Manganese in PDB 5gvw: Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4

The structure of Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4, PDB code: 5gvw 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)	50.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.119, 84.211, 130.113, 90.00, 89.97, 90.00
R / Rfree (%)	19.8 / 25.5

The binding sites of Manganese atom in the Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 (pdb code 5gvw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4, PDB code: 5gvw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Apo-Form 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 Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:79.2 occ:1.00 OD2 C:ASP106 2.5 42.9 1.0 O C:HOH718 2.5 33.5 1.0 OD1 C:ASP108 2.6 38.9 1.0 OD2 C:ASP108 2.7 43.6 1.0 NE2 C:HIS227 3.0 33.5 1.0 CG C:ASP108 3.0 40.8 1.0 CG C:ASP106 3.6 37.6 1.0 CE1 C:HIS227 3.7 33.1 1.0 O C:HOH667 3.9 37.0 1.0 CD2 C:HIS227 4.0 33.0 1.0 CB C:ASP106 4.3 37.5 1.0 CB C:ASP108 4.4 37.8 1.0 OD1 C:ASP106 4.5 33.9 1.0 CG2 C:ILE229 4.6 40.3 1.0 O C:HOH648 4.7 34.7 1.0 CA C:ILE229 4.8 37.4 1.0 NZ C:LYS233 4.8 40.9 1.0 ND1 C:HIS227 4.9 33.6 1.0 CB C:ILE229 4.9 40.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Apo-Form 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 Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:70.4 occ:1.00 O A:HOH691 2.4 38.0 1.0 OD1 A:ASP108 2.4 35.2 1.0 O A:HOH723 2.4 39.6 1.0 OD2 A:ASP106 2.5 39.0 1.0 NE2 A:HIS227 2.6 37.1 1.0 OD2 A:ASP108 2.6 37.5 1.0 CG A:ASP108 2.9 34.8 1.0 CG A:ASP106 3.4 34.7 1.0 CE1 A:HIS227 3.4 34.4 1.0 CD2 A:HIS227 3.7 35.3 1.0 CB A:ASP106 3.7 34.5 1.0 CB A:ASP108 4.4 32.0 1.0 OD1 A:ASP106 4.4 34.9 1.0 O A:HOH711 4.5 39.5 1.0 ND1 A:HIS227 4.6 34.5 1.0 CG2 A:ILE229 4.6 35.8 1.0 CG A:HIS227 4.8 33.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Apo-Form 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 3 of Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:66.0 occ:1.00 OD1 B:ASP108 2.5 37.9 1.0 OD2 B:ASP106 2.5 36.1 1.0 NE2 B:HIS227 2.6 36.8 1.0 OD2 B:ASP108 2.6 39.8 1.0 O B:HOH716 2.7 36.5 1.0 CG B:ASP108 2.9 37.3 1.0 CG B:ASP106 3.3 34.9 1.0 CE1 B:HIS227 3.4 35.1 1.0 CD2 B:HIS227 3.6 35.3 1.0 CB B:ASP106 3.7 34.6 1.0 O B:HOH660 4.3 38.8 1.0 CB B:ASP108 4.3 34.2 1.0 OD1 B:ASP106 4.4 39.4 1.0 O B:HOH663 4.4 32.4 1.0 CG2 B:ILE229 4.6 34.0 1.0 ND1 B:HIS227 4.6 35.4 1.0 CG B:HIS227 4.7 33.3 1.0 N B:ASP108 5.0 31.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Apo-Form 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 4 of Crystal Structure of the Apo-Form Glycosyltransferase Glye in Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:66.9 occ:1.00 OD1 D:ASP108 2.3 44.1 1.0 OD2 D:ASP106 2.3 42.6 1.0 NE2 D:HIS227 2.6 40.5 1.0 OD2 D:ASP108 2.6 39.4 1.0 O D:HOH691 2.6 22.7 1.0 CG D:ASP108 2.8 39.9 1.0 O D:HOH683 3.1 41.6 1.0 CG D:ASP106 3.2 40.2 1.0 CE1 D:HIS227 3.4 39.4 1.0 CD2 D:HIS227 3.6 38.7 1.0 CB D:ASP106 3.6 40.1 1.0 CB D:ASP108 4.3 36.7 1.0 OD1 D:ASP106 4.3 43.1 1.0 O D:HOH634 4.5 37.8 1.0 ND1 D:HIS227 4.6 37.6 1.0 CG D:HIS227 4.7 38.8 1.0 CG2 D:ILE229 4.8 40.5 1.0 NZ D:LYS233 4.9 45.2 1.0 N D:ASP108 5.0 32.4 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