Manganese in PDB 5u9z: Phosphoglycerol Transferase Gach From Streptococcus Pyogenes

The structure of Phosphoglycerol Transferase Gach From Streptococcus Pyogenes, PDB code: 5u9z 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)	49.51 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.870, 78.170, 172.660, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24

The binding sites of Manganese atom in the Phosphoglycerol Transferase Gach From Streptococcus Pyogenes (pdb code 5u9z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Phosphoglycerol Transferase Gach From Streptococcus Pyogenes, PDB code: 5u9z:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Phosphoglycerol Transferase Gach From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphoglycerol Transferase Gach From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:37.3 occ:1.00 OG1 A:THR530 2.1 37.9 1.0 OD2 A:ASP711 2.1 36.8 1.0 OE2 A:GLU488 2.1 41.4 1.0 NE2 A:HIS712 2.3 36.0 1.0 OE1 A:GLU488 2.3 39.0 1.0 O A:HOH1008 2.3 39.2 1.0 CD A:GLU488 2.5 39.1 1.0 HG23 A:THR530 3.1 47.3 1.0 CG A:ASP711 3.1 38.2 1.0 CD2 A:HIS712 3.2 36.7 1.0 CB A:THR530 3.2 37.7 1.0 CE1 A:HIS712 3.2 36.7 1.0 HD2 A:HIS712 3.3 44.1 1.0 HE1 A:HIS712 3.4 44.1 1.0 HA A:THR530 3.4 45.8 1.0 OD1 A:ASP711 3.5 37.2 1.0 CG2 A:THR530 3.5 39.3 1.0 H A:THR530 3.5 47.6 1.0 HG21 A:THR530 3.6 47.3 1.0 CA A:THR530 3.7 38.1 1.0 HG A:SER489 3.9 46.1 1.0 HB A:THR530 3.9 45.3 1.0 N A:THR530 4.0 39.6 1.0 CG A:GLU488 4.0 39.4 1.0 HA2 A:GLY528 4.0 48.7 1.0 H A:SER489 4.1 45.7 1.0 HA A:GLU488 4.1 47.2 1.0 ND1 A:HIS712 4.2 36.4 1.0 CG A:HIS712 4.2 36.5 1.0 O A:HOH1072 4.3 42.0 1.0 HD21 A:LEU486 4.3 48.0 1.0 HD2 A:HIS650 4.4 45.9 1.0 HG22 A:THR530 4.4 47.3 1.0 HG2 A:GLU488 4.4 47.4 1.0 HG3 A:GLU488 4.4 47.4 1.0 CB A:ASP711 4.4 38.4 1.0 HB2 A:ASP711 4.5 46.1 1.0 OG A:SER489 4.5 38.4 1.0 O A:HOH1055 4.6 40.2 1.0 O A:HOH1026 4.6 40.1 1.0 N A:SER489 4.6 38.0 1.0 HB2 A:GLU488 4.6 48.2 1.0 CB A:GLU488 4.7 40.0 1.0 CA A:GLU488 4.8 39.2 1.0 HB3 A:ASP711 4.8 46.1 1.0 CD2 A:HIS650 4.8 38.1 1.0 CA A:GLY528 4.9 40.5 1.0 HD1 A:HIS712 5.0 43.8 1.0 C A:GLY528 5.0 39.2 1.0

Manganese binding site 2 out of 2 in the Phosphoglycerol Transferase Gach From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphoglycerol Transferase Gach From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn901 b:35.4 occ:1.00 O B:HOH1041 2.0 36.3 1.0 OD2 B:ASP711 2.1 35.0 1.0 OG1 B:THR530 2.2 33.9 1.0 NE2 B:HIS712 2.2 32.1 1.0 OE2 B:GLU488 2.2 35.5 1.0 OE1 B:GLU488 2.4 34.6 1.0 CD B:GLU488 2.6 34.5 1.0 CD2 B:HIS712 3.1 31.7 1.0 CG B:ASP711 3.1 31.1 1.0 CE1 B:HIS712 3.1 33.4 1.0 HD2 B:HIS712 3.3 38.2 1.0 HG23 B:THR530 3.3 37.0 1.0 CB B:THR530 3.3 30.3 1.0 HE1 B:HIS712 3.3 40.1 1.0 HA B:THR530 3.4 37.4 1.0 OD1 B:ASP711 3.5 33.9 1.0 H B:THR530 3.5 39.2 1.0 CG2 B:THR530 3.7 30.8 1.0 CA B:THR530 3.8 31.0 1.0 HG B:SER489 3.8 44.1 1.0 HG21 B:THR530 3.9 37.0 1.0 N B:THR530 3.9 32.6 1.0 HA2 B:GLY528 4.1 40.7 1.0 HB B:THR530 4.1 36.5 1.0 CG B:GLU488 4.1 34.8 1.0 H B:SER489 4.1 42.8 1.0 HA B:GLU488 4.1 42.5 1.0 ND1 B:HIS712 4.1 33.4 1.0 CG B:HIS712 4.2 31.9 1.0 HD21 B:LEU486 4.4 40.1 1.0 HD2 B:HIS650 4.4 43.2 1.0 CB B:ASP711 4.4 29.9 1.0 O B:HOH1102 4.4 43.0 1.0 O B:HOH1138 4.4 36.8 1.0 HB2 B:ASP711 4.4 36.0 1.0 HG3 B:GLU488 4.5 41.8 1.0 OG B:SER489 4.5 36.6 1.0 HG2 B:GLU488 4.6 41.8 1.0 HG22 B:THR530 4.6 37.0 1.0 O B:HOH1026 4.6 34.2 1.0 N B:SER489 4.7 35.6 1.0 HB3 B:ASP711 4.8 36.0 1.0 HB2 B:GLU488 4.8 43.5 1.0 CA B:GLY528 4.8 33.8 1.0 CB B:GLU488 4.9 36.1 1.0 CA B:GLU488 4.9 35.3 1.0 CD2 B:HIS650 4.9 35.9 1.0 HD1 B:HIS712 4.9 40.2 1.0 C B:GLY528 4.9 33.9 1.0 H B:GLY529 5.0 39.9 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