Potassium in PDB 8tbt: Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2

Enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2

All present enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2:
2.7.1.40;

Protein crystallography data

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2, PDB code: 8tbt was solved by L.Jin, A.Padyana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.77 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.354, 174.038, 87.336, 90, 94.29, 90
R / Rfree (%) 19.8 / 25.3

Other elements in 8tbt:

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 (pdb code 8tbt). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2, PDB code: 8tbt:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8tbt

Go back to Potassium Binding Sites List in 8tbt
Potassium binding site 1 out of 4 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:54.6
occ:1.00
 OD1 A:ASP156 2.7 49.1 1.0
O A:HOH757 2.7 53.0 1.0
OD1 A:ASN118 2.8 41.1 1.0
O A:THR157 2.8 44.5 1.0
OG A:SER120 2.8 53.1 1.0
CB A:SER120 3.7 47.4 1.0
CG A:ASP156 3.7 47.5 1.0
OG A:SER286 3.8 40.7 1.0
C A:THR157 3.8 44.8 1.0
O A:ASP156 3.8 39.8 1.0
CG A:ASN118 3.8 43.0 1.0
NZ A:LYS313 3.9 46.6 1.0
N A:SER120 4.0 41.8 1.0
CA A:LYS158 4.2 48.9 1.0
C A:ASP156 4.3 39.4 1.0
NH2 A:ARG116 4.3 46.3 1.0
CA A:SER120 4.4 51.0 1.0
N A:LYS158 4.4 45.0 1.0
CB A:ASP156 4.4 45.0 1.0
O A:LYS158 4.4 49.1 1.0
ND2 A:ASN118 4.5 45.3 1.0
O A:HOH710 4.5 56.2 1.0
OD2 A:ASP156 4.5 50.5 1.0
OE2 A:GLU161 4.5 59.2 1.0
N A:THR157 4.7 43.4 1.0
N A:PHE119 4.7 40.3 1.0
C A:LYS158 4.7 47.0 1.0
CA A:THR157 4.9 44.2 1.0
C A:PHE119 4.9 43.6 1.0
CA A:ASN118 5.0 41.4 1.0
CA A:ASP156 5.0 41.0 1.0
CB A:ASN118 5.0 40.2 1.0

Potassium binding site 2 out of 4 in 8tbt

Go back to Potassium Binding Sites List in 8tbt
Potassium binding site 2 out of 4 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:55.0
occ:1.00
 OD1 B:ASP156 2.6 50.5 1.0
O B:HOH745 2.6 60.4 1.0
O B:THR157 2.7 55.6 1.0
OG B:SER120 2.8 54.5 1.0
OD1 B:ASN118 2.9 51.7 1.0
C B:THR157 3.6 55.4 1.0
CG B:ASP156 3.6 52.5 1.0
O B:ASP156 3.7 52.5 1.0
CG B:ASN118 3.8 46.7 1.0
CB B:SER120 3.9 50.6 1.0
OG B:SER286 3.9 50.6 1.0
CA B:LYS158 4.0 51.9 1.0
NZ B:LYS313 4.1 60.7 1.0
C B:ASP156 4.1 49.0 1.0
N B:SER120 4.1 51.7 1.0
N B:LYS158 4.2 54.9 1.0
CB B:ASP156 4.3 46.7 1.0
ND2 B:ASN118 4.3 47.2 1.0
O B:LYS158 4.4 57.4 1.0
OE2 B:GLU161 4.4 64.0 1.0
NH2 B:ARG116 4.4 49.2 1.0
OD2 B:ASP156 4.4 55.6 1.0
N B:THR157 4.4 48.5 1.0
CA B:SER120 4.6 51.8 1.0
CA B:THR157 4.6 51.3 1.0
C B:LYS158 4.6 54.9 1.0
O B:HOH709 4.6 161.0 1.0
N B:PHE119 4.8 49.4 1.0
CA B:ASP156 4.8 47.4 1.0
O B:HOH777 4.9 58.5 1.0
CA B:ASN118 4.9 44.7 1.0
CB B:ASN118 4.9 45.0 1.0
CB B:SER286 5.0 51.0 1.0

Potassium binding site 3 out of 4 in 8tbt

Go back to Potassium Binding Sites List in 8tbt
Potassium binding site 3 out of 4 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:74.0
occ:1.00
 O C:THR157 2.8 65.8 1.0
OD1 C:ASP156 2.9 62.9 1.0
OG C:SER120 2.9 71.9 1.0
OD1 C:ASN118 3.1 65.1 1.0
OG C:SER286 3.6 61.4 1.0
C C:THR157 3.7 66.3 1.0
CG C:ASP156 3.8 55.8 1.0
NZ C:LYS313 3.9 59.6 1.0
CB C:SER120 3.9 66.1 1.0
OE2 C:GLU161 4.0 74.9 1.0
O C:ASP156 4.0 62.9 1.0
CA C:LYS158 4.1 73.5 1.0
CG C:ASN118 4.2 62.7 1.0
N C:LYS158 4.3 72.9 1.0
O C:LYS158 4.3 66.5 1.0
C C:ASP156 4.3 61.6 1.0
N C:SER120 4.5 64.1 1.0
CB C:ASP156 4.5 55.7 1.0
C C:LYS158 4.6 69.5 1.0
NH2 C:ARG116 4.6 59.1 1.0
OD2 C:ASP156 4.6 66.2 1.0
N C:THR157 4.6 66.0 1.0
ND2 C:ASN118 4.7 61.8 1.0
CA C:SER120 4.7 69.0 1.0
CB C:SER286 4.7 55.3 1.0
CA C:THR157 4.8 65.2 1.0
O3 C:PYR602 4.9 61.0 1.0

Potassium binding site 4 out of 4 in 8tbt

Go back to Potassium Binding Sites List in 8tbt
Potassium binding site 4 out of 4 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K605

b:51.9
occ:1.00
 OD1 D:ASP156 2.6 39.2 1.0
OD1 D:ASN118 2.7 39.8 1.0
OG D:SER120 2.7 49.3 1.0
O D:THR157 2.8 33.7 1.0
O D:HOH770 2.9 47.2 1.0
CG D:ASP156 3.6 44.8 1.0
C D:THR157 3.7 38.6 1.0
O D:ASP156 3.8 34.6 1.0
CG D:ASN118 3.9 43.3 1.0
CB D:SER120 3.9 45.3 1.0
OG D:SER286 3.9 37.4 1.0
NZ D:LYS313 3.9 39.9 1.0
N D:SER120 4.0 44.1 1.0
C D:ASP156 4.1 36.4 1.0
CA D:LYS158 4.2 36.7 1.0
NH2 D:ARG116 4.3 38.7 1.0
CB D:ASP156 4.3 38.2 1.0
N D:LYS158 4.3 40.7 1.0
O D:LYS158 4.4 42.5 1.0
CA D:SER120 4.5 43.5 1.0
N D:THR157 4.5 35.3 1.0
N D:PHE119 4.5 37.5 1.0
OD2 D:ASP156 4.5 43.2 1.0
ND2 D:ASN118 4.6 42.1 1.0
C D:LYS158 4.7 43.6 1.0
CA D:THR157 4.7 36.5 1.0
CA D:ASP156 4.8 35.9 1.0
OE2 D:GLU161 4.8 55.5 1.0
C D:PHE119 4.9 40.7 1.0
CA D:ASN118 4.9 37.5 1.0
CB D:ASN118 4.9 36.3 1.0
C D:ASN118 4.9 38.7 1.0
O3 D:PYR603 5.0 46.1 1.0

Reference:

T.Liu, A.K.Padyana, E.T.Judd, L.Jin, D.Hammoudeh, C.Kung, L.Dang. Structure-Based Design of Ag-946, A Pyruvate Kinase Activator. Chemmedchem 00559 2023.
ISSN: ESSN 1860-7187
PubMed: 38109501
DOI: 10.1002/CMDC.202300559
Page generated: Tue Aug 13 00:55:01 2024

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