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

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp, PDB code: 8zly 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) 48.16 / 1.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.809, 403.204, 113.593, 90, 90, 90
R / Rfree (%) 16.5 / 20.5

Other elements in 8zly:

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

Magnesium (Mg) 15 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 and Udp (pdb code 8zly). 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 Oxalate and Fructose 1,6-Bisphosphate and Udp, PDB code: 8zly:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 1 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:41.7
occ:1.00
 OD1 A:ASP88 2.7 41.5 1.0
OD1 A:ASN56 2.7 32.0 1.0
O A:THR89 2.7 30.7 1.0
OG A:SER58 2.8 29.6 1.0
O A:HOH946 2.8 41.1 1.0
O A:HOH815 2.8 32.5 1.0
OG A:SER220 3.5 32.0 1.0
C A:THR89 3.6 33.9 1.0
CG A:ASP88 3.6 35.7 1.0
CG A:ASN56 3.7 32.5 1.0
CB A:SER58 3.8 30.9 1.0
O A:ASP88 3.9 31.1 1.0
ND2 A:ASN56 4.1 30.7 1.0
NZ A:LYS248 4.1 35.3 1.0
C A:ASP88 4.2 33.1 1.0
N A:LYS90 4.2 37.2 1.0
N A:SER58 4.2 32.9 1.0
CA A:LYS90 4.2 36.9 1.0
OD2 A:ASP88 4.4 38.0 1.0
CB A:ASP88 4.4 31.7 1.0
N A:THR89 4.4 30.6 1.0
NH2 A:ARG95 4.5 35.4 1.0
CA A:SER58 4.6 31.4 1.0
NH2 A:ARG54 4.6 29.4 1.0
O A:LYS90 4.6 36.1 1.0
CA A:THR89 4.6 33.9 1.0
OE2 A:GLU93 4.7 34.3 1.0
O A:HOH832 4.7 30.4 1.0
CB A:SER220 4.7 30.3 1.0
O1B A:UDP604 4.7 34.4 1.0
OE1 A:GLU93 4.8 37.2 1.0
C A:LYS90 4.8 32.9 1.0
CB A:ASN56 4.9 29.6 1.0
N A:PHE57 4.9 32.6 1.0
CA A:ASP88 4.9 29.7 1.0
CA A:ASN56 4.9 33.1 1.0

Potassium binding site 2 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 2 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:52.7
occ:1.00
 O B:HOH913 2.3 55.1 1.0
OD1 B:ASP88 2.6 42.5 1.0
OD1 B:ASN56 2.7 36.1 1.0
O B:HOH924 2.7 54.4 1.0
O B:THR89 2.8 36.2 1.0
OG B:SER58 2.9 42.3 1.0
CG B:ASN56 3.5 34.1 1.0
OG B:SER220 3.6 33.3 1.0
CG B:ASP88 3.7 39.5 1.0
C B:THR89 3.7 41.3 1.0
CB B:SER58 3.9 45.6 1.0
ND2 B:ASN56 3.9 33.2 1.0
NZ B:LYS248 4.1 36.9 1.0
O B:ASP88 4.2 32.6 1.0
C B:ASP88 4.3 39.0 1.0
N B:SER58 4.3 35.9 1.0
NH2 B:ARG54 4.3 33.4 1.0
CA B:LYS90 4.3 48.4 1.0
N B:LYS90 4.3 48.2 1.0
O1B B:UDP604 4.4 52.8 1.0
CB B:ASP88 4.4 35.1 1.0
OD2 B:ASP88 4.5 43.9 1.0
N B:THR89 4.5 36.8 1.0
NH2 B:ARG95 4.5 59.7 1.0
O B:LYS90 4.6 42.5 1.0
CA B:SER58 4.7 41.4 1.0
O B:HOH813 4.7 40.0 1.0
CB B:ASN56 4.7 34.5 1.0
CA B:THR89 4.8 38.5 1.0
CB B:SER220 4.8 35.1 1.0
C B:LYS90 4.8 43.6 1.0
N B:PHE57 4.9 37.5 1.0
CA B:ASP88 4.9 31.8 1.0
O B:HOH927 5.0 56.9 1.0
OE1 B:GLU93 5.0 72.5 1.0
CA B:ASN56 5.0 33.2 1.0

Potassium binding site 3 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 3 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K605

b:37.0
occ:1.00
 OD1 C:ASP88 2.6 29.9 1.0
OD1 C:ASN56 2.6 24.9 1.0
O C:THR89 2.7 23.2 1.0
OG C:SER58 2.8 24.8 1.0
O C:HOH915 3.1 36.6 1.0
O C:HOH762 3.2 33.1 1.0
CG C:ASP88 3.6 27.4 1.0
CG C:ASN56 3.6 23.8 1.0
OG C:SER220 3.6 23.5 1.0
C C:THR89 3.6 27.0 1.0
CB C:SER58 3.7 25.9 1.0
O C:ASP88 3.9 28.8 1.0
ND2 C:ASN56 4.1 25.3 1.0
C C:ASP88 4.1 26.2 1.0
N C:SER58 4.1 25.8 1.0
N C:LYS90 4.2 27.2 1.0
NZ C:LYS248 4.3 30.8 1.0
CA C:LYS90 4.3 29.4 1.0
OD2 C:ASP88 4.3 29.2 1.0
CB C:ASP88 4.4 24.9 1.0
NH2 C:ARG95 4.4 26.4 1.0
N C:THR89 4.4 25.2 1.0
CA C:SER58 4.5 26.7 1.0
NH2 C:ARG54 4.6 26.1 1.0
CA C:THR89 4.6 26.9 1.0
CB C:SER220 4.7 22.9 1.0
O C:LYS90 4.7 28.7 1.0
O1B C:UDP604 4.7 30.9 1.0
N C:PHE57 4.8 26.5 1.0
OE1 C:GLU93 4.8 28.6 1.0
CB C:ASN56 4.8 23.1 1.0
OE2 C:GLU93 4.8 32.2 1.0
CA C:ASP88 4.8 25.4 1.0
O C:HOH758 4.8 24.8 1.0
C C:LYS90 4.9 27.0 1.0
CA C:ASN56 4.9 25.2 1.0

Potassium binding site 4 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 4 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K605

b:42.6
occ:1.00
 OD1 D:ASP88 2.7 33.5 1.0
O D:HOH954 2.7 46.5 1.0
OD1 D:ASN56 2.7 29.0 1.0
O D:HOH777 2.7 33.8 1.0
O D:THR89 2.7 30.9 1.0
OG D:SER58 2.8 32.6 1.0
OG D:SER220 3.6 29.4 1.0
CG D:ASN56 3.6 26.0 1.0
CB D:SER58 3.7 32.5 1.0
C D:THR89 3.7 31.9 1.0
CG D:ASP88 3.7 33.0 1.0
ND2 D:ASN56 4.0 27.4 1.0
NZ D:LYS248 4.1 31.3 1.0
O D:ASP88 4.1 28.4 1.0
NH2 D:ARG95 4.2 45.1 1.0
CA D:LYS90 4.3 37.7 1.0
N D:LYS90 4.3 35.7 1.0
N D:SER58 4.3 28.8 1.0
C D:ASP88 4.3 29.4 1.0
NH2 D:ARG54 4.4 28.6 1.0
O2B D:UDP604 4.5 43.6 1.0
O D:LYS90 4.5 36.1 1.0
OD2 D:ASP88 4.5 31.7 1.0
CB D:ASP88 4.5 26.2 1.0
CA D:SER58 4.6 31.7 1.0
N D:THR89 4.6 27.8 1.0
O D:HOH760 4.6 30.2 1.0
OE2 D:GLU93 4.6 54.9 1.0
CB D:SER220 4.7 29.7 1.0
C D:LYS90 4.7 37.3 1.0
CA D:THR89 4.8 28.9 1.0
OE1 D:GLU93 4.8 54.7 1.0
CB D:ASN56 4.9 24.1 1.0
O D:HOH870 4.9 50.4 1.0
CZ D:ARG95 5.0 51.1 1.0
N D:PHE57 5.0 26.4 1.0

Potassium binding site 5 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 5 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K605

b:45.3
occ:1.00
 OD1 E:ASP88 2.6 35.5 1.0
OD1 E:ASN56 2.6 29.1 1.0
O E:THR89 2.7 28.0 1.0
OG E:SER58 2.7 29.4 1.0
O E:HOH922 2.9 36.8 1.0
O E:HOH728 3.3 47.1 1.0
OG E:SER220 3.6 31.3 1.0
C E:THR89 3.6 34.8 1.0
CG E:ASN56 3.6 26.5 1.0
CB E:SER58 3.6 32.2 1.0
CG E:ASP88 3.7 34.9 1.0
O E:ASP88 3.8 32.4 1.0
C E:ASP88 4.1 28.9 1.0
ND2 E:ASN56 4.1 26.4 1.0
N E:SER58 4.1 37.3 1.0
N E:LYS90 4.2 35.0 1.0
CA E:LYS90 4.2 35.0 1.0
NZ E:LYS248 4.2 33.0 1.0
NH2 E:ARG95 4.4 32.4 1.0
N E:THR89 4.4 29.7 1.0
CB E:ASP88 4.5 28.1 1.0
CA E:SER58 4.5 34.0 1.0
O E:LYS90 4.5 32.0 1.0
OD2 E:ASP88 4.6 34.6 1.0
CA E:THR89 4.6 33.2 1.0
CB E:SER220 4.7 29.9 1.0
O E:HOH852 4.7 28.1 1.0
NH2 E:ARG54 4.7 32.5 1.0
OE1 E:GLU93 4.7 36.5 1.0
OE2 E:GLU93 4.8 36.6 1.0
N E:PHE57 4.8 31.4 1.0
C E:LYS90 4.8 32.3 1.0
CB E:ASN56 4.8 29.7 1.0
O3B E:UDP604 4.8 30.2 1.0
CA E:ASP88 4.9 29.5 1.0
CA E:ASN56 4.9 30.1 1.0

Potassium binding site 6 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 6 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K605

b:44.4
occ:1.00
 O F:THR89 2.7 37.1 1.0
O F:HOH885 2.7 36.0 1.0
OG F:SER58 2.8 31.5 1.0
OD1 F:ASN56 2.8 31.0 1.0
OD1 F:ASP88 2.8 37.2 1.0
O F:HOH906 2.9 42.8 1.0
C F:THR89 3.6 37.0 1.0
OG F:SER220 3.6 32.4 1.0
CG F:ASN56 3.7 27.4 1.0
CB F:SER58 3.7 34.1 1.0
CG F:ASP88 3.7 32.4 1.0
O F:ASP88 3.9 33.6 1.0
ND2 F:ASN56 4.1 29.2 1.0
N F:SER58 4.2 34.0 1.0
C F:ASP88 4.2 33.2 1.0
CA F:LYS90 4.2 39.8 1.0
N F:LYS90 4.2 39.8 1.0
NZ F:LYS248 4.2 32.0 1.0
NH2 F:ARG95 4.2 45.0 1.0
N F:THR89 4.4 34.6 1.0
CB F:ASP88 4.5 28.8 1.0
NH2 F:ARG54 4.5 33.2 1.0
CA F:SER58 4.5 34.5 1.0
O F:LYS90 4.5 36.8 1.0
OD2 F:ASP88 4.6 34.7 1.0
CA F:THR89 4.6 36.5 1.0
OE1 F:GLU93 4.7 42.9 1.0
CB F:SER220 4.7 31.7 1.0
C F:LYS90 4.8 37.7 1.0
O2B F:UDP604 4.8 40.8 1.0
O F:HOH841 4.8 30.8 1.0
N F:PHE57 4.8 34.0 1.0
OE2 F:GLU93 4.8 44.7 1.0
CB F:ASN56 4.9 29.5 1.0
CA F:ASP88 4.9 27.4 1.0
CA F:ASN56 5.0 31.0 1.0

Potassium binding site 7 out of 8 in 8zly

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


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 and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K605

b:40.0
occ:1.00
 OD1 G:ASP88 2.6 33.1 1.0
O G:THR89 2.6 26.4 1.0
OD1 G:ASN56 2.7 29.8 1.0
OG G:SER58 2.7 28.1 1.0
O G:HOH1032 2.8 38.8 1.0
O G:HOH913 2.9 36.2 1.0
OG G:SER220 3.6 29.8 1.0
C G:THR89 3.6 30.5 1.0
CG G:ASN56 3.6 27.6 1.0
CB G:SER58 3.7 28.4 1.0
CG G:ASP88 3.7 30.6 1.0
O G:ASP88 3.9 28.4 1.0
ND2 G:ASN56 4.1 25.3 1.0
C G:ASP88 4.1 27.9 1.0
CA G:LYS90 4.2 29.8 1.0
N G:LYS90 4.2 30.2 1.0
N G:SER58 4.2 27.6 1.0
NZ G:LYS248 4.2 32.1 1.0
NH2 G:ARG95 4.4 32.7 1.0
N G:THR89 4.4 27.1 1.0
CB G:ASP88 4.5 28.1 1.0
OD2 G:ASP88 4.5 30.9 1.0
CA G:SER58 4.5 27.1 1.0
O G:LYS90 4.6 29.4 1.0
CA G:THR89 4.6 30.4 1.0
CB G:SER220 4.7 28.9 1.0
O2B G:UDP604 4.7 32.6 1.0
NH2 G:ARG54 4.8 31.4 1.0
C G:LYS90 4.8 29.9 1.0
O G:HOH742 4.8 29.3 1.0
OE2 G:GLU93 4.8 35.5 1.0
OE1 G:GLU93 4.8 35.2 1.0
CB G:ASN56 4.8 24.1 1.0
N G:PHE57 4.9 27.2 1.0
CA G:ASP88 4.9 28.3 1.0
CA G:ASN56 5.0 26.3 1.0

Potassium binding site 8 out of 8 in 8zly

Go back to Potassium Binding Sites List in 8zly
Potassium binding site 8 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Oxalate and Fructose 1,6-Bisphosphate and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K603

b:44.0
occ:1.00
 OD1 H:ASP88 2.5 36.6 1.0
O H:THR89 2.6 33.8 1.0
OD1 H:ASN56 2.7 31.5 1.0
OG H:SER58 2.8 39.4 1.0
O H:HOH1002 2.8 48.4 1.0
O H:HOH799 2.8 35.9 1.0
C H:THR89 3.5 39.1 1.0
OG H:SER220 3.6 31.9 1.0
CG H:ASP88 3.6 32.8 1.0
CG H:ASN56 3.6 30.6 1.0
CB H:SER58 3.8 43.1 1.0
O H:ASP88 3.9 30.0 1.0
NZ H:LYS248 4.0 38.7 1.0
CA H:LYS90 4.1 45.1 1.0
N H:LYS90 4.1 41.8 1.0
ND2 H:ASN56 4.1 30.3 1.0
C H:ASP88 4.2 32.3 1.0
N H:SER58 4.2 36.9 1.0
NH2 H:ARG54 4.2 33.4 1.0
O H:LYS90 4.3 44.7 1.0
OD2 H:ASP88 4.4 32.0 1.0
N H:THR89 4.4 32.2 1.0
CB H:ASP88 4.4 29.2 1.0
O H:HOH939 4.5 44.9 1.0
C H:LYS90 4.6 41.9 1.0
CA H:SER58 4.6 39.8 1.0
O H:HOH771 4.6 36.0 1.0
CA H:THR89 4.6 33.7 1.0
CB H:SER220 4.7 32.0 1.0
CB H:ASN56 4.8 30.4 1.0
OE1 H:GLU93 4.8 59.7 1.0
N H:PHE57 4.9 34.2 1.0
CA H:ASP88 4.9 30.7 1.0
CA H:ASN56 5.0 29.8 1.0

Reference:

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
Page generated: Tue Aug 13 01:20:46 2024

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