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

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate, PDB code: 8iax 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) 48.37 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 221.061, 86.644, 258.148, 90, 100.86, 90
R / Rfree (%) 18.3 / 22.1

Other elements in 8iax:

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

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate (pdb code 8iax). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate, PDB code: 8iax:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8iax

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Potassium binding site 1 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:38.5
occ:1.00
 OG A:SER58 2.7 37.1 1.0
OD1 A:ASP88 2.7 35.4 1.0
O1P A:PEP602 2.8 38.7 1.0
OD1 A:ASN56 2.8 31.3 1.0
O A:THR89 2.8 34.1 1.0
O A:HOH786 3.0 37.1 1.0
O A:HOH830 3.5 42.2 1.0
OG A:SER220 3.6 33.7 1.0
NZ A:LYS248 3.7 32.1 1.0
CG A:ASN56 3.7 30.9 1.0
CB A:SER58 3.8 39.1 1.0
CG A:ASP88 3.8 36.8 1.0
C A:THR89 3.9 34.4 1.0
ND2 A:ASN56 4.0 33.3 1.0
OE1 A:GLU93 4.2 51.8 1.0
NH2 A:ARG54 4.2 35.4 1.0
O A:HOH836 4.2 31.9 1.0
P A:PEP602 4.2 42.7 1.0
CA A:LYS90 4.3 35.3 1.0
N A:SER58 4.4 37.2 1.0
O A:ASP88 4.4 35.9 1.0
O A:LYS90 4.4 35.7 1.0
N A:LYS90 4.5 35.6 1.0
OD2 A:ASP88 4.5 36.3 1.0
C A:ASP88 4.5 34.7 1.0
CA A:SER58 4.6 35.9 1.0
CB A:ASP88 4.7 32.8 1.0
C A:LYS90 4.7 31.2 1.0
N A:THR89 4.7 35.0 1.0
CB A:SER220 4.8 31.8 1.0
O3P A:PEP602 4.8 35.3 1.0
O2 A:PEP602 4.9 39.9 1.0
CA A:THR89 5.0 34.1 1.0

Potassium binding site 2 out of 8 in 8iax

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Potassium binding site 2 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:37.6
occ:1.00
 OG B:SER58 2.6 33.9 1.0
OD1 B:ASP88 2.7 32.6 1.0
O B:THR89 2.7 30.3 1.0
OD1 B:ASN56 2.8 30.5 1.0
O B:HOH783 2.9 36.9 1.0
O3P B:PEP602 2.9 36.4 1.0
O B:HOH881 3.4 41.2 1.0
OG B:SER220 3.6 28.8 1.0
C B:THR89 3.7 32.6 1.0
CB B:SER58 3.7 34.6 1.0
CG B:ASP88 3.7 30.3 1.0
CG B:ASN56 3.8 30.2 1.0
NZ B:LYS248 3.8 33.3 1.0
ND2 B:ASN56 4.1 29.1 1.0
OE1 B:GLU93 4.1 49.2 1.0
CA B:LYS90 4.2 31.8 1.0
O B:ASP88 4.3 28.8 1.0
NH2 B:ARG54 4.3 32.5 1.0
N B:LYS90 4.3 31.6 1.0
N B:SER58 4.3 32.5 1.0
O B:LYS90 4.4 32.3 1.0
P B:PEP602 4.4 40.8 1.0
OD2 B:ASP88 4.4 31.7 1.0
C B:ASP88 4.5 31.7 1.0
O B:HOH773 4.5 31.2 1.0
CA B:SER58 4.6 33.6 1.0
CB B:ASP88 4.6 27.0 1.0
N B:THR89 4.6 28.1 1.0
C B:LYS90 4.7 30.3 1.0
CA B:THR89 4.8 32.7 1.0
CB B:SER220 4.8 27.5 1.0
O2P B:PEP602 5.0 38.2 1.0

Potassium binding site 3 out of 8 in 8iax

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Potassium binding site 3 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:38.3
occ:1.00
 OD1 C:ASP88 2.7 31.3 1.0
OG C:SER58 2.7 34.5 1.0
OD1 C:ASN56 2.8 31.0 1.0
O C:THR89 2.9 29.6 1.0
O3P C:PEP602 2.9 38.4 1.0
O C:HOH789 3.0 36.4 1.0
O C:HOH921 3.5 41.8 1.0
OG C:SER220 3.6 29.0 1.0
CB C:SER58 3.7 38.1 1.0
CG C:ASP88 3.7 34.6 1.0
NZ C:LYS248 3.7 29.1 1.0
CG C:ASN56 3.8 29.3 1.0
C C:THR89 3.8 34.6 1.0
NH2 C:ARG54 4.1 31.9 1.0
ND2 C:ASN56 4.1 33.6 1.0
OE1 C:GLU93 4.3 45.1 1.0
O C:ASP88 4.3 30.0 1.0
CA C:LYS90 4.3 32.7 1.0
N C:SER58 4.4 33.1 1.0
OD2 C:ASP88 4.4 31.1 1.0
O C:LYS90 4.4 36.3 1.0
P C:PEP602 4.4 39.3 1.0
N C:LYS90 4.4 31.2 1.0
O C:HOH746 4.5 29.7 1.0
C C:ASP88 4.5 28.5 1.0
CA C:SER58 4.6 35.4 1.0
CB C:ASP88 4.6 28.7 1.0
N C:THR89 4.7 28.7 1.0
CB C:SER220 4.7 29.9 1.0
C C:LYS90 4.8 33.6 1.0
CA C:THR89 4.9 29.5 1.0
O2P C:PEP602 4.9 35.6 1.0

Potassium binding site 4 out of 8 in 8iax

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Potassium binding site 4 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:50.0
occ:1.00
 OD1 D:ASP88 2.5 36.7 1.0
OD1 D:ASN56 2.5 32.9 1.0
OG D:SER58 2.6 35.2 1.0
O D:THR89 2.6 33.8 1.0
CG D:ASN56 3.5 33.4 1.0
O3P D:PEP602 3.5 43.8 1.0
CG D:ASP88 3.5 38.3 1.0
C D:THR89 3.6 38.3 1.0
CB D:SER58 3.7 42.4 1.0
OG D:SER220 3.7 35.0 1.0
O D:HOH1007 3.7 49.0 1.0
O D:ASP88 3.8 31.5 1.0
O D:HOH951 3.8 39.3 1.0
ND2 D:ASN56 4.0 30.5 1.0
NZ D:LYS248 4.0 30.6 1.0
C D:ASP88 4.1 33.0 1.0
N D:SER58 4.2 37.8 1.0
CA D:LYS90 4.2 37.6 1.0
N D:LYS90 4.3 38.6 1.0
O D:HOH715 4.3 46.6 1.0
CB D:ASP88 4.3 30.8 1.0
NH2 D:ARG54 4.3 33.3 1.0
N D:THR89 4.4 34.6 1.0
OD2 D:ASP88 4.4 33.2 1.0
CA D:SER58 4.4 40.7 1.0
O D:LYS90 4.4 36.3 1.0
CA D:THR89 4.6 36.0 1.0
C D:LYS90 4.7 31.5 1.0
N D:PHE57 4.7 34.6 1.0
CB D:ASN56 4.7 29.7 1.0
CA D:ASP88 4.8 29.6 1.0
CA D:ASN56 4.9 31.6 1.0
P D:PEP602 4.9 43.7 1.0
CB D:SER220 4.9 31.6 1.0
O D:HOH833 5.0 39.5 1.0
C D:ASN56 5.0 32.6 1.0

Potassium binding site 5 out of 8 in 8iax

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Potassium binding site 5 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K604

b:46.6
occ:1.00
 OG E:SER58 2.7 44.4 1.0
O3P E:PEP602 2.7 45.6 1.0
OD1 E:ASP88 2.7 42.4 1.0
OD1 E:ASN56 2.8 41.6 1.0
O E:THR89 2.9 40.4 1.0
O E:HOH818 3.0 47.7 1.0
O E:HOH723 3.1 52.8 1.0
OG E:SER220 3.7 41.1 1.0
NZ E:LYS248 3.7 42.3 1.0
CG E:ASN56 3.7 39.0 1.0
CB E:SER58 3.8 44.1 1.0
CG E:ASP88 3.8 46.5 1.0
C E:THR89 3.9 43.1 1.0
ND2 E:ASN56 4.1 39.4 1.0
P E:PEP602 4.1 46.8 1.0
OE1 E:GLU93 4.1 64.0 1.0
O E:HOH775 4.2 40.1 1.0
NH2 E:ARG54 4.3 38.8 1.0
CA E:LYS90 4.3 40.9 1.0
N E:SER58 4.4 39.0 1.0
N E:LYS90 4.5 41.9 1.0
OD2 E:ASP88 4.5 44.2 1.0
O E:LYS90 4.5 42.0 1.0
O E:ASP88 4.5 44.3 1.0
O2P E:PEP602 4.6 42.2 1.0
C E:ASP88 4.6 47.8 1.0
CA E:SER58 4.7 45.5 1.0
CB E:SER220 4.8 36.5 1.0
CB E:ASP88 4.8 39.8 1.0
C E:LYS90 4.8 37.9 1.0
N E:THR89 4.8 40.9 1.0
O2 E:PEP602 4.8 46.7 1.0
CB E:ASN56 5.0 34.5 1.0
CA E:THR89 5.0 45.3 1.0

Potassium binding site 6 out of 8 in 8iax

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Potassium binding site 6 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:42.0
occ:1.00
 OG F:SER58 2.6 37.4 1.0
OD1 F:ASP88 2.7 38.7 1.0
O F:THR89 2.7 37.4 1.0
OD1 F:ASN56 2.8 37.1 1.0
O F:HOH862 3.1 42.3 1.0
O1P F:PEP602 3.1 39.1 1.0
O F:HOH842 3.4 46.4 1.0
CB F:SER58 3.6 41.4 1.0
CG F:ASN56 3.7 34.7 1.0
CG F:ASP88 3.7 37.8 1.0
OG F:SER220 3.7 37.7 1.0
C F:THR89 3.8 35.4 1.0
NZ F:LYS248 3.8 36.1 1.0
ND2 F:ASN56 4.0 34.9 1.0
OE1 F:GLU93 4.1 62.6 1.0
NH2 F:ARG54 4.2 35.4 1.0
O F:ASP88 4.2 35.4 1.0
CA F:LYS90 4.3 34.7 1.0
N F:SER58 4.4 38.0 1.0
N F:LYS90 4.4 34.8 1.0
O F:LYS90 4.4 38.0 1.0
O F:HOH782 4.4 36.1 1.0
C F:ASP88 4.4 35.3 1.0
OD2 F:ASP88 4.4 37.8 1.0
P F:PEP602 4.5 44.3 1.0
CA F:SER58 4.5 40.1 1.0
CB F:ASP88 4.5 34.3 1.0
N F:THR89 4.6 33.2 1.0
C F:LYS90 4.7 36.0 1.0
CA F:THR89 4.8 36.5 1.0
CB F:SER220 4.8 36.3 1.0
O3P F:PEP602 4.9 43.4 1.0
CB F:ASN56 4.9 37.2 1.0
O F:HOH722 4.9 62.0 1.0

Potassium binding site 7 out of 8 in 8iax

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Potassium binding site 7 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:44.0
occ:1.00
 OD1 G:ASP88 2.6 31.9 1.0
OG G:SER58 2.7 38.6 1.0
O G:THR89 2.7 33.9 1.0
OD1 G:ASN56 2.8 31.8 1.0
O3P G:PEP602 2.9 43.8 1.0
O G:HOH793 3.0 41.8 1.0
O G:HOH860 3.5 46.3 1.0
OG G:SER220 3.6 31.2 1.0
CG G:ASP88 3.7 37.3 1.0
CB G:SER58 3.7 40.1 1.0
CG G:ASN56 3.7 31.6 1.0
NZ G:LYS248 3.8 32.4 1.0
C G:THR89 3.8 38.3 1.0
ND2 G:ASN56 4.1 36.1 1.0
NH2 G:ARG54 4.2 34.4 1.0
O G:ASP88 4.3 31.5 1.0
O G:LYS90 4.3 37.7 1.0
CA G:LYS90 4.3 34.0 1.0
OE1 G:GLU93 4.4 54.8 1.0
P G:PEP602 4.4 40.3 1.0
N G:LYS90 4.4 34.3 1.0
N G:SER58 4.4 40.3 1.0
OD2 G:ASP88 4.4 36.0 1.0
C G:ASP88 4.4 30.6 1.0
O G:HOH778 4.4 33.5 1.0
CB G:ASP88 4.6 32.9 1.0
CA G:SER58 4.6 39.6 1.0
N G:THR89 4.6 31.4 1.0
C G:LYS90 4.7 33.8 1.0
CB G:SER220 4.7 32.1 1.0
CA G:THR89 4.8 33.9 1.0
O1P G:PEP602 5.0 36.7 1.0
CB G:ASN56 5.0 34.8 1.0

Potassium binding site 8 out of 8 in 8iax

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Potassium binding site 8 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K604

b:50.5
occ:1.00
 OG H:SER58 2.5 36.6 1.0
OD1 H:ASP88 2.6 37.0 1.0
OD1 H:ASN56 2.6 38.7 1.0
O H:THR89 2.7 35.6 1.0
O3P H:PEP602 3.3 40.4 1.0
CG H:ASN56 3.6 34.1 1.0
CG H:ASP88 3.6 36.8 1.0
OG H:SER220 3.6 32.1 1.0
CB H:SER58 3.7 39.0 1.0
C H:THR89 3.7 38.0 1.0
NZ H:LYS248 3.9 34.7 1.0
ND2 H:ASN56 4.0 33.9 1.0
O H:ASP88 4.1 34.0 1.0
O H:HOH715 4.1 50.3 1.0
NH2 H:ARG54 4.2 36.2 1.0
N H:SER58 4.3 41.1 1.0
CA H:LYS90 4.3 40.6 1.0
OD2 H:ASP88 4.3 33.2 1.0
C H:ASP88 4.4 33.2 1.0
N H:LYS90 4.4 38.2 1.0
O H:LYS90 4.4 37.9 1.0
CA H:SER58 4.5 39.6 1.0
CB H:ASP88 4.5 31.5 1.0
N H:THR89 4.6 33.7 1.0
C H:LYS90 4.7 37.3 1.0
O H:HOH783 4.7 40.7 1.0
P H:PEP602 4.7 45.0 1.0
CA H:THR89 4.8 35.7 1.0
CB H:ASN56 4.8 32.6 1.0
CB H:SER220 4.9 33.2 1.0

Reference:

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
Page generated: Tue Aug 13 00:02:59 2024

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