Potassium in PDB 6v75: Crystal Structure of Human PKM2 in Complex with L-Aspartate
Enzymatic activity of Crystal Structure of Human PKM2 in Complex with L-Aspartate
All present enzymatic activity of Crystal Structure of Human PKM2 in Complex with L-Aspartate:
2.7.1.40;
Protein crystallography data
The structure of Crystal Structure of Human PKM2 in Complex with L-Aspartate, PDB code: 6v75
was solved by
S.Nandi,
M.Dey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.52 /
2.85
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.523,
157.955,
93.031,
90.00,
101.08,
90.00
|
R / Rfree (%)
|
24.6 /
28.4
|
Other elements in 6v75:
The structure of Crystal Structure of Human PKM2 in Complex with L-Aspartate also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
(pdb code 6v75). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Crystal Structure of Human PKM2 in Complex with L-Aspartate, PDB code: 6v75:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 1 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K601
b:65.8
occ:1.00
|
O
|
C:THR114
|
2.8
|
60.8
|
1.0
|
OD1
|
C:ASN75
|
2.9
|
44.7
|
1.0
|
OD1
|
C:ASP113
|
3.1
|
53.8
|
1.0
|
OG
|
C:SER77
|
3.2
|
60.5
|
1.0
|
CG
|
C:ASP113
|
3.8
|
55.2
|
1.0
|
C
|
C:THR114
|
3.8
|
58.4
|
1.0
|
CG
|
C:ASN75
|
3.9
|
44.3
|
1.0
|
NZ
|
C:LYS270
|
4.0
|
44.6
|
1.0
|
OG
|
C:SER243
|
4.1
|
47.0
|
1.0
|
CB
|
C:SER77
|
4.1
|
55.4
|
1.0
|
CA
|
C:LYS115
|
4.2
|
58.9
|
1.0
|
ND2
|
C:ASN75
|
4.2
|
43.6
|
1.0
|
N
|
C:LYS115
|
4.4
|
53.5
|
1.0
|
OD2
|
C:ASP113
|
4.4
|
51.3
|
1.0
|
O2
|
C:OXL609
|
4.5
|
64.6
|
1.0
|
OE2
|
C:GLU118
|
4.5
|
66.7
|
1.0
|
O
|
C:LYS115
|
4.5
|
51.1
|
1.0
|
CB
|
C:ASP113
|
4.6
|
53.9
|
1.0
|
NH2
|
C:ARG73
|
4.6
|
48.1
|
1.0
|
N
|
C:SER77
|
4.7
|
55.5
|
1.0
|
C
|
C:LYS115
|
4.8
|
57.1
|
1.0
|
N
|
C:THR114
|
4.8
|
50.7
|
1.0
|
C
|
C:ASP113
|
4.8
|
48.5
|
1.0
|
O
|
C:ASP113
|
4.9
|
49.5
|
1.0
|
CA
|
C:THR114
|
4.9
|
49.9
|
1.0
|
CA
|
C:SER77
|
5.0
|
56.9
|
1.0
|
MG
|
C:MG608
|
5.0
|
57.4
|
1.0
|
|
Potassium binding site 2 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 2 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K602
b:82.4
occ:1.00
|
CD
|
C:ARG106
|
3.3
|
51.2
|
1.0
|
O
|
C:LEU104
|
3.6
|
53.0
|
1.0
|
CD2
|
C:PHE98
|
4.1
|
54.9
|
1.0
|
CG
|
C:ARG106
|
4.2
|
49.5
|
1.0
|
CG
|
C:PHE98
|
4.3
|
54.8
|
1.0
|
CE2
|
C:PHE98
|
4.5
|
57.4
|
1.0
|
CB
|
C:PHE98
|
4.6
|
56.3
|
1.0
|
C
|
C:LEU104
|
4.7
|
60.1
|
1.0
|
CD1
|
C:PHE98
|
4.8
|
55.0
|
1.0
|
CG2
|
C:ILE65
|
4.9
|
48.9
|
1.0
|
CB
|
C:ARG106
|
4.9
|
40.5
|
1.0
|
N
|
C:ARG106
|
5.0
|
59.7
|
1.0
|
|
Potassium binding site 3 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 3 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K601
b:63.0
occ:1.00
|
O
|
A:THR114
|
2.7
|
55.4
|
1.0
|
OG
|
A:SER77
|
2.8
|
62.8
|
1.0
|
OD1
|
A:ASN75
|
2.9
|
52.9
|
1.0
|
OD1
|
A:ASP113
|
3.2
|
67.3
|
1.0
|
OG
|
A:SER243
|
3.5
|
61.1
|
1.0
|
C
|
A:THR114
|
3.9
|
55.0
|
1.0
|
CB
|
A:SER77
|
3.9
|
67.2
|
1.0
|
O
|
A:LYS115
|
3.9
|
68.7
|
1.0
|
OE2
|
A:GLU118
|
3.9
|
62.1
|
1.0
|
CG
|
A:ASN75
|
4.0
|
55.7
|
1.0
|
CG
|
A:ASP113
|
4.1
|
69.0
|
1.0
|
CA
|
A:LYS115
|
4.1
|
62.7
|
1.0
|
C
|
A:LYS115
|
4.4
|
62.7
|
1.0
|
CB
|
A:SER243
|
4.4
|
65.0
|
1.0
|
ND2
|
A:ASN75
|
4.5
|
64.6
|
1.0
|
N
|
A:LYS115
|
4.5
|
57.0
|
1.0
|
N
|
A:SER77
|
4.6
|
63.8
|
1.0
|
O
|
A:ASP113
|
4.6
|
58.5
|
1.0
|
CA
|
A:SER77
|
4.7
|
70.0
|
1.0
|
CB
|
A:ASP113
|
4.8
|
63.5
|
1.0
|
C
|
A:ASP113
|
4.8
|
58.7
|
1.0
|
OD2
|
A:ASP113
|
4.9
|
63.2
|
1.0
|
N
|
A:THR114
|
5.0
|
55.9
|
1.0
|
|
Potassium binding site 4 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 4 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K601
b:69.6
occ:1.00
|
OD1
|
B:ASN75
|
2.9
|
64.8
|
1.0
|
OD1
|
B:ASP113
|
3.1
|
72.7
|
1.0
|
O
|
B:THR114
|
3.2
|
65.0
|
1.0
|
OG
|
B:SER77
|
3.5
|
73.4
|
1.0
|
CG
|
B:ASP113
|
3.9
|
69.0
|
1.0
|
CG
|
B:ASN75
|
4.0
|
57.7
|
1.0
|
CB
|
B:SER77
|
4.0
|
64.3
|
1.0
|
OG
|
B:SER243
|
4.1
|
61.6
|
1.0
|
C
|
B:THR114
|
4.1
|
67.5
|
1.0
|
NZ
|
B:LYS270
|
4.2
|
58.1
|
1.0
|
CA
|
B:LYS115
|
4.4
|
68.0
|
1.0
|
ND2
|
B:ASN75
|
4.4
|
64.1
|
1.0
|
O
|
B:ASP113
|
4.5
|
70.9
|
1.0
|
N
|
B:SER77
|
4.5
|
71.4
|
1.0
|
OD2
|
B:ASP113
|
4.5
|
65.8
|
1.0
|
N
|
B:LYS115
|
4.6
|
67.6
|
1.0
|
CB
|
B:ASP113
|
4.6
|
63.3
|
1.0
|
O
|
B:LYS115
|
4.6
|
67.5
|
1.0
|
NH2
|
B:ARG73
|
4.6
|
66.2
|
1.0
|
C
|
B:ASP113
|
4.7
|
66.3
|
1.0
|
C
|
B:LYS115
|
4.9
|
63.6
|
1.0
|
CA
|
B:SER77
|
4.9
|
64.9
|
1.0
|
|
Potassium binding site 5 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 5 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K601
b:68.9
occ:1.00
|
OG
|
D:SER77
|
2.8
|
71.8
|
1.0
|
OD1
|
D:ASP113
|
3.0
|
70.4
|
1.0
|
OD1
|
D:ASN75
|
3.2
|
69.9
|
1.0
|
O
|
D:THR114
|
3.5
|
70.0
|
1.0
|
OE2
|
D:GLU118
|
3.6
|
74.2
|
1.0
|
CB
|
D:SER77
|
4.0
|
74.6
|
1.0
|
CG
|
D:ASP113
|
4.0
|
67.6
|
1.0
|
CA
|
D:LYS115
|
4.0
|
73.4
|
1.0
|
O
|
D:LYS115
|
4.1
|
71.5
|
1.0
|
CG
|
D:ASN75
|
4.1
|
66.8
|
1.0
|
NZ
|
D:LYS270
|
4.2
|
63.5
|
1.0
|
C
|
D:THR114
|
4.2
|
71.6
|
1.0
|
ND2
|
D:ASN75
|
4.4
|
63.1
|
1.0
|
C
|
D:LYS115
|
4.5
|
68.6
|
1.0
|
N
|
D:LYS115
|
4.5
|
73.6
|
1.0
|
O
|
D:ASP113
|
4.6
|
67.4
|
1.0
|
N
|
D:SER77
|
4.6
|
78.6
|
1.0
|
CB
|
D:SER243
|
4.7
|
66.5
|
1.0
|
OD2
|
D:ASP113
|
4.7
|
67.4
|
1.0
|
CD
|
D:GLU118
|
4.8
|
76.5
|
1.0
|
CA
|
D:SER77
|
4.8
|
78.1
|
1.0
|
CB
|
D:ASP113
|
4.8
|
66.0
|
1.0
|
NH2
|
D:ARG73
|
4.9
|
63.4
|
1.0
|
C
|
D:ASP113
|
4.9
|
66.6
|
1.0
|
|
Potassium binding site 6 out
of 6 in 6v75
Go back to
Potassium Binding Sites List in 6v75
Potassium binding site 6 out
of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K602
b:0.7
occ:1.00
|
OD2
|
D:ASP487
|
3.7
|
98.7
|
1.0
|
CG
|
D:ASP487
|
4.3
|
88.4
|
1.0
|
OD1
|
D:ASP487
|
4.5
|
79.8
|
1.0
|
CG1
|
D:VAL490
|
4.9
|
59.5
|
1.0
|
|
Reference:
S.Nandi,
M.Dey.
Biochemical and Structural Investigation of Pyurvate Kinase Muscle Isoform 2 Regulation By Amino Acids To Be Published.
Page generated: Mon Aug 12 17:56:50 2024
|