Potassium in PDB 8xw9: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp, PDB code: 8xw9 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)	40.73 / 1.75
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.464, 81.464, 398.91, 90, 90, 90
R / Rfree (%)	16 / 19.1

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp 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 Udp (pdb code 8xw9). 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 Udp, PDB code: 8xw9:
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 Udp


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:36.5 occ:1.00 O A:THR89 2.6 26.0 1.0 OD1 A:ASP88 2.6 33.8 1.0 OD1 A:ASN56 2.7 28.0 1.0 OG A:SER58 2.8 26.5 1.0 O A:HOH914 2.8 34.5 1.0 O A:HOH1013 3.0 40.6 1.0 OG A:SER220 3.6 28.0 1.0 C A:THR89 3.6 27.1 1.0 CG A:ASP88 3.7 34.4 1.0 CB A:SER58 3.7 26.4 1.0 CG A:ASN56 3.7 26.6 1.0 O A:ASP88 4.0 28.6 1.0 ND2 A:ASN56 4.1 26.8 1.0 CA A:LYS90 4.2 28.1 1.0 N A:SER58 4.2 27.8 1.0 C A:ASP88 4.2 27.3 1.0 NZ A:LYS248 4.2 30.8 1.0 N A:LYS90 4.2 26.6 1.0 NH2 A:ARG95 4.4 29.6 1.0 CB A:ASP88 4.4 26.1 1.0 OD2 A:ASP88 4.5 34.3 1.0 N A:THR89 4.5 26.3 1.0 CA A:SER58 4.5 29.5 1.0 NH2 A:ARG54 4.6 29.3 1.0 O A:LYS90 4.6 29.2 1.0 CB A:SER220 4.7 29.7 1.0 CA A:THR89 4.7 27.1 1.0 O A:HOH768 4.7 29.9 1.0 OE2 A:GLU93 4.8 36.5 1.0 O3B A:UDP606 4.8 30.6 1.0 OE1 A:GLU93 4.8 33.5 1.0 C A:LYS90 4.8 27.4 1.0 N A:PHE57 4.9 27.4 1.0 CB A:ASN56 4.9 25.1 1.0 CA A:ASP88 4.9 25.1 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 Udp


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:K602 b:36.2 occ:1.00 OD1 B:ASP88 2.6 33.2 1.0 OD1 B:ASN56 2.7 30.0 1.0 OG B:SER58 2.7 31.8 1.0 O B:THR89 2.8 26.4 1.0 O B:HOH988 2.8 41.6 1.0 O B:HOH795 2.9 35.5 1.0 CG B:ASP88 3.6 32.0 1.0 OG B:SER220 3.7 28.6 1.0 CG B:ASN56 3.7 30.3 1.0 CB B:SER58 3.7 33.5 1.0 C B:THR89 3.7 29.9 1.0 NZ B:LYS248 4.0 31.4 1.0 O B:ASP88 4.1 29.0 1.0 O B:HOH829 4.1 41.1 1.0 ND2 B:ASN56 4.1 30.8 1.0 CA B:LYS90 4.2 31.0 1.0 NH2 B:ARG54 4.2 30.9 1.0 N B:SER58 4.2 28.7 1.0 N B:LYS90 4.3 31.5 1.0 OD2 B:ASP88 4.3 32.2 1.0 O B:LYS90 4.3 32.7 1.0 C B:ASP88 4.4 30.9 1.0 OE2 B:GLU93 4.4 49.8 1.0 CB B:ASP88 4.5 27.7 1.0 CA B:SER58 4.5 31.9 1.0 O B:HOH820 4.6 32.1 1.0 N B:THR89 4.6 29.4 1.0 C B:LYS90 4.6 30.1 1.0 CA B:THR89 4.8 29.6 1.0 CB B:SER220 4.8 28.3 1.0 CB B:ASN56 4.9 30.3 1.0 N B:PHE57 5.0 27.1 1.0 CA B:ASP88 5.0 27.9 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