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

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate, PDB code: 8iau 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) 49.38 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.442, 114.66, 140.705, 88.95, 88.12, 76.52
R / Rfree (%) 20 / 24.6

Other elements in 8iau:

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

Magnesium (Mg) 7 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 7 in 8iau

Go back to Potassium Binding Sites List in 8iau
Potassium binding site 1 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:50.7
occ:1.00
 O A:THR89 2.5 34.4 1.0
OD1 A:ASP88 2.6 40.5 1.0
OD1 A:ASN56 2.7 29.5 1.0
O A:HOH828 2.8 50.5 1.0
OG A:SER58 2.9 35.9 1.0
OG A:SER220 3.5 35.9 1.0
C A:THR89 3.6 35.4 1.0
CG A:ASP88 3.6 43.4 1.0
NZ A:LYS248 3.8 34.1 1.0
CG A:ASN56 3.8 33.8 1.0
CB A:SER58 3.9 42.1 1.0
O A:ASP88 4.0 30.2 1.0
CA A:LYS90 4.1 40.1 1.0
N A:SER58 4.2 41.4 1.0
N A:LYS90 4.2 39.0 1.0
C A:ASP88 4.2 31.6 1.0
O A:HOH832 4.2 45.2 1.0
ND2 A:ASN56 4.3 27.6 1.0
NH2 A:ARG54 4.3 28.7 1.0
OE1 A:GLU93 4.4 50.7 1.0
O A:LYS90 4.4 36.6 1.0
CB A:ASP88 4.4 34.0 1.0
OD2 A:ASP88 4.4 38.4 1.0
N A:THR89 4.5 31.1 1.0
CA A:SER58 4.6 43.2 1.0
C A:LYS90 4.6 39.2 1.0
CA A:THR89 4.7 32.6 1.0
CB A:SER220 4.7 33.3 1.0
O A:HOH713 4.7 33.5 1.0
CA A:ASP88 4.8 32.4 1.0
CB A:ASN56 5.0 30.4 1.0

Potassium binding site 2 out of 7 in 8iau

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Potassium binding site 2 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:46.2
occ:1.00
 OD1 B:ASP88 2.6 38.3 1.0
OD1 B:ASN56 2.6 34.9 1.0
O B:THR89 2.6 37.1 1.0
OG B:SER58 2.7 44.6 1.0
O B:HOH819 2.8 44.8 1.0
O B:HOH721 3.1 35.7 1.0
CG B:ASP88 3.5 33.0 1.0
OG B:SER220 3.6 32.7 1.0
CG B:ASN56 3.6 40.8 1.0
C B:THR89 3.7 36.0 1.0
O B:HOH752 3.7 44.6 1.0
CB B:SER58 3.7 38.0 1.0
NZ B:LYS248 3.9 36.3 1.0
ND2 B:ASN56 4.1 36.0 1.0
N B:SER58 4.1 35.6 1.0
O B:ASP88 4.1 29.9 1.0
OD2 B:ASP88 4.2 36.9 1.0
C B:ASP88 4.3 29.5 1.0
CA B:LYS90 4.3 36.2 1.0
NH2 B:ARG54 4.3 35.7 1.0
N B:LYS90 4.3 37.6 1.0
OE1 B:GLU93 4.3 60.3 1.0
CB B:ASP88 4.3 32.5 1.0
O B:LYS90 4.4 33.5 1.0
N B:THR89 4.5 31.3 1.0
CA B:SER58 4.5 41.2 1.0
O B:HOH736 4.7 37.4 1.0
C B:LYS90 4.7 32.5 1.0
CA B:THR89 4.7 33.0 1.0
CB B:SER220 4.8 34.1 1.0
N B:PHE57 4.8 37.5 1.0
CB B:ASN56 4.9 38.9 1.0
CA B:ASP88 4.9 28.3 1.0
CA B:ASN56 5.0 38.5 1.0

Potassium binding site 3 out of 7 in 8iau

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Potassium binding site 3 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:71.8
occ:1.00
 OD1 C:ASP88 2.4 43.7 1.0
OG C:SER58 2.5 54.6 1.0
OD1 C:ASN56 2.5 41.3 1.0
O C:THR89 2.7 45.6 1.0
CG C:ASP88 3.4 47.3 1.0
CG C:ASN56 3.6 43.1 1.0
C C:THR89 3.6 48.1 1.0
CB C:SER58 3.7 59.0 1.0
OG C:SER220 3.7 43.0 1.0
O C:ASP88 3.8 41.9 1.0
NZ C:LYS248 3.9 40.5 1.0
C C:ASP88 4.0 42.5 1.0
O C:HOH784 4.0 62.2 1.0
CB C:ASP88 4.1 40.9 1.0
N C:SER58 4.1 52.9 1.0
NH2 C:ARG54 4.1 45.2 1.0
ND2 C:ASN56 4.1 45.0 1.0
OD2 C:ASP88 4.2 43.4 1.0
N C:THR89 4.3 47.8 1.0
N C:LYS90 4.3 45.5 1.0
CA C:LYS90 4.3 45.3 1.0
CA C:SER58 4.4 58.8 1.0
CA C:ASP88 4.6 43.6 1.0
CA C:THR89 4.6 48.9 1.0
CB C:ASN56 4.7 39.5 1.0
N C:PHE57 4.8 48.1 1.0
CA C:ASN56 4.8 45.6 1.0
O C:LYS90 4.8 40.5 1.0
CB C:SER220 4.9 41.5 1.0
C C:LYS90 5.0 40.6 1.0
C C:PHE57 5.0 53.4 1.0

Potassium binding site 4 out of 7 in 8iau

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Potassium binding site 4 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:65.0
occ:1.00
 O D:THR89 2.6 36.2 1.0
OD1 D:ASP88 2.6 40.0 1.0
OD1 D:ASN56 2.6 37.6 1.0
OG D:SER58 2.7 39.2 1.0
C D:THR89 3.5 42.4 1.0
CG D:ASP88 3.5 42.1 1.0
OG D:SER220 3.5 32.9 1.0
CB D:SER58 3.7 45.8 1.0
CG D:ASN56 3.7 38.2 1.0
O D:ASP88 3.8 31.9 1.0
NZ D:LYS248 3.9 31.4 1.0
C D:ASP88 4.0 29.2 1.0
N D:SER58 4.0 42.9 1.0
N D:LYS90 4.1 38.7 1.0
CA D:LYS90 4.2 38.4 1.0
OD2 D:ASP88 4.2 37.5 1.0
N D:THR89 4.2 30.4 1.0
CB D:ASP88 4.3 30.9 1.0
ND2 D:ASN56 4.3 35.2 1.0
CA D:SER58 4.4 48.5 1.0
O D:LYS90 4.4 34.3 1.0
NH2 D:ARG54 4.4 34.6 1.0
CA D:THR89 4.5 36.8 1.0
C D:LYS90 4.7 37.2 1.0
CB D:SER220 4.7 34.2 1.0
O D:HOH742 4.7 36.5 1.0
CA D:ASP88 4.7 31.8 1.0
N D:PHE57 4.8 38.7 1.0
CB D:ASN56 4.9 38.4 1.0
C D:PHE57 5.0 42.1 1.0
CA D:ASN56 5.0 35.0 1.0

Potassium binding site 5 out of 7 in 8iau

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Potassium binding site 5 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:64.8
occ:1.00
 O F:THR89 2.5 39.4 1.0
OD1 F:ASN56 2.6 40.7 1.0
OG F:SER58 2.8 50.5 1.0
OD1 F:ASP88 2.9 48.2 1.0
O F:HOH793 3.0 58.5 1.0
C F:THR89 3.5 48.9 1.0
OG F:SER220 3.6 38.1 1.0
CG F:ASN56 3.6 43.4 1.0
CB F:SER58 3.7 57.3 1.0
CG F:ASP88 3.7 53.7 1.0
O F:ASP88 3.9 43.3 1.0
NZ F:LYS248 3.9 52.3 1.0
CA F:LYS90 3.9 52.6 1.0
N F:LYS90 4.0 54.9 1.0
O F:HOH745 4.1 57.8 1.0
ND2 F:ASN56 4.1 41.4 1.0
N F:SER58 4.1 53.6 1.0
C F:ASP88 4.2 44.0 1.0
O F:LYS90 4.2 50.3 1.0
NH2 F:ARG54 4.4 38.7 1.0
CB F:ASP88 4.4 45.9 1.0
CA F:SER58 4.5 59.1 1.0
N F:THR89 4.5 46.5 1.0
C F:LYS90 4.5 51.8 1.0
OD2 F:ASP88 4.5 50.3 1.0
CA F:THR89 4.6 44.6 1.0
OE1 F:GLU93 4.7 76.3 1.0
CB F:SER220 4.8 48.7 1.0
N F:PHE57 4.8 48.6 1.0
CB F:ASN56 4.8 43.5 1.0
O F:HOH703 4.9 37.7 1.0
CA F:ASP88 4.9 39.8 1.0
CA F:ASN56 5.0 43.6 1.0

Potassium binding site 6 out of 7 in 8iau

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Potassium binding site 6 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:60.9
occ:1.00
 O G:THR89 2.5 46.4 1.0
OD1 G:ASN56 2.6 42.3 1.0
OD1 G:ASP88 2.7 43.0 1.0
OG G:SER58 2.9 51.1 1.0
O G:HOH725 3.0 53.9 1.0
C G:THR89 3.4 52.0 1.0
CG G:ASP88 3.6 43.6 1.0
OG G:SER220 3.7 42.9 1.0
O G:ASP88 3.8 38.0 1.0
CG G:ASN56 3.8 44.4 1.0
CB G:SER58 3.8 50.2 1.0
C G:ASP88 4.0 38.1 1.0
N G:LYS90 4.0 47.0 1.0
CA G:LYS90 4.0 54.4 1.0
NZ G:LYS248 4.1 37.5 1.0
N G:SER58 4.2 50.0 1.0
CB G:ASP88 4.2 37.7 1.0
N G:THR89 4.3 43.6 1.0
ND2 G:ASN56 4.4 37.9 1.0
NH2 G:ARG54 4.4 40.2 1.0
OD2 G:ASP88 4.4 40.1 1.0
O G:LYS90 4.5 43.1 1.0
CA G:THR89 4.5 46.1 1.0
CA G:SER58 4.6 51.7 1.0
C G:LYS90 4.6 45.6 1.0
CA G:ASP88 4.7 39.2 1.0
N G:PHE57 4.8 40.3 1.0
O G:HOH718 4.8 44.9 1.0
CB G:SER220 4.9 41.3 1.0
CB G:ASN56 4.9 42.0 1.0
CA G:ASN56 4.9 42.1 1.0

Potassium binding site 7 out of 7 in 8iau

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Potassium binding site 7 out of 7 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate 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 Oxalate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K604

b:74.2
occ:1.00
 OG H:SER58 2.3 72.6 1.0
OD1 H:ASN56 2.6 47.8 1.0
O H:THR89 2.7 48.9 1.0
OD1 H:ASP88 3.1 66.2 1.0
CG H:ASP88 3.6 64.7 1.0
CG H:ASN56 3.6 50.2 1.0
CB H:SER58 3.6 75.9 1.0
C H:THR89 3.7 66.3 1.0
OG H:SER220 3.8 51.5 1.0
NZ H:LYS248 3.9 55.5 1.0
O H:ASP88 4.0 59.6 1.0
NH2 H:ARG54 4.1 39.2 1.0
OD2 H:ASP88 4.1 55.1 1.0
ND2 H:ASN56 4.1 57.7 1.0
N H:SER58 4.1 61.8 1.0
C H:ASP88 4.3 56.9 1.0
CB H:ASP88 4.3 60.2 1.0
N H:LYS90 4.4 60.5 1.0
CA H:SER58 4.4 69.7 1.0
CA H:LYS90 4.4 65.0 1.0
N H:THR89 4.6 58.0 1.0
O H:LYS90 4.7 48.3 1.0
CB H:ASN56 4.7 50.1 1.0
CA H:THR89 4.8 60.7 1.0
N H:PHE57 4.8 55.2 1.0
CA H:ASN56 4.9 52.5 1.0
CA H:ASP88 4.9 58.4 1.0
CB H:SER220 4.9 49.0 1.0
C H:LYS90 4.9 57.1 1.0
OE2 H:GLU93 5.0 79.2 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 00:02:10 2024

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