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Potassium in PDB 8tbs: Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946

Enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946

All present enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946:
2.7.1.40;

Protein crystallography data

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946, PDB code: 8tbs 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) 29.44 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.32, 122.596, 378.458, 90, 90, 90
R / Rfree (%) 19.3 / 23.4

Other elements in 8tbs:

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946 also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946 (pdb code 8tbs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946, PDB code: 8tbs:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 8tbs

Go back to Potassium Binding Sites List in 8tbs
Potassium binding site 1 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:90.1
occ:1.00
 OG A:SER120 2.7 63.5 1.0
OD1 A:ASN118 2.8 56.3 1.0
OD1 A:ASP156 2.9 75.9 1.0
O A:THR157 2.9 57.7 1.0
O A:HOH730 3.2 60.1 1.0
OG A:SER286 3.8 52.2 1.0
CG A:ASP156 3.8 67.6 1.0
CB A:SER120 3.8 59.3 1.0
CG A:ASN118 3.9 50.0 1.0
NZ A:LYS313 4.0 57.2 1.0
C A:THR157 4.0 55.5 1.0
O A:LYS158 4.3 69.3 1.0
NH2 A:ARG116 4.3 51.7 1.0
CA A:LYS158 4.3 56.0 1.0
O A:ASP156 4.3 49.4 1.0
ND2 A:ASN118 4.4 52.0 1.0
N A:SER120 4.4 50.6 1.0
OD2 A:ASP156 4.6 73.7 1.0
O3 A:PYR604 4.6 65.2 1.0
CB A:ASP156 4.6 45.3 1.0
C A:LYS158 4.6 63.4 1.0
N A:LYS158 4.6 54.9 1.0
C A:ASP156 4.6 47.5 1.0
CA A:SER120 4.7 58.4 1.0
OE2 A:GLU161 4.8 103.9 1.0
CE A:LYS313 4.9 53.1 1.0
N A:THR157 5.0 54.7 1.0

Potassium binding site 2 out of 6 in 8tbs

Go back to Potassium Binding Sites List in 8tbs
Potassium binding site 2 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:98.9
occ:1.00
 OG B:SER120 3.0 76.8 1.0
OD1 B:ASN118 3.1 57.3 1.0
O B:THR157 3.2 56.0 1.0
O B:HOH713 3.4 65.2 1.0
OD2 B:ASP156 3.4 75.0 1.0
O B:HOH723 3.5 79.2 1.0
OG B:SER286 3.7 61.0 1.0
O B:HOH704 3.7 74.5 1.0
NZ B:LYS313 3.9 65.7 1.0
CG B:ASP156 3.9 66.0 1.0
CG B:ASN118 4.0 58.8 1.0
NH2 B:ARG116 4.1 63.3 1.0
OD1 B:ASP156 4.2 79.2 1.0
C B:THR157 4.3 59.7 1.0
CB B:SER120 4.3 68.1 1.0
ND2 B:ASN118 4.3 60.8 1.0
O B:LYS158 4.3 70.0 1.0
OE2 B:GLU161 4.5 101.2 1.0
CA B:LYS158 4.7 62.6 1.0
CB B:ASP156 4.7 53.9 1.0
O B:PYR605 4.7 77.5 1.0
CE B:LYS313 4.8 60.2 1.0
C B:LYS158 4.9 67.2 1.0
CB B:SER286 4.9 61.5 1.0
O B:HOH759 4.9 56.8 1.0
MN B:MN603 4.9 87.5 1.0
O B:ASP156 4.9 52.8 1.0
N B:LYS158 4.9 59.5 1.0
C B:ASP156 5.0 51.6 1.0

Potassium binding site 3 out of 6 in 8tbs

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Potassium binding site 3 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:103.0
occ:1.00
 OG C:SER120 3.0 68.0 1.0
OD1 C:ASN118 3.0 54.2 1.0
O C:HOH713 3.1 71.1 1.0
O C:THR157 3.1 63.0 1.0
OD1 C:ASP156 3.3 64.8 1.0
NZ C:LYS313 3.5 55.1 1.0
OG C:SER286 3.7 65.2 1.0
CG C:ASP156 3.8 62.3 1.0
CG C:ASN118 4.0 60.2 1.0
NH2 C:ARG116 4.1 55.7 1.0
CB C:SER120 4.1 62.6 1.0
C C:THR157 4.2 61.2 1.0
OD2 C:ASP156 4.2 71.6 1.0
OXT C:PYR604 4.4 72.9 1.0
CB C:ASP156 4.5 57.1 1.0
O C:HOH709 4.5 58.1 1.0
ND2 C:ASN118 4.5 64.4 1.0
O C:LYS158 4.5 59.9 1.0
O C:ASP156 4.6 53.4 1.0
OE2 C:GLU161 4.6 98.0 1.0
C C:ASP156 4.7 52.1 1.0
CA C:LYS158 4.7 68.2 1.0
N C:SER120 4.7 67.1 1.0
CB C:SER286 4.9 45.4 1.0
N C:LYS158 4.9 60.0 1.0
N C:THR157 5.0 46.5 1.0
C C:LYS158 5.0 68.5 1.0
CA C:SER120 5.0 62.4 1.0
CE C:LYS313 5.0 48.9 1.0

Potassium binding site 4 out of 6 in 8tbs

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Potassium binding site 4 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K603

b:140.9
occ:1.00
 OG E:SER120 3.0 79.3 1.0
O E:HOH732 3.6 76.4 1.0
NZ E:LYS313 3.6 72.5 1.0
O E:THR157 3.6 69.6 1.0
O3 E:PYR604 3.7 84.5 1.0
OD1 E:ASN118 3.7 82.1 1.0
MN E:MN602 3.9 93.0 1.0
OG E:SER286 4.0 66.4 1.0
OD2 E:ASP156 4.1 93.5 1.0
O E:LYS158 4.2 71.5 1.0
CB E:SER120 4.3 73.1 1.0
NH2 E:ARG116 4.4 71.8 1.0
CG E:ASN118 4.6 72.3 1.0
CG E:ASP156 4.6 76.6 1.0
CA E:LYS158 4.6 64.9 1.0
C E:THR157 4.7 77.3 1.0
ND2 E:ASN118 4.7 77.7 1.0
C E:LYS158 4.8 68.9 1.0
CE E:LYS313 4.9 69.8 1.0
CB E:SER286 4.9 73.9 1.0
CA E:PYR604 4.9 77.4 1.0
OD1 E:ASP156 5.0 85.8 1.0

Potassium binding site 5 out of 6 in 8tbs

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Potassium binding site 5 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:107.6
occ:1.00
 OD1 F:ASN118 2.9 49.2 1.0
OG F:SER120 3.0 52.4 1.0
OD1 F:ASP156 3.2 54.9 1.0
O F:THR157 3.3 41.6 1.0
NZ F:LYS313 3.8 51.5 1.0
CG F:ASP156 3.8 54.7 1.0
CG F:ASN118 3.9 50.1 1.0
CB F:SER120 3.9 47.0 1.0
O F:HOH768 3.9 67.4 1.0
NH2 F:ARG116 4.0 51.5 1.0
O3 F:PYR605 4.0 90.5 1.0
OG F:SER286 4.1 51.1 1.0
C F:THR157 4.2 42.0 1.0
ND2 F:ASN118 4.3 47.0 1.0
CB F:ASP156 4.4 41.8 1.0
O F:ASP156 4.4 42.6 1.0
N F:SER120 4.5 46.5 1.0
OD2 F:ASP156 4.5 64.7 1.0
C F:ASP156 4.6 41.8 1.0
O F:LYS158 4.7 49.0 1.0
CA F:LYS158 4.7 45.5 1.0
CA F:SER120 4.7 54.9 1.0
O F:HOH750 4.7 57.4 1.0
N F:LYS158 4.9 50.6 1.0
N F:THR157 4.9 41.4 1.0

Potassium binding site 6 out of 6 in 8tbs

Go back to Potassium Binding Sites List in 8tbs
Potassium binding site 6 out of 6 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K603

b:119.6
occ:1.00
 OG G:SER120 3.2 86.9 1.0
O G:HOH727 3.5 70.9 1.0
O G:THR157 3.5 74.3 1.0
NZ G:LYS313 3.5 70.7 1.0
O G:LYS158 3.6 78.2 1.0
OG G:SER286 3.7 71.6 1.0
O G:HOH729 3.9 73.2 1.0
O3 G:PYR604 3.9 78.8 1.0
MN G:MN602 3.9 133.7 1.0
OD1 G:ASP156 3.9 85.9 1.0
OD1 G:ASN118 4.0 77.0 1.0
C G:LYS158 4.3 78.5 1.0
CA G:LYS158 4.4 79.2 1.0
CB G:SER120 4.4 86.1 1.0
OE2 G:GLU161 4.5 109.7 1.0
CB G:SER286 4.5 71.8 1.0
C G:THR157 4.6 79.4 1.0
CE G:LYS313 4.7 68.6 1.0
CG G:ASN118 4.9 71.2 1.0
CG G:ASP156 4.9 87.9 1.0
N G:LYS158 5.0 85.5 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 00:54:49 2024

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