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Manganese in PDB 8tbu: Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12

Enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12

All present enzymatic activity of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12:
2.7.1.40;

Protein crystallography data

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12, PDB code: 8tbu 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) 49.88 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.323, 122.845, 378.582, 90, 90, 90
R / Rfree (%) 20.2 / 24.6

Other elements in 8tbu:

The structure of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 (pdb code 8tbu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12, PDB code: 8tbu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8tbu

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Manganese binding site 1 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:90.3
occ:1.00
 OD2 A:ASP339 1.9 96.6 1.0
OE2 A:GLU315 2.4 63.0 1.0
O A:HOH852 2.6 64.3 1.0
O A:PYR602 3.1 63.3 1.0
CG A:ASP339 3.1 84.7 1.0
O3 A:PYR602 3.2 72.2 1.0
CD A:GLU315 3.2 59.8 1.0
OE1 A:GLU315 3.4 59.5 1.0
C A:PYR602 4.0 65.8 1.0
CB A:ASP339 4.0 66.1 1.0
OD1 A:ASP339 4.0 92.3 1.0
CA A:PYR602 4.0 69.7 1.0
CE1 A:PHE287 4.2 62.9 1.0
CD1 A:PHE287 4.3 60.8 1.0
NZ A:LYS313 4.3 39.3 1.0
CG A:GLU315 4.6 53.9 1.0
OG A:SER286 4.8 36.0 1.0
CE A:LYS313 4.9 42.8 1.0

Manganese binding site 2 out of 8 in 8tbu

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Manganese binding site 2 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:73.5
occ:1.00
 OE2 B:GLU315 2.1 83.3 1.0
OD2 B:ASP339 2.3 64.9 1.0
O B:PYR601 2.6 63.2 1.0
O3 B:PYR601 2.6 82.2 1.0
O B:HOH865 3.0 56.3 1.0
CD B:GLU315 3.1 72.0 1.0
CG B:ASP339 3.3 62.4 1.0
C B:PYR601 3.4 68.7 1.0
CA B:PYR601 3.4 75.1 1.0
OE1 B:GLU315 3.4 78.1 1.0
CB B:ASP339 3.8 56.5 1.0
NZ B:LYS313 4.1 54.3 1.0
CE1 B:PHE287 4.4 55.8 1.0
OD1 B:ASP339 4.4 64.2 1.0
CG B:GLU315 4.4 58.5 1.0
OXT B:PYR601 4.6 64.2 1.0
CE B:LYS313 4.7 55.4 1.0
CD1 B:PHE287 4.7 55.8 1.0
N B:ASP339 4.7 42.6 1.0
CB B:PYR601 4.8 72.3 1.0
CB B:GLU315 4.9 50.8 1.0
CA B:ASP339 4.9 47.7 1.0
CB B:ALA336 5.0 43.9 1.0
O B:HOH830 5.0 61.9 1.0

Manganese binding site 3 out of 8 in 8tbu

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Manganese binding site 3 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn603

b:61.8
occ:1.00
 OE1 C:GLU315 2.1 71.7 1.0
OD2 C:ASP339 2.4 57.3 1.0
OXT C:PYR601 2.4 67.7 1.0
O3 C:PYR601 2.6 86.8 1.0
O C:HOH851 3.0 61.2 1.0
C C:PYR601 3.1 70.5 1.0
CD C:GLU315 3.1 64.2 1.0
CA C:PYR601 3.1 77.8 1.0
CG C:ASP339 3.4 54.4 1.0
OE2 C:GLU315 3.5 67.7 1.0
O C:HOH837 3.5 69.2 1.0
CB C:ASP339 3.7 49.0 1.0
O C:HOH704 4.0 75.8 1.0
NZ C:LYS313 4.2 47.9 1.0
O C:PYR601 4.3 67.0 1.0
CE1 C:PHE287 4.4 66.3 1.0
N C:ASP339 4.4 41.0 1.0
CB C:PYR601 4.5 76.3 1.0
CG C:GLU315 4.5 53.4 1.0
OD1 C:ASP339 4.5 57.6 1.0
CE C:LYS313 4.6 47.9 1.0
CB C:ALA336 4.6 43.6 1.0
O C:HOH852 4.7 82.7 1.0
CA C:ASP339 4.7 45.6 1.0
CB C:GLU315 4.9 46.8 1.0
CD1 C:PHE287 5.0 64.4 1.0

Manganese binding site 4 out of 8 in 8tbu

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Manganese binding site 4 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn603

b:83.8
occ:1.00
 O D:HOH767 2.4 72.7 1.0
O D:HOH780 2.6 77.9 1.0
O D:HOH907 2.6 79.1 1.0
OD2 D:ASP339 2.6 66.0 1.0
OD1 D:ASP339 2.8 63.9 1.0
OE2 D:GLU315 2.8 50.7 1.0
CG D:ASP339 2.9 62.0 1.0
O D:HOH878 3.6 57.8 1.0
CD D:GLU315 3.8 45.9 1.0
O D:HOH830 3.8 71.5 1.0
O D:HOH788 4.0 77.8 1.0
OE1 D:GLU315 4.0 45.4 1.0
CB D:ASP339 4.1 52.0 1.0
O D:HOH822 4.3 59.3 1.0

Manganese binding site 5 out of 8 in 8tbu

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Manganese binding site 5 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn603

b:123.6
occ:1.00
 OD2 E:ASP339 2.3 106.7 1.0
O E:PYR601 2.4 101.7 1.0
OE2 E:GLU315 2.4 93.8 1.0
CE2 E:PHE287 2.8 92.8 1.0
OXT E:PYR601 2.8 99.9 1.0
CG E:ASP339 2.8 101.2 1.0
C E:PYR601 2.9 101.6 1.0
CD E:GLU315 3.1 94.0 1.0
OE1 E:GLU315 3.1 96.0 1.0
OD1 E:ASP339 3.2 104.7 1.0
CZ E:PHE287 3.3 92.7 1.0
CD2 E:PHE287 3.5 94.1 1.0
CB E:ASP339 3.9 92.7 1.0
CA E:PYR601 4.3 102.2 1.0
CE1 E:PHE287 4.4 94.8 1.0
O E:HOH752 4.4 70.7 1.0
NZ E:LYS313 4.4 76.0 1.0
CG E:GLU315 4.5 89.7 1.0
CG E:PHE287 4.5 93.8 1.0
OG E:SER286 4.8 79.9 1.0
O E:HOH702 4.8 63.2 1.0
CB E:SER286 4.8 80.9 1.0
CD1 E:PHE287 4.8 95.5 1.0
CB E:GLU315 4.8 84.5 1.0
CE E:LYS313 4.9 74.7 1.0

Manganese binding site 6 out of 8 in 8tbu

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Manganese binding site 6 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn604

b:123.3
occ:1.00
 O F:PYR602 1.9 110.3 1.0
C F:PYR602 2.3 98.1 1.0
OD2 F:ASP339 2.5 79.2 1.0
OE2 F:GLU315 2.8 63.0 1.0
CA F:PYR602 3.0 91.5 1.0
OXT F:PYR602 3.0 96.1 1.0
CG F:ASP339 3.1 75.3 1.0
OD1 F:ASP339 3.4 76.7 1.0
CD F:GLU315 3.5 59.3 1.0
OE1 F:GLU315 3.5 59.7 1.0
CB F:PYR602 3.5 89.2 1.0
O3 F:PYR602 3.9 89.4 1.0
CB F:ASP339 4.1 65.7 1.0
NZ F:LYS313 4.5 34.9 1.0
OG F:SER286 4.7 39.3 1.0
O F:HOH728 4.8 50.5 1.0
CG F:GLU315 4.9 53.4 1.0

Manganese binding site 7 out of 8 in 8tbu

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Manganese binding site 7 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn603

b:101.7
occ:1.00
 OD2 G:ASP339 2.0 130.0 1.0
OXT G:PYR601 2.7 95.5 1.0
CG G:ASP339 2.9 115.9 1.0
O3 G:PYR601 3.0 100.2 1.0
OE1 G:GLU315 3.4 86.9 1.0
OD1 G:ASP339 3.5 124.8 1.0
O G:HOH789 3.5 75.8 1.0
C G:PYR601 3.6 97.3 1.0
OE2 G:GLU315 3.7 88.5 1.0
NZ G:LYS313 3.7 70.5 1.0
CA G:PYR601 3.8 99.2 1.0
CD G:GLU315 3.8 86.4 1.0
CB G:ASP339 4.1 91.4 1.0
CE G:LYS313 4.5 69.1 1.0
O G:PYR601 4.8 97.1 1.0

Manganese binding site 8 out of 8 in 8tbu

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Manganese binding site 8 out of 8 in the Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Human Erythrocyte Pyruvate Kinase in Complex with An Allosteric Activator Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn603

b:94.1
occ:1.00
 O H:HOH848 2.4 66.1 1.0
OD2 H:ASP339 2.6 66.9 1.0
O H:HOH783 3.4 51.5 1.0
OE2 H:GLU315 3.4 68.1 1.0
CG H:ASP339 3.5 63.7 1.0
OE1 H:GLU315 3.8 66.9 1.0
O H:HOH912 3.8 53.6 1.0
CD H:GLU315 3.9 63.7 1.0
OD1 H:ASP339 4.0 66.1 1.0
CB H:ASP339 4.4 54.2 1.0
O H:LYS158 5.0 42.3 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: Sun Oct 6 13:56:20 2024

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