Potassium in PDB 8xw8: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp, PDB code: 8xw8 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)	47.30 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.335, 256.08, 88.575, 90, 90.04, 90
R / Rfree (%)	19.8 / 23.4

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

Magnesium

(Mg)

8 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 Gdp (pdb code 8xw8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 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 Gdp, PDB code: 8xw8:
Jump to Potassium binding site number: 1; 2; 3; 4;

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


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 Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:37.3 occ:1.00 OD1 A:ASP88 2.5 23.3 1.0 O A:HOH947 2.6 32.4 1.0 OD1 A:ASN56 2.7 21.2 1.0 O A:THR89 2.7 18.9 1.0 O A:HOH1066 2.8 37.0 1.0 OG A:SER58 2.8 20.0 1.0 CB A:SER58 3.5 23.5 1.0 OG A:SER220 3.6 17.3 1.0 C A:THR89 3.6 20.3 1.0 CG A:ASP88 3.6 23.2 1.0 CG A:ASN56 3.7 22.1 1.0 O A:ASP88 3.8 21.0 1.0 C A:ASP88 4.1 18.8 1.0 CA A:LYS90 4.1 24.1 1.0 N A:SER58 4.2 23.2 1.0 ND2 A:ASN56 4.2 20.0 1.0 N A:LYS90 4.2 21.4 1.0 NZ A:LYS248 4.3 21.8 1.0 NH2 A:ARG95 4.4 26.0 1.0 CB A:ASP88 4.4 20.3 1.0 CA A:SER58 4.4 22.6 1.0 OD2 A:ASP88 4.4 22.5 1.0 N A:THR89 4.5 19.0 1.0 O A:LYS90 4.6 21.3 1.0 CA A:THR89 4.6 19.3 1.0 NH2 A:ARG54 4.7 19.1 1.0 CB A:SER220 4.7 17.5 1.0 OE2 A:GLU93 4.8 34.2 1.0 O A:HOH778 4.8 19.1 1.0 C A:LYS90 4.8 24.2 1.0 O1B A:GDP605 4.8 22.0 1.0 CA A:ASP88 4.8 19.3 1.0 N A:PHE57 4.9 22.4 1.0 CB A:ASN56 4.9 21.2 1.0 OE1 A:GLU93 4.9 29.5 1.0 CA A:ASN56 5.0 20.1 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp


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 Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:K603 b:37.7 occ:1.00 OD1 B:ASP88 2.5 23.3 1.0 O B:HOH948 2.6 30.5 1.0 OD1 B:ASN56 2.7 17.9 1.0 OG B:SER58 2.7 20.1 1.0 O B:HOH1045 2.8 33.2 1.0 O B:THR89 2.8 18.0 1.0 OG B:SER220 3.6 19.2 1.0 CB B:SER58 3.6 23.1 1.0 CG B:ASP88 3.6 23.8 1.0 C B:THR89 3.6 20.7 1.0 CG B:ASN56 3.6 20.4 1.0 O B:ASP88 3.8 20.3 1.0 ND2 B:ASN56 4.1 18.5 1.0 C B:ASP88 4.1 18.5 1.0 CA B:LYS90 4.1 24.9 1.0 N B:SER58 4.2 23.2 1.0 N B:LYS90 4.2 21.9 1.0 NZ B:LYS248 4.3 20.2 1.0 NH2 B:ARG95 4.3 24.2 1.0 OD2 B:ASP88 4.4 23.6 1.0 CB B:ASP88 4.4 19.6 1.0 CA B:SER58 4.4 22.8 1.0 N B:THR89 4.5 18.7 1.0 O B:LYS90 4.6 22.4 1.0 CA B:THR89 4.6 19.2 1.0 CB B:SER220 4.7 18.3 1.0 NH2 B:ARG54 4.7 19.6 1.0 O2B B:GDP605 4.8 21.4 1.0 C B:LYS90 4.8 22.8 1.0 OE2 B:GLU93 4.8 36.0 1.0 CA B:ASP88 4.8 19.9 1.0 O B:HOH775 4.8 17.9 1.0 N B:PHE57 4.9 21.1 1.0 CB B:ASN56 4.9 19.3 1.0 OE1 B:GLU93 4.9 29.0 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:K603 b:50.8 occ:1.00 OD1 C:ASN56 2.3 33.1 1.0 O C:HOH959 2.4 46.0 1.0 O C:THR89 2.5 38.4 1.0 OD1 C:ASP88 2.7 34.8 1.0 O C:HOH964 2.8 40.9 1.0 OG C:SER58 3.2 41.2 1.0 CG C:ASN56 3.3 31.2 1.0 CB C:SER58 3.4 43.6 1.0 CG C:ASP88 3.5 32.6 1.0 C C:THR89 3.7 46.1 1.0 ND2 C:ASN56 3.7 33.8 1.0 OG C:SER220 3.7 33.4 1.0 NZ C:LYS248 4.1 30.4 1.0 O C:ASP88 4.1 30.0 1.0 NH2 C:ARG54 4.1 26.8 1.0 N C:SER58 4.2 41.2 1.0 OD2 C:ASP88 4.3 35.7 1.0 C C:ASP88 4.3 27.6 1.0 CB C:ASP88 4.3 31.8 1.0 CA C:SER58 4.4 41.5 1.0 CA C:LYS90 4.4 45.5 1.0 N C:LYS90 4.5 47.9 1.0 CB C:ASN56 4.5 32.0 1.0 N C:THR89 4.5 32.9 1.0 O1B C:GDP605 4.5 45.8 1.0 NH2 C:ARG95 4.5 56.3 1.0 O C:HOH754 4.7 28.3 1.0 CA C:THR89 4.7 37.4 1.0 CA C:ASN56 4.8 33.0 1.0 N C:PHE57 4.8 39.5 1.0 CA C:ASP88 4.9 27.7 1.0 CB C:SER220 4.9 31.8 1.0

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:K603 b:53.3 occ:1.00 OD1 D:ASN56 2.4 34.4 1.0 O D:HOH959 2.5 43.5 1.0 OD1 D:ASP88 2.6 37.0 1.0 O D:THR89 2.9 43.1 1.0 OG D:SER58 3.2 42.1 1.0 CB D:SER58 3.4 45.2 1.0 CG D:ASN56 3.4 31.4 1.0 CG D:ASP88 3.6 35.0 1.0 OG D:SER220 3.7 32.4 1.0 C D:THR89 3.8 45.7 1.0 ND2 D:ASN56 3.9 34.1 1.0 NZ D:LYS248 4.2 29.5 1.0 O D:ASP88 4.2 31.2 1.0 NH2 D:ARG54 4.2 25.4 1.0 N D:SER58 4.3 40.8 1.0 C D:ASP88 4.3 29.1 1.0 CB D:ASP88 4.3 35.9 1.0 OD2 D:ASP88 4.3 39.5 1.0 CA D:SER58 4.4 40.5 1.0 N D:LYS90 4.4 47.0 1.0 CA D:LYS90 4.4 40.5 1.0 O D:HOH911 4.4 23.5 1.0 N D:THR89 4.5 34.2 1.0 O3B D:GDP605 4.6 51.0 1.0 CB D:ASN56 4.6 32.7 1.0 NH2 D:ARG95 4.7 51.0 1.0 CA D:THR89 4.7 38.0 1.0 CB D:SER220 4.9 31.1 1.0 CA D:ASN56 4.9 33.1 1.0 CA D:ASP88 4.9 30.2 1.0 N D:PHE57 4.9 37.9 1.0 O D:HOH766 4.9 42.5 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