Atomistry » Potassium » PDB 8g7m-8jxo » 8iax
Atomistry »
  Potassium »
    PDB 8g7m-8jxo »
      8iax »

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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Go back to Potassium Binding Sites List in 8iax
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy