Magnesium in PDB 8iau: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate, PDB code: 8iau 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)	49.38 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.442, 114.66, 140.705, 88.95, 88.12, 76.52
R / Rfree (%)	20 / 24.6

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate also contains other interesting chemical elements:

Potassium

(K)

7 atoms

The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate (pdb code 8iau). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate, PDB code: 8iau:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


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 and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:38.3 occ:1.00 O A:HOH708 1.9 35.0 1.0 OE1 A:GLU250 2.0 37.8 1.0 OD1 A:ASP274 2.1 33.6 1.0 O2 A:OXL603 2.1 45.4 1.0 O A:HOH713 2.1 33.5 1.0 O1 A:OXL603 2.2 38.3 1.0 C2 A:OXL603 2.9 60.1 1.0 C1 A:OXL603 2.9 49.5 1.0 CD A:GLU250 3.0 35.4 1.0 CG A:ASP274 3.2 32.0 1.0 OE2 A:GLU250 3.4 36.2 1.0 CB A:ASP274 3.6 32.6 1.0 O4 A:OXL603 4.1 55.3 1.0 O3 A:OXL603 4.1 45.3 1.0 O A:HOH828 4.2 50.5 1.0 NZ A:LYS248 4.2 34.1 1.0 N A:ASP274 4.2 31.3 1.0 OD2 A:ASP274 4.3 38.4 1.0 CG A:GLU250 4.3 37.7 1.0 CE2 A:PHE221 4.4 40.9 1.0 CE A:LYS248 4.5 32.7 1.0 CB A:ALA271 4.5 29.5 1.0 CA A:ASP274 4.6 30.8 1.0 CB A:GLU250 4.8 40.1 1.0 CD2 A:PHE221 5.0 39.0 1.0 CZ A:PHE221 5.0 44.1 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


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 and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:39.4 occ:1.00 OD1 B:ASP274 2.0 37.7 1.0 O2 B:OXL603 2.0 42.9 1.0 O B:HOH717 2.1 33.7 1.0 O1 B:OXL603 2.2 37.2 1.0 O B:HOH736 2.2 37.4 1.0 OE1 B:GLU250 2.2 42.2 1.0 C2 B:OXL603 2.8 47.9 1.0 C1 B:OXL603 2.9 44.6 1.0 CG B:ASP274 3.1 34.8 1.0 CD B:GLU250 3.2 40.1 1.0 CB B:ASP274 3.6 35.3 1.0 OE2 B:GLU250 3.6 37.0 1.0 O4 B:OXL603 4.1 49.3 1.0 O B:HOH819 4.1 44.8 1.0 O3 B:OXL603 4.1 44.6 1.0 OD2 B:ASP274 4.2 39.7 1.0 NZ B:LYS248 4.3 36.3 1.0 N B:ASP274 4.4 30.7 1.0 CE2 B:PHE221 4.4 43.0 1.0 O B:HOH721 4.5 35.7 1.0 CE B:LYS248 4.5 37.0 1.0 CB B:ALA271 4.5 35.7 1.0 CG B:GLU250 4.6 34.6 1.0 CA B:ASP274 4.6 30.8 1.0 CB B:GLU250 5.0 39.5 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


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 and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:58.1 occ:1.00 O C:HOH723 1.9 46.0 1.0 OD1 C:ASP274 2.0 32.8 1.0 OE1 C:GLU250 2.1 44.3 1.0 O3 C:OXL603 2.1 48.9 1.0 O C:HOH714 2.1 38.8 1.0 O4 C:OXL603 2.3 42.7 1.0 C1 C:OXL603 3.0 54.3 1.0 C2 C:OXL603 3.1 45.6 1.0 CD C:GLU250 3.1 47.2 1.0 CG C:ASP274 3.1 36.0 1.0 OE2 C:GLU250 3.4 39.0 1.0 CB C:ASP274 3.7 37.6 1.0 O1 C:OXL603 4.2 57.7 1.0 OD2 C:ASP274 4.2 39.6 1.0 NZ C:LYS248 4.2 40.5 1.0 O2 C:OXL603 4.3 43.0 1.0 O C:HOH784 4.4 62.2 1.0 N C:ASP274 4.4 38.1 1.0 CE2 C:PHE221 4.5 57.2 1.0 CG C:GLU250 4.5 48.8 1.0 CE C:LYS248 4.5 41.7 1.0 CA C:ASP274 4.7 34.5 1.0 CB C:ALA271 4.8 47.4 1.0 CD2 C:PHE221 4.9 53.1 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


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 and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:40.5 occ:1.00 O D:HOH710 1.8 40.0 1.0 OE1 D:GLU250 1.9 37.1 1.0 OD1 D:ASP274 2.0 35.8 1.0 O D:HOH742 2.1 36.5 1.0 O3 D:OXL603 2.1 40.3 1.0 O4 D:OXL603 2.2 40.6 1.0 C1 D:OXL603 2.9 51.3 1.0 C2 D:OXL603 2.9 48.3 1.0 CD D:GLU250 3.0 35.8 1.0 CG D:ASP274 3.1 38.7 1.0 OE2 D:GLU250 3.4 38.8 1.0 CB D:ASP274 3.5 35.4 1.0 O1 D:OXL603 4.1 39.7 1.0 O2 D:OXL603 4.2 55.2 1.0 N D:ASP274 4.2 31.8 1.0 OD2 D:ASP274 4.2 38.7 1.0 CG D:GLU250 4.3 36.9 1.0 NZ D:LYS248 4.3 31.4 1.0 CA D:ASP274 4.5 31.5 1.0 CE2 D:PHE221 4.5 42.5 1.0 CE D:LYS248 4.6 32.5 1.0 CB D:ALA271 4.6 31.7 1.0 CB D:GLU250 4.9 38.1 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:51.4 occ:1.00 OE1 F:GLU250 1.7 48.8 1.0 OD1 F:ASP274 2.0 51.6 1.0 O2 F:OXL603 2.1 46.4 1.0 O F:HOH734 2.1 46.7 1.0 O F:HOH703 2.2 37.7 1.0 O1 F:OXL603 2.3 42.9 1.0 C2 F:OXL603 2.9 66.5 1.0 CD F:GLU250 2.9 47.7 1.0 C1 F:OXL603 3.0 61.1 1.0 CG F:ASP274 3.0 46.9 1.0 OE2 F:GLU250 3.5 47.0 1.0 CB F:ASP274 3.6 38.1 1.0 CG F:GLU250 4.1 57.9 1.0 OD2 F:ASP274 4.1 51.9 1.0 O4 F:OXL603 4.1 66.4 1.0 O3 F:OXL603 4.2 56.7 1.0 N F:ASP274 4.2 34.0 1.0 NZ F:LYS248 4.2 52.3 1.0 O F:HOH793 4.3 58.5 1.0 CE F:LYS248 4.4 51.4 1.0 CE2 F:PHE221 4.5 61.5 1.0 CA F:ASP274 4.5 34.9 1.0 CB F:ALA271 4.6 40.3 1.0 CZ F:PHE221 4.9 57.6 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:50.3 occ:1.00 O G:HOH733 1.9 41.2 1.0 OD1 G:ASP274 2.0 48.3 1.0 OE1 G:GLU250 2.0 44.3 1.0 O G:HOH718 2.2 44.9 1.0 O4 G:OXL603 2.2 38.7 1.0 O3 G:OXL603 2.2 49.9 1.0 C2 G:OXL603 3.0 54.1 1.0 C1 G:OXL603 3.0 60.3 1.0 CD G:GLU250 3.0 48.3 1.0 CG G:ASP274 3.1 44.6 1.0 OE2 G:GLU250 3.3 52.8 1.0 CB G:ASP274 3.7 46.7 1.0 OD2 G:ASP274 4.1 54.0 1.0 O2 G:OXL603 4.2 49.8 1.0 O1 G:OXL603 4.2 61.4 1.0 NZ G:LYS248 4.3 37.5 1.0 N G:ASP274 4.4 39.5 1.0 CG G:GLU250 4.4 51.3 1.0 O G:HOH794 4.4 68.9 1.0 CA G:ASP274 4.6 44.3 1.0 CB G:ALA271 4.7 43.6 1.0 CE G:LYS248 4.7 37.6 1.0 CE2 G:PHE221 4.7 61.0 1.0 O G:HOH725 4.8 53.9 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:58.8 occ:1.00 O1 H:OXL603 2.1 65.5 1.0 OD1 H:ASP274 2.1 63.7 1.0 O H:HOH704 2.1 55.9 1.0 O2 H:OXL603 2.3 74.3 1.0 OE1 H:GLU250 2.5 60.3 1.0 C1 H:OXL603 2.9 69.8 1.0 C2 H:OXL603 3.0 73.7 1.0 CG H:ASP274 3.3 54.0 1.0 CD H:GLU250 3.4 65.8 1.0 OE2 H:GLU250 3.5 62.9 1.0 NZ H:LYS248 3.9 55.5 1.0 CB H:ASP274 4.0 49.9 1.0 O3 H:OXL603 4.1 57.9 1.0 OD2 H:ASP274 4.2 51.9 1.0 CE H:LYS248 4.2 52.0 1.0 O4 H:OXL603 4.3 73.0 1.0 N H:ASP274 4.7 42.7 1.0 CE2 H:PHE221 4.7 76.3 1.0 CB H:ALA271 4.7 51.7 1.0 CG H:GLU250 4.8 61.5 1.0 CA H:ASP274 5.0 44.7 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