Magnesium in PDB 8xw6: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Atp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Atp, PDB code: 8xw6 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)	46.96 / 1.99
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.58, 81.58, 402, 90, 90, 90
R / Rfree (%)	17.8 / 21.1

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

Potassium

(K)

2 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 and Atp (pdb code 8xw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Atp, PDB code: 8xw6:
Jump to Magnesium binding site number: 1; 2; 3;

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


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 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:56.5 occ:1.00 O A:HOH889 2.0 48.1 1.0 O A:HOH907 2.1 52.9 1.0 O2A A:ATP605 2.1 49.5 1.0 O1G A:ATP605 2.2 51.9 1.0 O2B A:ATP605 2.3 58.9 1.0 O A:HOH747 2.5 48.5 1.0 PB A:ATP605 3.3 49.9 1.0 PG A:ATP605 3.4 55.7 1.0 PA A:ATP605 3.4 52.2 1.0 O3B A:ATP605 3.6 54.9 1.0 O3A A:ATP605 3.6 53.6 1.0 OG A:SER340 3.9 43.8 1.0 O3G A:ATP605 4.0 42.3 1.0 OD1 A:ASP153 4.1 92.8 1.0 CB A:SER340 4.1 40.2 1.0 C1 A:OXL604 4.2 62.3 1.0 O A:HOH930 4.3 53.6 1.0 O3 A:OXL604 4.4 63.3 1.0 C2 A:OXL604 4.4 53.9 1.0 O5' A:ATP605 4.4 50.8 1.0 OG1 A:THR306 4.4 43.3 1.0 C5' A:ATP605 4.5 61.7 1.0 O1A A:ATP605 4.5 58.9 1.0 O1 A:OXL604 4.6 47.9 1.0 NH2 A:ARG54 4.6 53.7 1.0 O2 A:OXL604 4.6 49.1 1.0 O1B A:ATP605 4.6 63.1 1.0 O2G A:ATP605 4.7 47.3 1.0 CG2 A:THR306 4.7 41.5 1.0 O4 A:OXL604 4.8 60.4 1.0 O A:HOH869 4.8 53.1 1.0 CG A:ASP153 4.9 91.3 1.0 OD2 A:ASP153 4.9 101.0 1.0 NH1 A:ARG54 4.9 48.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Atp


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 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:44.2 occ:1.00 O A:HOH734 1.9 38.6 1.0 OD1 A:ASP274 1.9 45.5 1.0 O3G A:ATP605 2.1 42.3 1.0 OE1 A:GLU250 2.2 41.3 1.0 O1 A:OXL604 2.2 47.9 1.0 O2 A:OXL604 2.5 49.1 1.0 CG A:ASP274 3.1 42.9 1.0 CD A:GLU250 3.1 39.7 1.0 C1 A:OXL604 3.1 62.3 1.0 C2 A:OXL604 3.2 53.9 1.0 OE2 A:GLU250 3.3 43.5 1.0 PG A:ATP605 3.4 55.7 1.0 CB A:ASP274 3.6 42.0 1.0 O2G A:ATP605 3.9 47.3 1.0 NZ A:LYS248 3.9 50.1 1.0 O1G A:ATP605 4.1 51.9 1.0 OD2 A:ASP274 4.2 49.5 1.0 O A:HOH869 4.2 53.1 1.0 CE A:LYS248 4.3 46.3 1.0 O A:HOH889 4.3 48.1 1.0 CE2 A:PHE221 4.3 46.7 1.0 O3 A:OXL604 4.4 63.3 1.0 O4 A:OXL604 4.4 60.4 1.0 CZ A:PHE221 4.4 47.4 1.0 O A:HOH799 4.5 41.5 1.0 N A:ASP274 4.5 40.4 1.0 CG A:GLU250 4.5 39.9 1.0 CB A:ALA271 4.7 43.6 1.0 CA A:ASP274 4.7 41.5 1.0 CB A:GLU250 4.8 45.3 1.0 O3B A:ATP605 4.9 54.9 1.0

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


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 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:47.6 occ:1.00 OD1 B:ASP274 2.0 41.1 1.0 O B:HOH765 2.0 49.1 1.0 OE1 B:GLU250 2.1 43.8 1.0 O B:HOH732 2.1 44.7 1.0 O1 B:OXL603 2.2 52.1 1.0 O2 B:OXL603 2.3 54.7 1.0 C1 B:OXL603 3.0 52.3 1.0 C2 B:OXL603 3.0 61.6 1.0 CG B:ASP274 3.1 46.9 1.0 CD B:GLU250 3.1 43.6 1.0 OE2 B:GLU250 3.5 42.0 1.0 CB B:ASP274 3.6 47.9 1.0 O B:HOH864 4.0 51.0 1.0 NZ B:LYS248 4.1 48.7 1.0 OD2 B:ASP274 4.2 48.8 1.0 O3 B:OXL603 4.2 53.2 1.0 O4 B:OXL603 4.3 66.8 1.0 N B:ASP274 4.4 39.9 1.0 CE2 B:PHE221 4.4 56.9 1.0 CG B:GLU250 4.5 44.8 1.0 CE B:LYS248 4.5 46.2 1.0 CB B:ALA271 4.5 44.4 1.0 CA B:ASP274 4.7 41.8 1.0 CZ B:PHE221 4.7 56.2 1.0 CB B:GLU250 4.8 47.6 1.0 O B:HOH713 4.8 46.2 1.0

A.Taguchi, R.Nakashima, K.Nishino. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J.Mol.Biol. 68708 2024.
ISSN: ESSN 1089-8638
PubMed: 39009072
DOI: 10.1016/J.JMB.2024.168708