Magnesium in PDB 4azc: Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh

The structure of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4azc was solved by B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.81 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.200, 115.600, 132.000, 90.00, 99.40, 90.00
R / Rfree (%)	19 / 24

The binding sites of Magnesium atom in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh (pdb code 4azc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4azc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2043 b:15.3 occ:1.00 O A:HOH3036 3.0 16.7 1.0 N A:TYR959 3.3 16.9 1.0 NZ A:LYS642 3.3 10.9 1.0 O A:HOH3592 3.3 40.7 1.0 O A:HOH3492 3.4 37.0 1.0 ND2 A:ASN710 3.5 15.4 1.0 CE A:LYS642 3.5 12.6 1.0 CA A:GLU958 3.8 17.4 1.0 C A:GLU958 4.0 17.3 1.0 O A:ALA957 4.1 16.6 1.0 CB A:TYR959 4.2 16.3 1.0 CG A:GLU958 4.2 19.0 1.0 O A:HOH3270 4.2 30.9 1.0 O A:HOH3021 4.2 19.0 1.0 CA A:TYR959 4.2 17.0 1.0 O A:TYR959 4.5 17.3 1.0 CB A:GLU958 4.5 18.1 1.0 O A:HOH3020 4.5 11.3 1.0 CG A:ASN710 4.7 17.6 1.0 O A:HOH3022 4.7 12.1 1.0 N A:GLU958 4.8 17.1 1.0 C A:TYR959 4.8 17.2 1.0 C A:ALA957 4.9 16.9 1.0

Magnesium binding site 2 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2044 b:16.1 occ:1.00 O A:HOH3593 3.1 22.4 1.0 N A:VAL765 3.2 19.0 1.0 O A:HOH3594 3.4 28.7 1.0 CG2 A:VAL765 3.7 17.1 1.0 CB A:LYS764 3.7 21.1 1.0 CA A:LYS764 3.8 20.8 1.0 CB A:VAL765 3.9 17.8 1.0 C A:LYS764 4.0 20.0 1.0 CA A:VAL765 4.1 17.4 1.0 O A:HOH3399 4.1 32.1 1.0 O A:VAL765 4.8 15.6 1.0 O A:HOH3180 4.8 27.2 1.0 O A:HOH3398 4.9 25.0 1.0 CG A:LYS764 4.9 22.6 1.0

Magnesium binding site 3 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2045 b:22.4 occ:1.00 O A:MET947 2.6 8.4 1.0 O A:ASN898 2.9 9.9 1.0 CE1 A:TYR902 3.3 10.4 1.0 OG A:SER949 3.3 9.5 1.0 N A:SER949 3.4 10.4 1.0 CD1 A:TYR902 3.4 10.5 1.0 CA A:LEU948 3.5 10.2 1.0 C A:MET947 3.6 9.7 1.0 C A:THR897 3.6 9.0 1.0 O A:THR897 3.6 9.2 1.0 C A:ASN898 3.7 9.3 1.0 C A:LEU948 3.8 10.3 1.0 CB A:TRP901 3.8 11.1 1.0 CB A:SER949 3.9 9.8 1.0 N A:ASN898 3.9 8.9 1.0 CG2 A:THR897 3.9 7.8 1.0 N A:LEU948 4.0 9.6 1.0 CE3 A:TRP901 4.0 9.0 1.0 CA A:THR897 4.1 9.8 1.0 CA A:SER949 4.2 9.8 1.0 CA A:ASN898 4.4 9.5 1.0 C A:TRP901 4.4 11.2 1.0 N A:TYR902 4.4 11.2 1.0 CA A:TRP901 4.5 10.9 1.0 CZ A:TYR902 4.6 11.3 1.0 N A:GLY899 4.6 9.6 1.0 N A:TRP901 4.7 10.4 1.0 CB A:THR897 4.7 9.9 1.0 CB A:LEU948 4.7 10.8 1.0 CG A:TRP901 4.7 10.5 1.0 CD2 A:TRP901 4.7 10.5 1.0 CG A:TYR902 4.7 10.9 1.0 O A:LEU948 4.8 10.6 1.0 O A:TRP901 4.9 11.0 1.0 CA A:GLY899 4.9 9.4 1.0 CA A:TYR902 5.0 11.5 1.0 CG A:LEU948 5.0 12.2 1.0 CA A:MET947 5.0 9.8 1.0

Magnesium binding site 4 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2046 b:25.7 occ:1.00 OH A:TYR854 2.8 12.1 1.0 CG A:GLN862 3.0 17.3 0.5 NZ A:LYS890 3.4 23.0 1.0 NZ A:LYS865 3.4 26.5 1.0 CZ A:TYR854 3.6 9.0 1.0 CE1 A:TYR854 3.7 11.3 1.0 CE A:LYS865 3.7 24.0 1.0 CB A:GLN862 3.8 16.4 0.5 CG A:GLN862 3.9 17.6 0.5 CE A:LYS890 4.0 21.7 1.0 CD A:LYS890 4.0 19.4 1.0 OE1 A:GLN862 4.0 20.4 0.5 CD A:GLN862 4.2 18.7 0.3 CB A:GLN862 4.3 16.4 0.5 NE2 A:GLN862 4.3 19.0 0.3 CB A:ASP859 4.4 18.6 1.0 CD A:GLN862 4.4 20.3 0.7 CA A:GLN862 4.6 16.3 0.5 CA A:GLN862 4.6 16.4 0.5 OD2 A:ASP859 4.7 20.9 1.0 O A:HOH3302 4.8 28.4 1.0 O A:ASP859 4.8 19.9 1.0 CE2 A:TYR854 4.9 11.2 1.0 CD1 A:TYR854 4.9 10.1 1.0 CG A:ASP859 5.0 19.8 1.0

Magnesium binding site 5 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2045 b:16.6 occ:1.00 NZ B:LYS642 3.1 18.9 1.0 O B:HOH3391 3.2 36.3 1.0 N B:TYR959 3.2 22.9 1.0 O B:HOH3027 3.3 22.6 1.0 O B:HOH3399 3.4 43.7 1.0 CE B:LYS642 3.5 19.0 1.0 ND2 B:ASN710 3.6 24.9 1.0 CA B:GLU958 3.7 23.6 1.0 O B:ALA957 3.9 24.6 1.0 C B:GLU958 3.9 23.1 1.0 CB B:TYR959 4.1 21.9 1.0 CG B:GLU958 4.2 24.4 1.0 CA B:TYR959 4.2 22.3 1.0 O B:HOH3018 4.3 17.7 1.0 O B:TYR959 4.5 21.8 1.0 CB B:GLU958 4.5 23.8 1.0 O B:HOH3017 4.5 19.9 1.0 N B:GLU958 4.6 23.7 1.0 C B:ALA957 4.7 24.1 1.0 C B:TYR959 4.8 22.2 1.0 CG B:ASN710 4.8 26.2 1.0 O B:HOH3019 4.8 20.9 1.0

Magnesium binding site 6 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2042 b:13.4 occ:1.00 O C:HOH3036 3.1 17.8 1.0 NZ C:LYS642 3.2 12.2 1.0 N C:TYR959 3.3 18.4 1.0 O C:HOH3459 3.5 42.4 1.0 ND2 C:ASN710 3.6 18.4 1.0 CE C:LYS642 3.6 12.0 1.0 CA C:GLU958 3.8 18.3 1.0 O C:ALA957 4.0 17.6 1.0 C C:GLU958 4.0 18.1 1.0 CB C:TYR959 4.1 18.2 1.0 CG C:GLU958 4.2 20.4 1.0 CA C:TYR959 4.2 18.3 1.0 O C:HOH3257 4.2 31.7 1.0 O C:HOH3020 4.3 9.9 1.0 O C:HOH3021 4.5 12.9 1.0 O C:TYR959 4.5 18.3 1.0 CB C:GLU958 4.6 18.6 1.0 N C:GLU958 4.7 18.0 1.0 CG C:ASN710 4.8 19.4 1.0 C C:ALA957 4.8 17.9 1.0 O C:HOH3022 4.8 14.8 1.0 C C:TYR959 4.9 18.4 1.0

Magnesium binding site 7 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2043 b:16.4 occ:1.00 O C:HOH3278 3.2 31.8 1.0 N C:TYR825 3.3 13.5 1.0 N C:GLY826 3.4 13.1 1.0 C C:GLN823 3.4 15.2 1.0 CA C:GLN823 3.5 15.3 1.0 O C:HOH3221 3.6 58.7 1.0 CB C:TYR825 3.6 12.6 1.0 N C:LEU824 3.7 14.6 1.0 CA C:TYR825 3.7 13.1 1.0 O C:HOH3226 3.8 16.5 1.0 O C:GLN823 3.9 15.0 1.0 C C:TYR825 4.0 13.4 1.0 C C:LEU824 4.2 14.0 1.0 CB C:GLN823 4.2 15.2 1.0 CA C:GLY826 4.4 13.7 1.0 CA C:LEU824 4.4 14.1 1.0 O C:LEU819 4.5 14.7 1.0 N C:GLN823 4.6 16.1 1.0 O C:LYS820 4.7 16.9 1.0 CA C:LYS820 4.7 16.2 1.0 CG C:GLN823 4.8 14.7 1.0 CG C:TYR825 4.8 12.7 1.0 CG2 C:VAL861 5.0 19.0 1.0

Magnesium binding site 8 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2044 b:26.4 occ:1.00 OH C:TYR854 2.8 14.1 1.0 NZ C:LYS865 3.1 27.8 1.0 NZ C:LYS890 3.3 20.6 1.0 CG C:GLN862 3.4 17.1 1.0 CZ C:TYR854 3.6 13.2 1.0 CE1 C:TYR854 3.6 14.3 1.0 CE C:LYS865 3.6 24.2 1.0 O C:HOH3422 3.9 44.1 1.0 CE C:LYS890 4.1 19.6 1.0 O C:HOH3276 4.1 40.7 1.0 CB C:GLN862 4.3 15.8 1.0 CD C:LYS890 4.3 18.7 1.0 CB C:ASP859 4.3 20.1 1.0 CD C:GLN862 4.5 16.6 0.5 CA C:GLN862 4.5 16.1 1.0 O C:ASP859 4.7 20.7 1.0 NE2 C:GLN862 4.8 16.8 0.2 CE2 C:TYR854 4.8 13.6 1.0 CD1 C:TYR854 4.9 12.7 1.0 OD2 C:ASP859 5.0 22.3 0.8 O C:HOH3345 5.0 40.9 1.0

B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston. Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh. Org.Biomol.Chem. V. 11 7907 2013.
ISSN: ISSN 1477-0520
PubMed: 24132305
DOI: 10.1039/C3OB41579A