Potassium in PDB 8xw7: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp, PDB code: 8xw7 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)	47.21 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	123.184, 255.539, 88.133, 90, 90, 90
R / Rfree (%)	18.6 / 22.7

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

Magnesium

(Mg)

4 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 Adp (pdb code 8xw7). 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 Adp, PDB code: 8xw7:
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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:56.7 occ:1.00 OD1 A:ASP88 2.6 42.5 1.0 O A:HOH821 2.7 56.4 1.0 OD1 A:ASN56 2.8 39.6 1.0 O A:HOH839 2.8 44.9 1.0 O A:THR89 2.9 38.6 1.0 OG A:SER58 2.9 45.6 1.0 OG A:SER220 3.4 39.2 1.0 CG A:ASP88 3.5 43.7 1.0 C A:THR89 3.7 38.1 1.0 CB A:SER58 3.7 46.5 1.0 CG A:ASN56 3.7 42.6 1.0 NZ A:LYS248 4.0 42.6 1.0 O A:ASP88 4.2 40.9 1.0 ND2 A:ASN56 4.2 37.0 1.0 OD2 A:ASP88 4.2 47.4 1.0 CA A:LYS90 4.2 46.3 1.0 N A:LYS90 4.3 44.1 1.0 C A:ASP88 4.3 37.6 1.0 CB A:ASP88 4.3 38.2 1.0 NH2 A:ARG95 4.4 49.4 1.0 N A:SER58 4.4 47.6 1.0 CB A:SER220 4.5 39.1 1.0 O A:HOH727 4.5 40.2 1.0 N A:THR89 4.5 38.0 1.0 O A:LYS90 4.6 40.2 1.0 NH2 A:ARG54 4.6 42.6 1.0 CA A:SER58 4.6 47.6 1.0 O3B A:ADP606 4.7 47.0 1.0 CA A:THR89 4.8 38.0 1.0 C A:LYS90 4.8 42.7 1.0 OE1 A:GLU93 4.8 49.9 1.0 CA A:ASP88 4.9 36.8 1.0 CB A:ASN56 4.9 39.1 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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:K603 b:70.0 occ:1.00 OD1 B:ASN56 2.3 53.8 1.0 OG B:SER58 2.8 67.8 1.0 OD1 B:ASP88 2.8 54.6 1.0 O B:THR89 3.0 73.1 1.0 CG B:ASN56 3.4 54.9 1.0 CG B:ASP88 3.6 57.1 1.0 OG B:SER220 3.6 50.8 1.0 C B:THR89 3.8 69.4 1.0 CB B:SER58 3.8 71.0 1.0 NZ B:LYS248 3.9 56.1 1.0 ND2 B:ASN56 4.0 53.1 1.0 O B:ASP88 4.1 52.7 1.0 N B:LYS90 4.3 74.6 1.0 OD2 B:ASP88 4.3 69.8 1.0 CB B:ASP88 4.3 53.4 1.0 NH2 B:ARG54 4.3 50.3 1.0 CA B:LYS90 4.3 73.0 1.0 C B:ASP88 4.3 50.8 1.0 O1B B:ADP606 4.5 90.6 1.0 N B:SER58 4.5 70.7 1.0 O B:LYS90 4.5 75.1 1.0 N B:THR89 4.6 53.2 1.0 O B:HOH713 4.6 52.3 1.0 CB B:ASN56 4.7 51.8 1.0 CA B:SER58 4.7 68.8 1.0 CB B:SER220 4.8 56.5 1.0 C B:LYS90 4.8 67.7 1.0 CA B:THR89 4.8 54.5 1.0 N B:PHE57 4.8 67.8 1.0 NH2 B:ARG95 4.9 96.0 1.0 CA B:ASP88 4.9 52.1 1.0 CA B:ASN56 4.9 56.9 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