Calcium 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:

Manganese

(Mn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Streptococcus Pyogenes Phosphoglycerol Transferase Gach in Complex with Sn-Glycerol-1-Phosphate, PDB code: 6dgm:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca903 b:44.1 occ:1.00 O A:ASP472 2.4 39.3 1.0 OD1 A:ASP764 2.4 29.3 1.0 O A:HOH1200 2.5 43.6 1.0 O A:HOH1163 2.7 48.8 1.0 O A:HOH1350 2.7 48.3 1.0 CG A:ASP764 3.1 29.1 1.0 OD2 A:ASP764 3.1 32.1 1.0 HB3 A:ASP472 3.6 46.3 1.0 C A:ASP472 3.6 37.5 1.0 HA A:ARG473 3.7 39.1 1.0 HD3 A:ARG473 4.0 33.0 1.0 O A:HOH1094 4.0 40.5 1.0 CB A:ASP472 4.4 38.6 1.0 CB A:ASP764 4.5 26.0 1.0 HG3 A:LYS474 4.5 67.3 1.0 N A:ARG473 4.5 35.9 1.0 CA A:ASP472 4.5 36.3 1.0 O A:HOH1342 4.5 41.7 1.0 CA A:ARG473 4.5 32.6 1.0 H A:LYS474 4.6 41.8 1.0 HB2 A:ASP764 4.6 31.2 1.0 HA A:ASP472 4.7 43.6 1.0 HB2 A:ASP472 4.7 46.3 1.0 HA A:ASP764 4.8 29.4 1.0 O A:HOH1299 4.9 41.1 1.0 CD A:ARG473 4.9 27.5 1.0 HE3 A:LYS474 4.9 82.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca903 b:20.2 occ:1.00 O B:ASP472 2.3 18.7 1.0 OD1 B:ASP764 2.3 20.4 1.0 O B:HOH1273 2.4 34.6 1.0 O B:HOH1111 2.4 25.7 1.0 CG B:ASP764 3.1 19.7 1.0 OD2 B:ASP764 3.3 21.1 1.0 HB3 B:ASP472 3.4 24.6 1.0 C B:ASP472 3.5 18.1 1.0 HA B:ARG473 3.7 21.3 1.0 HD3 B:ARG473 4.0 21.4 1.0 O B:HOH1248 4.0 38.4 1.0 CB B:ASP472 4.2 20.5 1.0 O B:HOH1379 4.3 27.3 1.0 CA B:ASP472 4.4 18.6 1.0 N B:ARG473 4.4 19.0 1.0 CA B:ARG473 4.5 17.8 1.0 CB B:ASP764 4.5 17.6 1.0 HA B:ASP472 4.5 22.4 1.0 HB2 B:ASP472 4.6 24.6 1.0 HB2 B:ASP764 4.6 21.1 1.0 H B:LYS474 4.6 22.4 1.0 HA B:ASP764 4.7 19.4 1.0 O B:HOH1270 4.8 26.1 1.0 CD B:ARG473 4.9 17.8 1.0 HE B:ARG473 5.0 20.6 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