Magnesium in PDB 8iat: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate, PDB code: 8iat was solved by R.Nakashima, A.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.051, 118.353, 99.82, 90, 108.93, 90
R / Rfree (%)	19.9 / 24.6

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate (pdb code 8iat). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate, PDB code: 8iat:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:32.2 occ:1.00 O A:HOH787 2.0 33.6 1.0 O A:HOH822 2.0 30.4 1.0 O4 A:OXL601 2.1 36.9 1.0 OD1 A:ASP274 2.1 35.0 1.0 O3 A:OXL601 2.2 32.2 1.0 OE1 A:GLU250 2.2 31.0 1.0 C2 A:OXL601 2.9 43.2 1.0 C1 A:OXL601 2.9 38.5 1.0 CD A:GLU250 3.1 30.4 1.0 CG A:ASP274 3.2 36.3 1.0 OE2 A:GLU250 3.5 34.0 1.0 CB A:ASP274 3.7 32.7 1.0 NZ A:LYS248 4.0 31.4 1.0 O A:HOH881 4.1 43.5 1.0 O2 A:OXL601 4.1 44.6 1.0 O1 A:OXL601 4.1 33.0 1.0 O A:HOH953 4.2 37.4 1.0 OD2 A:ASP274 4.3 38.5 1.0 O A:HOH996 4.3 53.8 1.0 CE2 A:PHE221 4.3 50.5 1.0 N A:ASP274 4.4 33.3 1.0 O A:HOH841 4.4 33.5 1.0 CE A:LYS248 4.5 30.6 1.0 CG A:GLU250 4.5 36.2 1.0 CB A:ALA271 4.6 32.1 1.0 CA A:ASP274 4.6 30.6 1.0 CZ A:PHE221 4.7 47.1 1.0 CB A:GLU250 4.9 36.1 1.0 O A:HOH844 5.0 44.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:30.8 occ:1.00 OE1 B:GLU250 2.0 29.8 1.0 OD1 B:ASP274 2.0 31.3 1.0 O B:HOH807 2.0 36.3 1.0 O2 B:OXL601 2.1 38.7 1.0 O1 B:OXL601 2.1 28.6 1.0 O B:HOH755 2.1 30.9 1.0 C1 B:OXL601 2.9 35.9 1.0 C2 B:OXL601 2.9 39.4 1.0 CD B:GLU250 3.0 28.6 1.0 CG B:ASP274 3.1 32.7 1.0 OE2 B:GLU250 3.4 30.7 1.0 CB B:ASP274 3.5 31.8 1.0 O3 B:OXL601 4.1 33.0 1.0 O4 B:OXL601 4.1 40.0 1.0 OD2 B:ASP274 4.2 36.0 1.0 N B:ASP274 4.3 30.7 1.0 O B:HOH966 4.3 58.9 1.0 NZ B:LYS248 4.3 28.8 1.0 O B:HOH949 4.3 37.2 1.0 CG B:GLU250 4.4 32.6 1.0 O B:HOH951 4.4 50.4 1.0 CE2 B:PHE221 4.5 34.5 1.0 CA B:ASP274 4.5 30.3 1.0 CB B:ALA271 4.6 28.7 1.0 CE B:LYS248 4.7 28.8 1.0 CB B:GLU250 4.9 33.3 1.0 CD2 B:PHE221 5.0 34.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:37.6 occ:1.00 O3 C:OXL601 1.9 44.9 1.0 OD1 C:ASP274 1.9 38.3 1.0 O C:HOH734 2.1 36.5 1.0 O C:HOH745 2.2 34.5 1.0 OE1 C:GLU250 2.2 46.2 1.0 O4 C:OXL601 2.2 34.9 1.0 C1 C:OXL601 2.7 44.2 1.0 C2 C:OXL601 2.9 36.2 1.0 CG C:ASP274 3.1 35.3 1.0 CD C:GLU250 3.2 51.6 1.0 OE2 C:GLU250 3.6 45.5 1.0 CB C:ASP274 3.7 35.0 1.0 O C:HOH817 3.8 49.3 1.0 O1 C:OXL601 3.9 46.8 1.0 O2 C:OXL601 4.1 41.1 1.0 OD2 C:ASP274 4.1 41.7 1.0 NZ C:LYS248 4.3 43.9 1.0 CE2 C:PHE221 4.3 55.6 1.0 N C:ASP274 4.3 35.2 1.0 O C:HOH752 4.4 44.0 1.0 CE C:LYS248 4.4 41.1 1.0 O C:HOH813 4.5 50.2 1.0 CB C:ALA271 4.5 39.6 1.0 CG C:GLU250 4.5 42.4 1.0 CA C:ASP274 4.7 35.6 1.0 CZ C:PHE221 4.9 50.5 1.0 CB C:GLU250 5.0 49.1 1.0 CD2 C:PHE221 5.0 57.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:41.3 occ:1.00 O D:HOH764 2.0 43.0 1.0 OD1 D:ASP274 2.0 38.0 1.0 O D:HOH834 2.1 38.3 1.0 O1 D:OXL601 2.1 43.7 1.0 OE1 D:GLU250 2.2 44.0 1.0 O2 D:OXL601 2.2 48.0 1.0 C1 D:OXL601 3.0 45.2 1.0 C2 D:OXL601 3.0 52.1 1.0 CG D:ASP274 3.1 40.9 1.0 CD D:GLU250 3.2 43.2 1.0 CB D:ASP274 3.6 38.4 1.0 OE2 D:GLU250 3.6 41.0 1.0 O D:HOH837 4.0 48.0 1.0 O3 D:OXL601 4.2 38.0 1.0 OD2 D:ASP274 4.2 42.6 1.0 NZ D:LYS248 4.2 41.2 1.0 O4 D:OXL601 4.3 48.0 1.0 N D:ASP274 4.3 41.3 1.0 CE2 D:PHE221 4.4 57.2 1.0 CE D:LYS248 4.5 42.6 1.0 CG D:GLU250 4.5 44.8 1.0 CB D:ALA271 4.6 42.4 1.0 CA D:ASP274 4.6 37.5 1.0 O D:HOH720 4.6 48.8 1.0 CB D:GLU250 4.8 45.0 1.0 CZ D:PHE221 4.9 55.0 1.0

A.Taguchi, R.Nakashima, K.Nishino. Functional and Structural Characterization of Streptococcus Pneumoniae Pyruvate Kinase Involved in Fosfomycin Resistance. J.Biol.Chem. 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.104892