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:
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: Mon Aug 12 05:23:31 2024
|