Manganese in PDB 5gvv: Crystal Structure of the Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4

The structure of Crystal Structure of the Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4, PDB code: 5gvv was solved by Y.L.Jiang, H.Jin, R.L.Zhao, H.B.Yang, Y.Chen, C.Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.170, 88.210, 128.360, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.7

The binding sites of Manganese atom in the Crystal Structure of the Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 (pdb code 5gvv). 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 Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4, PDB code: 5gvv:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4


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 Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:32.6 occ:1.00 O3B A:UDP502 2.0 19.0 1.0 OD2 A:ASP106 2.1 14.3 1.0 OD1 A:ASP108 2.1 12.4 1.0 NE2 A:HIS227 2.1 13.6 1.0 O1A A:UDP502 2.1 17.6 1.0 OD2 A:ASP108 2.2 11.9 1.0 CG A:ASP108 2.5 15.7 1.0 CG A:ASP106 3.0 18.4 1.0 CE1 A:HIS227 3.1 15.6 1.0 CD2 A:HIS227 3.1 12.7 1.0 PB A:UDP502 3.3 28.3 1.0 PA A:UDP502 3.4 25.2 1.0 CB A:ASP106 3.4 15.3 1.0 O3A A:UDP502 3.6 30.2 1.0 CB A:ASP108 3.9 13.3 1.0 O3' A:UDP502 4.0 24.0 1.0 O2B A:UDP502 4.1 21.9 1.0 OD1 A:ASP106 4.2 16.7 1.0 ND1 A:HIS227 4.2 11.2 1.0 O2A A:UDP502 4.2 25.8 1.0 CG A:HIS227 4.3 12.7 1.0 O1B A:UDP502 4.4 31.1 1.0 O A:HOH717 4.4 26.9 1.0 O A:HOH623 4.4 25.8 1.0 O5' A:UDP502 4.4 27.5 1.0 C5' A:UDP502 4.6 28.8 1.0 CG2 A:ILE229 4.6 14.3 1.0 N A:ASP108 4.7 12.8 1.0 C3' A:UDP502 4.8 24.6 1.0 CA A:ASP108 4.8 12.3 1.0 O A:ASP108 4.8 14.4 1.0 CA A:ASP106 4.8 14.7 1.0 NZ A:LYS233 4.8 15.5 1.0 CA A:ILE229 4.9 14.8 1.0 C A:ASP108 5.0 11.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4


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 Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn501 b:29.3 occ:1.00 O2B F:UDP502 2.0 16.3 1.0 O2A F:UDP502 2.1 19.1 1.0 NE2 F:HIS227 2.1 12.9 1.0 OD1 F:ASP108 2.1 14.7 1.0 OD2 F:ASP106 2.1 15.8 1.0 OD2 F:ASP108 2.2 12.2 1.0 CG F:ASP108 2.5 15.0 1.0 CE1 F:HIS227 3.1 10.2 1.0 CG F:ASP106 3.1 18.3 1.0 CD2 F:HIS227 3.1 12.3 1.0 PB F:UDP502 3.3 25.0 1.0 PA F:UDP502 3.4 24.1 1.0 CB F:ASP106 3.4 15.6 1.0 O3A F:UDP502 3.7 25.5 1.0 CB F:ASP108 4.0 13.8 1.0 O3' F:UDP502 4.1 19.7 1.0 O1B F:UDP502 4.1 23.6 1.0 ND1 F:HIS227 4.2 10.4 1.0 OD1 F:ASP106 4.2 18.2 1.0 O1A F:UDP502 4.2 20.5 1.0 CG F:HIS227 4.3 13.0 1.0 O F:HOH667 4.3 26.0 1.0 O3B F:UDP502 4.3 29.0 1.0 O F:HOH608 4.4 27.9 1.0 O5' F:UDP502 4.4 29.4 1.0 C5' F:UDP502 4.5 25.6 1.0 CG2 F:ILE229 4.5 11.2 1.0 N F:ASP108 4.7 12.8 1.0 NZ F:LYS233 4.7 11.6 1.0 CA F:ILE229 4.7 11.8 1.0 C3' F:UDP502 4.8 23.0 1.0 CA F:ASP108 4.8 13.5 1.0 O F:ASP108 4.9 14.8 1.0 CA F:ASP106 4.9 12.8 1.0 O F:TYR228 5.0 9.3 1.0

Y.L.Jiang, H.Jin, H.B.Yang, R.L.Zhao, S.Wang, Y.Chen, C.Z.Zhou. Defining the Enzymatic Pathway For Polymorphic O-Glycosylation of the Pneumococcal Serine-Rich Repeat Protein Psrp. J. Biol. Chem. V. 292 6213 2017.
ISSN: ESSN 1083-351X
PubMed: 28246170
DOI: 10.1074/JBC.M116.770446