 25.9 1.0 N2 A:NDG405 4.8 45.4 1.0 O A:ASP325 4.8 30.2 1.0 C A:SER327 4.8 34.8 1.0 OH A:TYR75 4.8 28.7 1.0

Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn 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 B:Mn403 b:35.3 occ:1.00 O2B B:UDP404 1.9 39.5 1.0 O B:HOH520 2.1 31.1 1.0 OG B:SER327 2.1 39.5 1.0 O2A B:UDP404 2.2 33.9 1.0 OD2 B:ASP228 2.2 31.9 1.0 OD1 B:ASP325 2.4 38.2 1.0 CG B:ASP228 3.1 31.5 1.0 CB B:SER327 3.3 38.1 1.0 PB B:UDP404 3.3 48.4 1.0 PA B:UDP404 3.3 39.9 1.0 OD1 B:ASP228 3.5 30.6 1.0 H8C1 B:NDG405 3.6 44.4 1.0 CG B:ASP325 3.6 44.2 1.0 O3A B:UDP404 3.6 42.2 1.0 HA B:NDG405 3.7 50.8 1.0 H8C3 B:NDG405 3.9 44.4 1.0 O B:HOH502 4.0 40.2 1.0 N B:SER327 4.1 37.2 1.0 O3B B:UDP404 4.2 53.2 1.0 O B:HOH540 4.2 31.9 1.0 O1A B:UDP404 4.2 39.4 1.0 CA B:SER327 4.2 37.9 1.0 C8 B:NDG405 4.2 37.0 1.0 CA B:ASP325 4.3 37.4 1.0 OD2 B:ASP226 4.3 30.9 1.0 O1B B:UDP404 4.3 49.2 1.0 CB B:ASP228 4.4 28.3 1.0 OD2 B:ASP325 4.4 44.6 1.0 CB B:ASP325 4.4 38.7 1.0 O5' B:UDP404 4.5 39.9 1.0 C B:ASP325 4.6 36.3 1.0 N2 B:NDG405 4.6 42.4 1.0 C5' B:UDP404 4.6 34.3 1.0 N B:SER328 4.8 41.2 1.0 OH B:TYR75 4.8 33.4 1.0 C B:SER327 4.9 41.3 1.0 O B:ASP325 4.9 40.5 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