Magnesium in PDB 5a6b: GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac

The structure of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac, PDB code: 5a6b was solved by M.Cid, C.S.Robb, M.A.Higgins, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.699, 136.937, 201.446, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.3

The binding sites of Magnesium atom in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac (pdb code 5a6b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac, PDB code: 5a6b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1628 b:27.7 occ:1.00 O A:HOH2046 3.1 31.3 1.0 OG A:SER38 3.2 25.6 1.0 NE2 A:GLN57 3.3 24.0 1.0 NH1 A:ARG53 3.5 40.4 1.0 CD A:ARG53 3.6 36.7 1.0 CE A:LYS54 3.7 40.7 1.0 CB A:SER38 3.9 22.8 1.0 OE1 A:GLN57 4.0 27.0 1.0 CD A:GLN57 4.1 25.6 1.0 CD A:LYS54 4.3 35.2 1.0 CZ A:ARG53 4.3 40.3 1.0 CA A:SER38 4.3 24.8 1.0 NE A:ARG53 4.3 38.8 1.0 CB A:ALA81 4.4 26.7 1.0 NZ A:LYS54 4.4 43.3 1.0 CG A:ARG53 4.5 30.3 1.0 CB A:ARG53 4.5 30.5 1.0 CG A:LYS54 4.5 32.5 1.0 N A:ALA81 4.9 26.0 1.0 N A:SER38 5.0 27.4 1.0

Magnesium binding site 2 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1628 b:22.5 occ:1.00 OG B:SER574 3.0 24.4 1.0 O B:HOH2461 3.2 27.5 1.0 NH1 B:ARG571 3.2 18.0 1.0 CD B:ARG575 3.6 21.4 1.0 CB B:SER574 3.7 23.6 1.0 N B:ARG575 3.8 22.3 1.0 C B:SER574 3.8 22.8 1.0 CG B:ARG575 3.9 21.4 1.0 CD B:ARG571 3.9 17.0 1.0 O B:SER574 4.1 21.3 1.0 CA B:ARG575 4.1 22.0 1.0 CA B:SER574 4.4 20.7 1.0 CZ B:ARG571 4.4 16.1 1.0 CG2 B:VAL578 4.4 29.1 1.0 O A:HOH2357 4.6 34.3 1.0 CB B:ARG575 4.6 19.9 1.0 NE B:ARG571 4.6 17.6 1.0 O B:HOH2459 4.8 22.7 1.0 O B:ARG571 4.8 18.2 1.0 CD1 A:LEU547 4.9 20.4 1.0 NE B:ARG575 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1628 b:21.2 occ:1.00 O C:HOH2051 3.0 23.0 1.0 OG C:SER38 3.1 20.0 1.0 NH1 C:ARG53 3.3 30.6 1.0 NE2 C:GLN57 3.3 21.0 1.0 CD C:ARG53 3.8 25.9 1.0 CE C:LYS54 3.9 28.0 1.0 CB C:SER38 4.0 19.9 1.0 OE1 C:GLN57 4.1 21.4 1.0 CD C:GLN57 4.1 18.3 1.0 CZ C:ARG53 4.2 30.4 1.0 NZ C:LYS54 4.3 29.6 1.0 CA C:SER38 4.3 21.6 1.0 CD C:LYS54 4.3 26.9 1.0 NE C:ARG53 4.4 28.8 1.0 CB C:ARG53 4.5 23.7 1.0 CB C:ALA81 4.5 22.8 1.0 O C:HOH2045 4.5 38.9 1.0 CG C:ARG53 4.5 26.1 1.0 CG C:LYS54 4.6 25.6 1.0 N C:SER38 5.0 21.3 1.0 N C:ALA81 5.0 22.6 1.0

M.Robb, C.S.Robb, M.A.Higgins, J.K.Hobbs, J.C.Paton, A.B.Boraston. A Second Beta-Hexosaminidase Encoded in the Streptococcus Pneumoniae Genome Provides An Expanded Biochemical Ability to Degrade Host Glycans. J. Biol. Chem. V. 290 30888 2015.
ISSN: ESSN 1083-351X
PubMed: 26491009
DOI: 10.1074/JBC.M115.688630