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Potassium in PDB 1t5a: Human Pyruvate Kinase M2

Enzymatic activity of Human Pyruvate Kinase M2

All present enzymatic activity of Human Pyruvate Kinase M2:
2.7.1.40;

Protein crystallography data

The structure of Human Pyruvate Kinase M2, PDB code: 1t5a was solved by J.D.Dombrauckas, B.D.Santarsiero, A.D.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.209, 145.006, 159.260, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 27.8

Other elements in 1t5a:

The structure of Human Pyruvate Kinase M2 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human Pyruvate Kinase M2 (pdb code 1t5a). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Human Pyruvate Kinase M2, PDB code: 1t5a:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1t5a

Go back to Potassium Binding Sites List in 1t5a
Potassium binding site 1 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K701

b:66.4
occ:1.00
 OD2 A:ASP113 3.1 69.2 1.0
O A:THR114 3.2 65.6 1.0
OD1 A:ASN75 3.5 59.3 1.0
OG A:SER243 3.6 57.1 1.0
O A:HOH729 3.6 66.4 1.0
CB A:SER77 3.7 46.3 1.0
OG A:SER77 3.8 46.3 1.0
NZ A:LYS270 4.0 62.0 1.0
OE1 A:GLU118 4.0 89.2 1.0
C A:THR114 4.1 65.6 1.0
CG A:ASP113 4.1 69.2 1.0
CA A:LYS115 4.2 76.7 1.0
CG A:ASN75 4.4 59.3 1.0
O A:ASP113 4.4 77.4 1.0
O A:LYS115 4.4 76.7 1.0
MG A:MG601 4.4 66.4 1.0
N A:LYS115 4.6 76.7 1.0
O1 A:OXL533 4.7 66.4 1.0
CB A:SER243 4.7 57.1 1.0
C A:LYS115 4.7 76.7 1.0
ND2 A:ASN75 4.7 59.3 1.0
N A:SER77 4.7 99.0 1.0
NH1 A:ARG73 4.8 55.6 1.0
CA A:SER77 4.8 99.0 1.0
OD1 A:ASP113 4.9 69.2 1.0
C A:ASP113 4.9 77.4 1.0

Potassium binding site 2 out of 4 in 1t5a

Go back to Potassium Binding Sites List in 1t5a
Potassium binding site 2 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K702

b:66.4
occ:1.00
 O B:HOH723 3.0 66.4 1.0
OD2 B:ASP113 3.0 70.1 1.0
OD1 B:ASN75 3.0 66.3 1.0
O B:THR114 3.2 62.8 1.0
OG B:SER77 3.4 99.0 1.0
CB B:SER77 3.5 99.0 1.0
CG B:ASN75 3.9 66.3 1.0
OG B:SER243 4.0 40.6 1.0
CG B:ASP113 4.1 70.1 1.0
O B:ASP113 4.1 65.8 1.0
C B:THR114 4.1 62.8 1.0
OE1 B:GLU118 4.2 76.3 1.0
NZ B:LYS270 4.3 77.3 1.0
CA B:LYS115 4.3 98.1 1.0
ND2 B:ASN75 4.3 66.3 1.0
N B:SER77 4.3 87.1 1.0
CA B:SER77 4.5 87.1 1.0
N B:LYS115 4.6 98.1 1.0
MG B:MG602 4.6 66.4 1.0
NH1 B:ARG73 4.6 46.5 1.0
O B:LYS115 4.7 98.1 1.0
C B:ASP113 4.7 65.8 1.0
CB B:ASP113 4.8 70.1 1.0
C B:LYS115 4.9 98.1 1.0
OD1 B:ASP113 4.9 70.1 1.0
O1 B:OXL533 5.0 66.4 1.0
N B:PHE76 5.0 80.8 1.0

Potassium binding site 3 out of 4 in 1t5a

Go back to Potassium Binding Sites List in 1t5a
Potassium binding site 3 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K703

b:66.4
occ:1.00
 OD2 C:ASP113 2.9 70.9 1.0
OD1 C:ASN75 3.0 74.7 1.0
O C:THR114 3.0 51.5 1.0
O C:HOH725 3.4 66.4 1.0
OG C:SER77 3.5 87.9 1.0
CB C:SER77 3.5 87.9 1.0
O C:ASP113 3.7 64.6 1.0
C C:THR114 3.9 51.5 1.0
CG C:ASN75 3.9 74.7 1.0
CG C:ASP113 3.9 70.9 1.0
OG C:SER243 4.0 35.3 1.0
CA C:LYS115 4.2 47.1 1.0
N C:SER77 4.2 98.9 1.0
NZ C:LYS270 4.3 48.4 1.0
ND2 C:ASN75 4.4 74.7 1.0
N C:LYS115 4.4 47.1 1.0
OE1 C:GLU118 4.4 62.7 1.0
C C:ASP113 4.4 64.6 1.0
CA C:SER77 4.4 98.9 1.0
NH1 C:ARG73 4.5 52.2 1.0
CB C:ASP113 4.6 70.9 1.0
MG C:MG603 4.7 66.4 1.0
OD1 C:ASP113 4.7 70.9 1.0
N C:PHE76 4.8 75.0 1.0
O C:LYS115 4.8 47.1 1.0
C C:LYS115 4.9 47.1 1.0
CA C:ASN75 4.9 61.2 1.0
N C:THR114 5.0 51.5 1.0
C C:PHE76 5.0 75.0 1.0
CA C:THR114 5.0 51.5 1.0
CB C:ASN75 5.0 74.7 1.0

Potassium binding site 4 out of 4 in 1t5a

Go back to Potassium Binding Sites List in 1t5a
Potassium binding site 4 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K704

b:66.4
occ:1.00
 OD2 D:ASP113 3.2 63.7 1.0
O D:THR114 3.3 51.2 1.0
OD1 D:ASN75 3.4 41.6 1.0
OG D:SER77 3.5 59.8 1.0
CB D:SER77 3.6 59.8 1.0
OG D:SER243 3.8 69.7 1.0
OE1 D:GLU118 3.9 91.6 1.0
MG D:MG604 4.1 66.4 1.0
NZ D:LYS270 4.1 46.1 1.0
CG D:ASN75 4.2 41.6 1.0
CG D:ASP113 4.3 63.7 1.0
C D:THR114 4.3 51.2 1.0
CA D:LYS115 4.3 66.6 1.0
ND2 D:ASN75 4.5 41.6 1.0
O D:LYS115 4.5 66.6 1.0
O D:ASP113 4.5 62.4 1.0
O4 D:OXL533 4.6 66.4 1.0
N D:SER77 4.7 52.4 1.0
CA D:SER77 4.7 52.4 1.0
N D:LYS115 4.7 66.6 1.0
C D:LYS115 4.8 66.6 1.0
NH1 D:ARG73 4.8 42.3 1.0
CB D:SER243 4.8 69.7 1.0
OD1 D:ASP113 5.0 63.7 1.0

Reference:

J.D.Dombrauckas, B.D.Santarsiero, A.D.Mesecar. Structural Basis For Tumor Pyruvate Kinase M2 Allosteric Regulation and Catalysis. Biochemistry V. 44 9417 2005.
ISSN: ISSN 0006-2960
PubMed: 15996096
DOI: 10.1021/BI0474923
Page generated: Sun Dec 13 23:02:07 2020

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