Potassium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium 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 Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K601 b:46.5 occ:1.00 OD1 A:ASP88 2.7 47.6 1.0 OD1 A:ASN56 2.7 41.3 1.0 O A:THR89 2.7 40.8 1.0 O2G A:ATP605 2.8 47.3 1.0 OG A:SER58 2.8 41.8 1.0 O A:HOH799 2.9 41.5 1.0 OG A:SER220 3.4 40.2 1.0 CG A:ASN56 3.6 45.6 1.0 CG A:ASP88 3.7 48.5 1.0 C A:THR89 3.7 40.5 1.0 CB A:SER58 3.7 44.2 1.0 ND2 A:ASN56 3.9 46.3 1.0 NZ A:LYS248 4.0 50.1 1.0 PG A:ATP605 4.2 55.7 1.0 O A:ASP88 4.2 42.3 1.0 CA A:LYS90 4.3 41.2 1.0 N A:LYS90 4.3 39.4 1.0 C A:ASP88 4.3 42.8 1.0 O A:HOH734 4.4 38.6 1.0 OD2 A:ASP88 4.4 57.3 1.0 N A:SER58 4.4 46.0 1.0 NH2 A:ARG95 4.4 46.8 1.0 O A:LYS90 4.5 44.1 1.0 CB A:SER220 4.5 42.3 1.0 N A:THR89 4.5 39.2 1.0 CB A:ASP88 4.5 38.9 1.0 O3B A:ATP605 4.6 54.9 1.0 NH2 A:ARG54 4.6 53.7 1.0 CA A:SER58 4.7 46.7 1.0 CA A:THR89 4.7 42.1 1.0 C A:LYS90 4.8 41.6 1.0 OE1 A:GLU93 4.9 47.5 1.0 CB A:ASN56 4.9 40.4 1.0 OE2 A:GLU93 4.9 48.9 1.0 O3G A:ATP605 5.0 42.3 1.0

Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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 B:K601 b:55.0 occ:1.00 O B:HOH713 2.6 46.2 1.0 OD1 B:ASP88 2.6 47.4 1.0 OG B:SER58 2.7 44.3 1.0 OD1 B:ASN56 2.8 44.0 1.0 O B:THR89 2.8 43.7 1.0 O B:HOH864 3.0 51.0 1.0 OG B:SER220 3.6 43.5 1.0 CG B:ASP88 3.7 45.8 1.0 CB B:SER58 3.7 48.9 1.0 CG B:ASN56 3.8 46.9 1.0 C B:THR89 3.8 41.8 1.0 NZ B:LYS248 3.9 48.7 1.0 ND2 B:ASN56 4.2 42.4 1.0 CA B:LYS90 4.3 49.8 1.0 NH2 B:ARG54 4.3 46.8 1.0 O B:ASP88 4.3 39.7 1.0 N B:SER58 4.3 47.5 1.0 OE2 B:GLU93 4.3 67.5 1.0 O B:LYS90 4.4 44.8 1.0 C B:ASP88 4.4 41.0 1.0 N B:LYS90 4.4 48.5 1.0 OD2 B:ASP88 4.4 47.3 1.0 O B:HOH732 4.4 44.7 1.0 CB B:ASP88 4.5 38.6 1.0 CA B:SER58 4.6 53.1 1.0 N B:THR89 4.6 43.8 1.0 C B:LYS90 4.7 45.2 1.0 CB B:SER220 4.7 47.7 1.0 CA B:THR89 4.9 41.6 1.0 CB B:ASN56 5.0 44.9 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