Manganese in PDB 6dgm: Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate

The structure of Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate, PDB code: 6dgm was solved by R.J.Edgar, N.Korotkova, K.V.Korotkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.53 / 1.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.650, 82.970, 130.360, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.5

The structure of Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate (pdb code 6dgm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate, PDB code: 6dgm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:17.5 occ:1.00 OG1 A:THR530 2.1 25.2 1.0 OD2 A:ASP711 2.1 17.6 1.0 NE2 A:HIS712 2.2 18.1 1.0 OE1 A:GLU488 2.2 16.9 1.0 O2P A:1GP902 2.3 28.9 1.0 OE2 A:GLU488 2.3 16.1 1.0 CD A:GLU488 2.6 16.6 1.0 CE1 A:HIS712 3.0 15.2 1.0 CG A:ASP711 3.1 15.0 1.0 CD2 A:HIS712 3.1 15.6 1.0 HE1 A:HIS712 3.2 18.3 1.0 CB A:THR530 3.3 21.1 1.0 HD2 A:HIS712 3.3 18.7 1.0 H A:THR530 3.4 22.8 1.0 OD1 A:ASP711 3.4 15.1 1.0 HG23 A:THR530 3.4 25.1 1.0 P A:1GP902 3.5 28.9 1.0 CG2 A:THR530 3.7 20.9 1.0 HG21 A:THR530 3.7 25.1 1.0 HA A:THR530 3.7 22.3 1.0 HA2 A:GLY528 3.8 20.7 1.0 HG A:SER489 3.8 19.7 1.0 CA A:THR530 3.9 18.5 1.0 N A:THR530 3.9 19.0 1.0 O1P A:1GP902 4.0 29.6 1.0 H A:SER489 4.0 16.7 1.0 HB A:THR530 4.0 25.4 1.0 O A:HOH1047 4.1 22.6 1.0 HA A:GLU488 4.1 17.2 1.0 O3P A:1GP902 4.1 27.9 1.0 CG A:GLU488 4.1 15.7 1.0 ND1 A:HIS712 4.1 15.4 1.0 H12 A:1GP902 4.1 34.3 1.0 CG A:HIS712 4.2 15.0 1.0 HD2 A:HIS650 4.3 22.3 1.0 HD21 A:LEU486 4.3 17.2 1.0 CB A:ASP711 4.4 13.5 1.0 HB2 A:ASP711 4.4 16.3 1.0 HG3 A:GLU488 4.5 18.9 1.0 OG A:SER489 4.5 16.4 1.0 HG2 A:GLU488 4.5 18.9 1.0 N A:SER489 4.6 13.9 1.0 CA A:GLY528 4.6 17.2 1.0 O A:HOH1046 4.6 15.2 1.0 HG22 A:THR530 4.6 25.1 1.0 C1 A:1GP902 4.7 28.6 1.0 HO3P A:1GP902 4.7 33.5 1.0 O4P A:1GP902 4.8 32.7 1.0 CA A:GLU488 4.8 14.3 1.0 HB3 A:ASP711 4.8 16.3 1.0 H A:GLY529 4.8 23.5 1.0 C A:GLY528 4.8 18.4 1.0 CB A:GLU488 4.8 14.4 1.0 HB2 A:GLU488 4.8 17.3 1.0 CD2 A:HIS650 4.9 18.6 1.0 N A:GLY529 4.9 19.6 1.0 HD1 A:HIS712 4.9 18.5 1.0 HE2 A:HIS650 5.0 22.7 1.0

Manganese binding site 2 out of 2 in the Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn901 b:20.4 occ:1.00 OG1 B:THR530 2.1 22.7 1.0 OD2 B:ASP711 2.1 16.5 1.0 NE2 B:HIS712 2.1 16.8 1.0 OE1 B:GLU488 2.2 19.1 1.0 OE2 B:GLU488 2.3 17.7 1.0 O2P B:1GP902 2.3 29.5 1.0 CD B:GLU488 2.6 16.9 1.0 CE1 B:HIS712 3.1 13.6 1.0 CG B:ASP711 3.1 13.5 1.0 CD2 B:HIS712 3.1 14.1 1.0 HE1 B:HIS712 3.2 16.3 1.0 CB B:THR530 3.3 19.0 1.0 HD2 B:HIS712 3.3 17.0 1.0 H B:THR530 3.4 19.3 1.0 OD1 B:ASP711 3.4 13.3 1.0 HG23 B:THR530 3.5 21.1 1.0 P B:1GP902 3.5 30.5 1.0 HA B:THR530 3.7 20.0 1.0 CG2 B:THR530 3.7 17.6 1.0 HG21 B:THR530 3.7 21.1 1.0 CA B:THR530 3.8 16.6 1.0 HG B:SER489 3.8 18.6 1.0 HA2 B:GLY528 3.9 17.7 1.0 O1P B:1GP902 3.9 33.0 1.0 N B:THR530 3.9 16.1 1.0 H B:SER489 3.9 15.3 1.0 HB B:THR530 4.0 22.8 1.0 O B:HOH1017 4.0 24.7 1.0 CG B:GLU488 4.1 15.3 1.0 O3P B:1GP902 4.1 32.2 1.0 HA B:GLU488 4.1 16.3 1.0 ND1 B:HIS712 4.1 13.1 1.0 HD2 B:HIS650 4.2 22.7 1.0 CG B:HIS712 4.2 13.6 1.0 H12 B:1GP902 4.3 37.2 1.0 HD21 B:LEU486 4.3 16.8 1.0 CB B:ASP711 4.4 12.9 1.0 HB2 B:ASP711 4.4 15.5 1.0 HG3 B:GLU488 4.4 18.4 1.0 HG2 B:GLU488 4.5 18.4 1.0 OG B:SER489 4.5 15.5 1.0 N B:SER489 4.5 12.8 1.0 O B:HOH1065 4.6 16.5 1.0 HG22 B:THR530 4.7 21.1 1.0 CA B:GLY528 4.7 14.7 1.0 C1 B:1GP902 4.7 30.9 1.0 HO3P B:1GP902 4.7 38.6 1.0 HB3 B:ASP711 4.8 15.5 1.0 CD2 B:HIS650 4.8 18.9 1.0 O4P B:1GP902 4.8 33.2 1.0 H B:GLY529 4.8 19.6 1.0 CA B:GLU488 4.8 13.6 1.0 CB B:GLU488 4.8 14.7 1.0 HB2 B:GLU488 4.9 17.6 1.0 C B:GLY528 4.9 15.6 1.0 HO3 B:1GP902 4.9 22.5 1.0 HE2 B:HIS650 4.9 23.0 1.0 N B:GLY529 4.9 16.3 1.0 HD1 B:HIS712 4.9 15.8 1.0

R.J.Edgar, V.P.Van Hensbergen, A.Ruda, A.G.Turner, P.Deng, Y.Le Breton, N.M.El-Sayed, A.T.Belew, K.S.Mciver, A.G.Mcewan, A.J.Morris, G.Lambeau, M.J.Walker, J.S.Rush, K.V.Korotkov, G.Widmalm, N.M.Van Sorge, N.Korotkova. Discovery of Glycerol Phosphate Modification on Streptococcal Rhamnose Polysaccharides. Nat.Chem.Biol. V. 15 463 2019.
ISSN: ESSN 1552-4469
PubMed: 30936502
DOI: 10.1038/S41589-019-0251-4