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Manganese 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:

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

Manganese binding site 1 out of 4 in 8tbt

Go back to Manganese Binding Sites List in 8tbt
Manganese 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 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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:98.6
occ:1.00
 OD2 A:ASP339 1.8 57.7 1.0
O A:HOH710 2.2 56.2 1.0
OE2 A:GLU315 2.2 57.3 1.0
O A:PYR602 2.3 58.1 1.0
O3 A:PYR602 2.4 51.5 1.0
C A:PYR602 3.0 48.9 1.0
CA A:PYR602 3.0 45.7 1.0
CG A:ASP339 3.0 50.3 1.0
CD A:GLU315 3.2 41.7 1.0
OE1 A:GLU315 3.5 40.3 1.0
CB A:ASP339 3.8 39.2 1.0
NZ A:LYS313 3.8 46.6 1.0
O A:HOH748 3.9 61.7 1.0
OD1 A:ASP339 4.0 52.4 1.0
OXT A:PYR602 4.2 44.4 1.0
CE A:LYS313 4.2 53.0 1.0
O A:HOH757 4.3 53.0 1.0
CE2 A:PHE287 4.4 54.7 1.0
CB A:PYR602 4.5 49.5 1.0
N A:ASP339 4.5 40.8 1.0
CZ A:PHE287 4.5 61.1 1.0
CG A:GLU315 4.6 42.6 1.0
CB A:ALA336 4.7 44.0 1.0
CA A:ASP339 4.8 45.5 1.0

Manganese binding site 2 out of 4 in 8tbt

Go back to Manganese Binding Sites List in 8tbt
Manganese 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 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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:163.3
occ:1.00
 O B:HOH709 1.7 161.0 1.0
OD2 B:ASP339 1.8 97.6 1.0
O3 B:PYR603 1.9 120.7 1.0
OE2 B:GLU315 2.1 70.0 1.0
OXT B:PYR603 2.2 65.6 1.0
O B:HOH757 2.6 78.0 1.0
CA B:PYR603 2.7 85.2 1.0
C B:PYR603 2.8 65.5 1.0
CG B:ASP339 3.0 65.8 1.0
CD B:GLU315 3.2 58.9 1.0
OE1 B:GLU315 3.5 54.5 1.0
CB B:ASP339 3.9 49.3 1.0
OD1 B:ASP339 4.0 63.3 1.0
NZ B:LYS313 4.0 60.7 1.0
O B:PYR603 4.1 51.6 1.0
CB B:PYR603 4.1 83.7 1.0
O B:HOH745 4.2 60.4 1.0
CE2 B:PHE287 4.4 66.9 1.0
CG B:GLU315 4.5 52.8 1.0
CE B:LYS313 4.5 54.0 1.0
CZ B:PHE287 4.6 67.1 1.0
N B:ASP339 4.7 44.6 1.0
CB B:ALA336 4.8 47.9 1.0
CA B:ASP339 4.9 45.0 1.0

Manganese binding site 3 out of 4 in 8tbt

Go back to Manganese Binding Sites List in 8tbt
Manganese 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 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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn603

b:57.1
occ:1.00
 OD2 C:ASP339 2.0 53.2 1.0
O C:HOH702 2.2 52.3 1.0
O3 C:PYR602 2.2 61.0 1.0
OE2 C:GLU315 2.2 63.7 1.0
OXT C:PYR602 2.3 53.5 1.0
CA C:PYR602 2.9 66.7 1.0
C C:PYR602 2.9 53.8 1.0
CG C:ASP339 3.1 59.6 1.0
CD C:GLU315 3.2 58.1 1.0
OE1 C:GLU315 3.4 57.7 1.0
CB C:ASP339 3.7 57.1 1.0
O C:PYR602 4.2 51.9 1.0
NZ C:LYS313 4.2 59.6 1.0
OD1 C:ASP339 4.2 60.1 1.0
CB C:PYR602 4.3 65.7 1.0
N C:ASP339 4.4 46.5 1.0
CE2 C:PHE287 4.4 64.8 1.0
CG C:GLU315 4.5 58.0 1.0
CE C:LYS313 4.6 56.6 1.0
CA C:ASP339 4.7 50.9 1.0
CB C:ALA336 4.7 52.2 1.0
CD2 C:PHE287 4.9 62.9 1.0

Manganese binding site 4 out of 4 in 8tbt

Go back to Manganese Binding Sites List in 8tbt
Manganese 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 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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn604

b:72.6
occ:1.00
 O D:PYR603 1.6 72.2 1.0
OD2 D:ASP339 1.9 55.7 1.0
OE2 D:GLU315 1.9 73.3 1.0
O3 D:PYR603 2.4 46.1 1.0
C D:PYR603 2.6 51.8 1.0
CA D:PYR603 2.9 48.7 1.0
O D:HOH786 2.9 61.0 1.0
CD D:GLU315 3.0 42.1 1.0
CG D:ASP339 3.1 39.4 1.0
OE1 D:GLU315 3.4 36.3 1.0
CB D:ASP339 3.7 39.7 1.0
OXT D:PYR603 3.8 36.3 1.0
O D:HOH770 4.0 47.2 1.0
OD1 D:ASP339 4.1 45.0 1.0
NZ D:LYS313 4.2 39.9 1.0
CE1 D:PHE287 4.3 45.6 1.0
CG D:GLU315 4.3 39.7 1.0
CB D:PYR603 4.3 54.3 1.0
CE D:LYS313 4.5 38.7 1.0
O D:HOH799 4.5 54.4 1.0
N D:ASP339 4.6 37.9 1.0
CD1 D:PHE287 4.8 43.1 1.0
CB D:ALA336 4.8 35.4 1.0
CA D:ASP339 4.8 40.2 1.0
CB D:GLU315 5.0 35.8 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 13:56:15 2024

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