Atomistry » Potassium » PDB 8vj8-9bz1 » 8zly
Atomistry »
  Potassium »
    PDB 8vj8-9bz1 »
      8zly »

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

Go back to Potassium Binding Sites List in 8zly
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy