Magnesium in PDB 8hmr: Crystal Structure of PKM2 Mutant L144P
Enzymatic activity of Crystal Structure of PKM2 Mutant L144P
Protein crystallography data
The structure of Crystal Structure of PKM2 Mutant L144P, PDB code: 8hmr
was solved by
S.Upadhyay,
A.Kumar,
A.K.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.01 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.4,
151.769,
89.85,
90,
100.59,
90
|
R / Rfree (%)
|
26.3 /
29.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of PKM2 Mutant L144P
(pdb code 8hmr). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of PKM2 Mutant L144P, PDB code: 8hmr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8hmr
Go back to
Magnesium Binding Sites List in 8hmr
Magnesium binding site 1 out
of 4 in the Crystal Structure of PKM2 Mutant L144P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of PKM2 Mutant L144P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:75.7
occ:1.00
|
OD2
|
A:ASP296
|
2.2
|
42.9
|
1.0
|
O3
|
A:OXL601
|
2.2
|
35.3
|
1.0
|
OE1
|
A:GLU272
|
2.7
|
51.8
|
1.0
|
CG
|
A:ASP296
|
3.1
|
42.5
|
1.0
|
CD
|
A:GLU272
|
3.2
|
52.7
|
1.0
|
C1
|
A:OXL601
|
3.4
|
34.8
|
1.0
|
OE2
|
A:GLU272
|
3.5
|
52.7
|
1.0
|
CE2
|
A:PHE244
|
3.5
|
66.4
|
1.0
|
CZ
|
A:PHE244
|
3.5
|
65.6
|
1.0
|
O4
|
A:OXL601
|
3.6
|
33.7
|
1.0
|
NZ
|
A:LYS270
|
3.7
|
38.8
|
1.0
|
CB
|
A:ASP296
|
3.9
|
41.3
|
1.0
|
OD1
|
A:ASP296
|
4.0
|
42.4
|
1.0
|
C2
|
A:OXL601
|
4.0
|
33.7
|
1.0
|
CG
|
A:GLU272
|
4.3
|
52.8
|
1.0
|
CD2
|
A:PHE244
|
4.3
|
64.8
|
1.0
|
CE1
|
A:PHE244
|
4.4
|
61.1
|
1.0
|
O1
|
A:OXL601
|
4.5
|
35.1
|
1.0
|
CE
|
A:LYS270
|
4.5
|
38.1
|
1.0
|
OG
|
A:SER243
|
4.8
|
47.2
|
1.0
|
CB
|
A:SER243
|
4.8
|
50.5
|
1.0
|
OE2
|
A:GLU118
|
4.9
|
53.2
|
1.0
|
CB
|
A:GLU272
|
5.0
|
48.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8hmr
Go back to
Magnesium Binding Sites List in 8hmr
Magnesium binding site 2 out
of 4 in the Crystal Structure of PKM2 Mutant L144P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of PKM2 Mutant L144P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:74.4
occ:1.00
|
O1
|
B:OXL602
|
2.2
|
54.7
|
1.0
|
OD2
|
B:ASP296
|
2.7
|
45.7
|
1.0
|
OE1
|
B:GLU272
|
2.7
|
46.0
|
1.0
|
CE2
|
B:PHE244
|
3.2
|
62.7
|
1.0
|
CD
|
B:GLU272
|
3.4
|
46.8
|
1.0
|
C1
|
B:OXL602
|
3.4
|
48.0
|
1.0
|
NZ
|
B:LYS270
|
3.4
|
49.7
|
1.0
|
OE2
|
B:GLU272
|
3.5
|
46.4
|
1.0
|
CZ
|
B:PHE244
|
3.5
|
62.6
|
1.0
|
CG
|
B:ASP296
|
3.7
|
47.8
|
1.0
|
O3
|
B:OXL602
|
4.0
|
47.3
|
1.0
|
CD2
|
B:PHE244
|
4.1
|
60.9
|
1.0
|
CE
|
B:LYS270
|
4.2
|
50.0
|
1.0
|
OG
|
B:SER243
|
4.3
|
56.3
|
1.0
|
OD1
|
B:ASP296
|
4.4
|
50.6
|
1.0
|
CB
|
B:SER243
|
4.4
|
56.8
|
1.0
|
O2
|
B:OXL602
|
4.5
|
45.9
|
1.0
|
C2
|
B:OXL602
|
4.5
|
46.3
|
1.0
|
CG
|
B:GLU272
|
4.6
|
47.2
|
1.0
|
CE1
|
B:PHE244
|
4.6
|
60.8
|
1.0
|
CB
|
B:ASP296
|
4.6
|
47.4
|
1.0
|
OE2
|
B:GLU118
|
4.9
|
67.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8hmr
Go back to
Magnesium Binding Sites List in 8hmr
Magnesium binding site 3 out
of 4 in the Crystal Structure of PKM2 Mutant L144P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of PKM2 Mutant L144P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg605
b:62.2
occ:1.00
|
OE1
|
C:GLU272
|
2.4
|
70.3
|
1.0
|
OD2
|
C:ASP296
|
2.4
|
48.9
|
1.0
|
O2
|
C:OXL601
|
2.5
|
48.6
|
1.0
|
O1
|
C:OXL601
|
2.7
|
53.1
|
1.0
|
CD
|
C:GLU272
|
3.1
|
73.3
|
1.0
|
NZ
|
C:LYS270
|
3.2
|
62.0
|
1.0
|
OE2
|
C:GLU272
|
3.3
|
78.4
|
1.0
|
C2
|
C:OXL601
|
3.4
|
49.6
|
1.0
|
C1
|
C:OXL601
|
3.5
|
50.7
|
1.0
|
CG
|
C:ASP296
|
3.6
|
49.1
|
1.0
|
CE
|
C:LYS270
|
3.8
|
62.7
|
1.0
|
CE2
|
C:PHE244
|
3.9
|
67.7
|
1.0
|
CZ
|
C:PHE244
|
4.0
|
68.0
|
1.0
|
CB
|
C:ASP296
|
4.3
|
47.1
|
1.0
|
CG
|
C:GLU272
|
4.3
|
72.6
|
1.0
|
OD1
|
C:ASP296
|
4.5
|
52.0
|
1.0
|
O4
|
C:OXL601
|
4.6
|
47.8
|
1.0
|
CD2
|
C:PHE244
|
4.7
|
65.9
|
1.0
|
OG
|
C:SER243
|
4.7
|
49.0
|
1.0
|
O3
|
C:OXL601
|
4.7
|
50.1
|
1.0
|
CB
|
C:SER243
|
4.9
|
51.8
|
1.0
|
CE1
|
C:PHE244
|
4.9
|
67.6
|
1.0
|
CB
|
C:GLU272
|
4.9
|
67.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8hmr
Go back to
Magnesium Binding Sites List in 8hmr
Magnesium binding site 4 out
of 4 in the Crystal Structure of PKM2 Mutant L144P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of PKM2 Mutant L144P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg603
b:66.7
occ:1.00
|
O4
|
D:OXL602
|
2.3
|
59.4
|
1.0
|
OD2
|
D:ASP296
|
2.4
|
58.0
|
1.0
|
OE1
|
D:GLU272
|
2.7
|
78.6
|
1.0
|
O3
|
D:OXL602
|
3.0
|
54.8
|
1.0
|
C2
|
D:OXL602
|
3.3
|
56.6
|
1.0
|
CG
|
D:ASP296
|
3.5
|
60.7
|
1.0
|
CD
|
D:GLU272
|
3.5
|
77.7
|
1.0
|
NZ
|
D:LYS270
|
3.5
|
58.3
|
1.0
|
C1
|
D:OXL602
|
3.6
|
55.4
|
1.0
|
OE2
|
D:GLU272
|
3.8
|
82.8
|
1.0
|
CB
|
D:ASP296
|
4.1
|
60.5
|
1.0
|
CE2
|
D:PHE244
|
4.1
|
90.0
|
1.0
|
CE
|
D:LYS270
|
4.2
|
55.1
|
1.0
|
CZ
|
D:PHE244
|
4.2
|
88.4
|
1.0
|
OD1
|
D:ASP296
|
4.4
|
64.2
|
1.0
|
O2
|
D:OXL602
|
4.5
|
53.7
|
1.0
|
CG
|
D:GLU272
|
4.6
|
73.0
|
1.0
|
O1
|
D:OXL602
|
4.7
|
55.4
|
1.0
|
|
Reference:
S.Upadhyay,
A.Kumar,
A.K.Patel.
Structural and Mechanistic Insights Into Cancer Patient-Derived Mutations in Pyruvate Kinase Muscle Isoform 2 To Be Published.
Page generated: Fri Apr 7 11:27:55 2023
|