Potassium in PDB 8iat: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate, PDB code: 8iat 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)	48.30 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.051, 118.353, 99.82, 90, 108.93, 90
R / Rfree (%)	19.9 / 24.6

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 (pdb code 8iat). 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, PDB code: 8iat:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:K604 b:37.7 occ:1.00 OD1 A:ASP88 2.5 34.8 1.0 O A:HOH953 2.6 37.4 1.0 OD1 A:ASN56 2.7 31.7 1.0 OG A:SER58 2.7 31.9 1.0 O A:THR89 2.7 29.0 1.0 O A:HOH841 2.9 33.5 1.0 OG A:SER220 3.6 33.0 1.0 CG A:ASP88 3.6 32.5 1.0 CG A:ASN56 3.7 31.9 1.0 C A:THR89 3.7 30.2 1.0 CB A:SER58 3.7 35.9 1.0 NZ A:LYS248 4.0 31.4 1.0 O A:ASP88 4.1 30.8 1.0 NH2 A:ARG54 4.1 37.0 1.0 ND2 A:ASN56 4.2 31.0 1.0 CA A:LYS90 4.2 32.2 1.0 N A:SER58 4.2 34.0 1.0 C A:ASP88 4.3 30.4 1.0 N A:LYS90 4.3 30.6 1.0 OD2 A:ASP88 4.3 33.1 1.0 O A:HOH924 4.3 43.2 1.0 CB A:ASP88 4.4 28.5 1.0 O A:LYS90 4.5 30.3 1.0 OE1 A:GLU93 4.5 48.3 1.0 N A:THR89 4.5 30.6 1.0 CA A:SER58 4.5 34.4 1.0 O A:HOH787 4.6 33.6 1.0 C A:LYS90 4.7 30.0 1.0 CA A:THR89 4.8 32.0 1.0 CB A:SER220 4.8 31.5 1.0 CB A:ASN56 4.8 29.8 1.0 N A:PHE57 4.9 33.1 1.0 CA A:ASP88 4.9 29.0 1.0 CA A:ASN56 5.0 33.2 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:K604 b:48.8 occ:1.00 O B:HOH949 2.6 37.2 1.0 OG B:SER58 2.7 34.3 1.0 O B:THR89 2.7 28.4 1.0 OD1 B:ASN56 2.7 30.7 1.0 OD1 B:ASP88 2.8 36.8 1.0 O B:HOH951 2.9 50.4 1.0 CG B:ASP88 3.5 31.1 1.0 CG B:ASN56 3.6 31.4 1.0 C B:THR89 3.7 31.2 1.0 CB B:SER58 3.8 32.4 1.0 NH2 B:ARG54 3.9 34.5 1.0 NZ B:LYS248 3.9 28.8 1.0 O B:ASP88 4.0 24.8 1.0 OG B:SER220 4.0 30.9 1.0 ND2 B:ASN56 4.1 33.4 1.0 C B:ASP88 4.1 22.7 1.0 CB B:ASP88 4.1 25.2 1.0 OD2 B:ASP88 4.3 33.2 1.0 CA B:LYS90 4.3 29.4 1.0 N B:LYS90 4.3 29.0 1.0 O B:HOH879 4.3 56.0 1.0 N B:THR89 4.4 25.5 1.0 N B:SER58 4.4 31.3 1.0 CA B:THR89 4.7 28.4 1.0 CA B:SER58 4.7 34.3 1.0 O B:LYS90 4.7 31.0 1.0 CA B:ASP88 4.7 23.3 1.0 CB B:ASN56 4.8 28.8 1.0 C B:LYS90 4.9 28.7 1.0 CZ B:ARG54 5.0 28.5 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:K604 b:50.4 occ:1.00 O C:HOH817 2.7 49.3 1.0 OD1 C:ASP88 2.7 40.7 1.0 O C:THR89 2.8 42.2 1.0 O C:HOH752 2.8 44.0 1.0 OG C:SER58 2.8 42.5 1.0 OD1 C:ASN56 2.9 42.1 1.0 OG C:SER220 3.5 39.0 1.0 C C:THR89 3.6 58.5 1.0 CG C:ASP88 3.8 43.3 1.0 NZ C:LYS248 3.8 43.9 1.0 CB C:SER58 3.8 49.2 1.0 CG C:ASN56 3.9 38.1 1.0 CA C:LYS90 4.1 48.5 1.0 O C:HOH828 4.2 61.2 1.0 NH2 C:ARG54 4.2 37.6 1.0 O C:LYS90 4.2 48.0 1.0 ND2 C:ASN56 4.2 43.6 1.0 N C:LYS90 4.2 50.1 1.0 OE1 C:GLU93 4.3 53.8 1.0 O C:ASP88 4.4 52.8 1.0 N C:THR89 4.4 48.1 1.0 OD2 C:ASP88 4.5 47.5 1.0 N C:SER58 4.5 47.2 1.0 C C:ASP88 4.5 47.2 1.0 C C:LYS90 4.5 49.6 1.0 O C:HOH745 4.5 34.5 1.0 CA C:THR89 4.7 53.9 1.0 CA C:SER58 4.7 47.1 1.0 CB C:ASP88 4.7 38.2 1.0 CB C:SER220 4.7 42.4 1.0 O3 C:OXL601 5.0 44.9 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:K604 b:48.2 occ:1.00 OD1 D:ASP88 2.6 43.5 1.0 O D:HOH837 2.7 48.0 1.0 OD1 D:ASN56 2.7 41.9 1.0 OG D:SER58 2.7 46.5 1.0 O D:HOH720 2.7 48.8 1.0 O D:THR89 2.8 40.9 1.0 OG D:SER220 3.6 41.8 1.0 CG D:ASP88 3.6 43.3 1.0 C D:THR89 3.7 46.6 1.0 CG D:ASN56 3.7 42.9 1.0 CB D:SER58 3.7 41.6 1.0 NZ D:LYS248 3.8 41.2 1.0 CA D:LYS90 4.2 47.4 1.0 NH2 D:ARG54 4.2 41.6 1.0 ND2 D:ASN56 4.2 41.3 1.0 O D:ASP88 4.2 47.1 1.0 N D:LYS90 4.2 43.1 1.0 N D:SER58 4.3 49.7 1.0 OE1 D:GLU93 4.3 47.2 1.0 C D:ASP88 4.3 41.0 1.0 O D:LYS90 4.3 47.5 1.0 OD2 D:ASP88 4.4 44.8 1.0 O D:HOH798 4.4 46.5 1.0 CB D:ASP88 4.5 38.7 1.0 N D:THR89 4.5 44.8 1.0 O D:HOH834 4.5 38.3 1.0 CA D:SER58 4.5 44.9 1.0 C D:LYS90 4.6 45.5 1.0 CA D:THR89 4.7 45.1 1.0 CB D:SER220 4.8 40.0 1.0 N D:PHE57 4.9 46.4 1.0 CB D:ASN56 5.0 41.0 1.0 CA D:ASP88 5.0 37.4 1.0

A.Taguchi, R.Nakashima, K.Nishino. Functional and Structural Characterization of Streptococcus Pneumoniae Pyruvate Kinase Involved in Fosfomycin Resistance. J.Biol.Chem. 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.104892