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Manganese 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:

Potassium (K) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 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 Ag-946, PDB code: 8tbs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:61.8
occ:1.00
 OE2 A:GLU315 1.8 69.4 1.0
O A:PYR604 2.1 59.8 1.0
OD2 A:ASP339 2.1 60.7 1.0
O3 A:PYR604 2.2 65.2 1.0
C A:PYR604 2.8 57.0 1.0
CA A:PYR604 2.9 60.0 1.0
CD A:GLU315 2.9 56.9 1.0
CG A:ASP339 3.2 52.5 1.0
OE1 A:GLU315 3.5 58.6 1.0
CB A:ASP339 3.6 47.6 1.0
NZ A:LYS313 4.1 57.2 1.0
OXT A:PYR604 4.1 50.7 1.0
O A:HOH730 4.1 60.1 1.0
CG A:GLU315 4.1 50.8 1.0
OD1 A:ASP339 4.3 58.3 1.0
CB A:PYR604 4.3 65.6 1.0
N A:ASP339 4.4 42.1 1.0
CA A:ASP339 4.6 49.5 1.0
CB A:ALA336 4.7 39.8 1.0
CE2 A:PHE287 4.8 60.0 1.0
CE A:LYS313 4.8 53.1 1.0
CB A:GLU315 5.0 47.2 1.0

Manganese binding site 2 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:87.5
occ:1.00
 O B:PYR605 2.0 77.5 1.0
OXT B:PYR605 2.1 66.3 1.0
OD2 B:ASP339 2.2 70.8 1.0
OE1 B:GLU315 2.3 62.1 1.0
C B:PYR605 2.3 78.4 1.0
O B:HOH713 2.7 65.2 1.0
O B:HOH723 2.8 79.2 1.0
CG B:ASP339 3.3 58.6 1.0
CD B:GLU315 3.3 57.4 1.0
OE2 B:GLU315 3.6 59.6 1.0
CA B:PYR605 3.7 72.5 1.0
CB B:ASP339 3.9 60.9 1.0
NZ B:LYS313 4.1 65.7 1.0
O B:HOH704 4.2 74.5 1.0
OD1 B:ASP339 4.3 68.2 1.0
CE1 B:PHE287 4.3 66.6 1.0
O3 B:PYR605 4.5 51.6 1.0
N B:ASP339 4.6 44.9 1.0
CB B:PYR605 4.6 72.6 1.0
CG B:GLU315 4.6 50.1 1.0
CE B:LYS313 4.8 60.2 1.0
CA B:ASP339 4.9 49.0 1.0
K B:K604 4.9 98.9 1.0
CD1 B:PHE287 4.9 62.5 1.0
CB B:ALA336 4.9 55.4 1.0

Manganese binding site 3 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:67.7
occ:1.00
 O C:PYR604 1.9 62.9 1.0
OXT C:PYR604 2.0 72.9 1.0
OD2 C:ASP339 2.1 71.6 1.0
OE1 C:GLU315 2.1 52.6 1.0
C C:PYR604 2.2 68.2 1.0
O C:HOH709 2.4 58.1 1.0
CD C:GLU315 3.1 58.9 1.0
CG C:ASP339 3.1 60.7 1.0
OE2 C:GLU315 3.5 55.0 1.0
CA C:PYR604 3.6 60.5 1.0
CB C:ASP339 3.6 52.8 1.0
O C:HOH713 4.0 71.1 1.0
NZ C:LYS313 4.1 55.1 1.0
O C:HOH754 4.2 65.7 1.0
OD1 C:ASP339 4.2 70.2 1.0
O3 C:PYR604 4.3 52.6 1.0
CE1 C:PHE287 4.4 71.5 1.0
N C:ASP339 4.4 44.4 1.0
CG C:GLU315 4.5 53.3 1.0
CB C:PYR604 4.6 56.9 1.0
CA C:ASP339 4.6 52.2 1.0
CE C:LYS313 4.7 48.9 1.0
CB C:ALA336 4.8 48.3 1.0
CD1 C:PHE287 4.8 63.9 1.0
CB C:GLU315 4.9 49.7 1.0

Manganese binding site 4 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn603

b:99.5
occ:1.00
 OD2 D:ASP339 2.1 83.4 1.0
O3 D:PYR604 2.2 84.2 1.0
OE1 D:GLU315 2.4 70.5 1.0
O D:HOH712 2.6 71.7 1.0
OXT D:PYR604 3.0 68.8 1.0
CA D:PYR604 3.2 78.8 1.0
CG D:ASP339 3.3 66.2 1.0
CD D:GLU315 3.3 54.5 1.0
C D:PYR604 3.4 74.2 1.0
OE2 D:GLU315 3.6 49.0 1.0
NZ D:LYS313 3.9 56.1 1.0
CB D:ASP339 4.1 51.3 1.0
OD1 D:ASP339 4.2 67.0 1.0
CE D:LYS313 4.3 48.9 1.0
O D:HOH717 4.4 72.9 1.0
CB D:PYR604 4.5 58.9 1.0
O D:PYR604 4.6 62.7 1.0
CG D:GLU315 4.7 54.4 1.0
CB D:ALA336 5.0 47.2 1.0

Manganese binding site 5 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:93.0
occ:1.00
 OD2 E:ASP339 2.0 77.4 1.0
O E:PYR604 2.4 76.1 1.0
OE1 E:GLU315 2.5 71.7 1.0
O3 E:PYR604 2.6 84.5 1.0
O E:HOH732 2.8 76.4 1.0
C E:PYR604 3.1 75.2 1.0
CA E:PYR604 3.1 77.4 1.0
CG E:ASP339 3.3 72.9 1.0
CD E:GLU315 3.4 71.9 1.0
OE2 E:GLU315 3.6 66.7 1.0
NZ E:LYS313 3.6 72.5 1.0
K E:K603 3.9 140.9 1.0
CB E:ASP339 4.1 63.6 1.0
OD1 E:ASP339 4.2 84.6 1.0
CE E:LYS313 4.2 69.8 1.0
CE2 E:PHE287 4.4 77.9 1.0
OXT E:PYR604 4.4 71.2 1.0
CB E:PYR604 4.5 61.6 1.0
CG E:GLU315 4.8 63.5 1.0
N E:ASP339 4.8 59.1 1.0
CD2 E:PHE287 4.9 80.3 1.0
CB E:ALA336 4.9 54.7 1.0

Manganese binding site 6 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn603

b:160.9
occ:1.00
 OE1 F:GLU315 2.2 72.8 1.0
OD2 F:ASP339 2.4 70.8 1.0
O F:HOH750 2.6 57.4 1.0
OXT F:PYR605 3.0 81.2 1.0
O F:HOH770 3.1 48.0 1.0
CD F:GLU315 3.3 57.0 1.0
CG F:ASP339 3.5 66.6 1.0
NZ F:LYS313 3.7 51.5 1.0
O3 F:PYR605 3.8 90.5 1.0
OE2 F:GLU315 3.8 52.3 1.0
C F:PYR605 3.9 75.7 1.0
CB F:ASP339 3.9 53.7 1.0
CE F:LYS313 4.2 44.5 1.0
CA F:PYR605 4.2 85.8 1.0
N F:ASP339 4.4 44.6 1.0
CB F:ALA336 4.5 41.9 1.0
CG F:GLU315 4.5 46.6 1.0
OD1 F:ASP339 4.6 67.1 1.0
O F:PYR605 4.8 74.1 1.0
CA F:ASP339 4.8 48.9 1.0

Manganese binding site 7 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn602

b:133.7
occ:1.00
 O3 G:PYR604 2.1 78.8 1.0
OE2 G:GLU315 2.1 84.6 1.0
OD2 G:ASP339 2.3 82.9 1.0
O G:HOH729 2.5 73.2 1.0
OXT G:PYR604 2.8 70.7 1.0
CG G:ASP339 3.0 74.3 1.0
CA G:PYR604 3.1 75.4 1.0
CD G:GLU315 3.1 74.2 1.0
C G:PYR604 3.4 71.1 1.0
OE1 G:GLU315 3.4 69.4 1.0
OD1 G:ASP339 3.6 83.8 1.0
K G:K603 3.9 119.6 1.0
CB G:ASP339 4.0 69.6 1.0
O G:HOH727 4.2 70.9 1.0
NZ G:LYS313 4.2 70.7 1.0
CE1 G:PHE287 4.4 74.4 1.0
CB G:PYR604 4.4 67.6 1.0
CG G:GLU315 4.5 68.4 1.0
CE G:LYS313 4.5 68.6 1.0
O G:PYR604 4.7 63.7 1.0
N G:ASP339 4.8 56.8 1.0
CD1 G:PHE287 4.9 81.1 1.0

Manganese binding site 8 out of 8 in 8tbs

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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 Ag-946


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 Ag-946 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn603

b:210.1
occ:1.00
 OE1 H:GLU315 2.2 74.7 1.0
OD2 H:ASP339 2.8 78.2 1.0
OXT H:PYR604 3.1 86.6 1.0
O H:HOH799 3.2 56.8 1.0
CD H:GLU315 3.3 60.4 1.0
NZ H:LYS313 3.4 37.4 1.0
O H:HOH765 3.5 45.8 1.0
CG H:ASP339 3.8 77.3 1.0
CE H:LYS313 3.8 44.5 1.0
OE2 H:GLU315 3.9 63.6 1.0
O H:HOH762 4.1 72.8 1.0
CB H:ASP339 4.1 58.7 1.0
C H:PYR604 4.1 81.5 1.0
CB H:ALA336 4.3 41.7 1.0
CG H:GLU315 4.5 47.2 1.0
O H:PYR604 4.7 80.8 1.0
N H:ASP339 4.7 41.1 1.0
O H:HOH794 4.8 64.6 1.0
OD1 H:ASP339 4.9 83.0 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 13:56:21 2024

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