Magnesium in PDB 8p5i: Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
Enzymatic activity of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
All present enzymatic activity of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51:
2.7.11.1;
Protein crystallography data
The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51, PDB code: 8p5i
was solved by
T.Battista,
M.S.Semrau,
A.Heroux,
G.Lolli,
P.Storici,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
96.40 /
1.83
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.47,
109.54,
96.52,
90,
92.84,
90
|
|
R / Rfree (%)
|
16.6 /
18.9
|
Other elements in 8p5i:
The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
(pdb code 8p5i). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51, PDB code: 8p5i:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 1 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:29.8
occ:1.00
|
H
|
A:ASP199
|
2.0
|
19.7
|
1.0
|
|
HB2
|
A:TYR198
|
2.7
|
19.4
|
1.0
|
|
OE2
|
A:GLU191
|
2.8
|
20.4
|
1.0
|
|
OD1
|
A:ASP199
|
2.9
|
23.4
|
1.0
|
|
N
|
A:ASP199
|
2.9
|
19.3
|
1.0
|
|
HA
|
A:TYR198
|
2.9
|
19.6
|
1.0
|
|
HB2
|
A:HIS263
|
3.0
|
25.6
|
1.0
|
|
HG3
|
A:GLU191
|
3.0
|
20.2
|
1.0
|
|
H
|
A:ALA202
|
3.3
|
18.1
|
1.0
|
|
HB3
|
A:HIS263
|
3.3
|
25.5
|
1.0
|
|
HB2
|
A:ALA202
|
3.3
|
19.2
|
1.0
|
|
HB2
|
A:LYS201
|
3.4
|
23.0
|
1.0
|
|
CA
|
A:TYR198
|
3.4
|
19.7
|
1.0
|
|
CB
|
A:TYR198
|
3.5
|
19.7
|
1.0
|
|
CB
|
A:HIS263
|
3.5
|
26.6
|
1.0
|
|
CD
|
A:GLU191
|
3.6
|
21.2
|
1.0
|
|
CG
|
A:HIS263
|
3.6
|
23.2
|
1.0
|
|
HH12
|
A:ARG266
|
3.6
|
19.4
|
1.0
|
|
O
|
A:ASP199
|
3.6
|
21.3
|
1.0
|
|
C
|
A:TYR198
|
3.6
|
19.5
|
1.0
|
|
CG
|
A:ASP199
|
3.7
|
28.1
|
1.0
|
|
N
|
A:ALA202
|
3.7
|
17.3
|
1.0
|
|
CG
|
A:GLU191
|
3.7
|
19.7
|
1.0
|
|
HB3
|
A:TYR198
|
3.8
|
19.4
|
1.0
|
|
CA
|
A:ASP199
|
3.8
|
20.3
|
1.0
|
|
ND1
|
A:HIS263
|
3.9
|
28.8
|
1.0
|
|
C
|
A:ASP199
|
3.9
|
20.5
|
1.0
|
|
HD1
|
A:HIS263
|
3.9
|
28.8
|
0.0
|
|
H
|
A:LYS201
|
4.0
|
18.4
|
1.0
|
|
HG2
|
A:GLU191
|
4.0
|
20.2
|
1.0
|
|
CD2
|
A:HIS263
|
4.1
|
27.6
|
1.0
|
|
CB
|
A:ALA202
|
4.1
|
19.4
|
1.0
|
|
HA
|
A:ALA202
|
4.2
|
19.2
|
1.0
|
|
CB
|
A:ASP199
|
4.3
|
21.8
|
1.0
|
|
CA
|
A:ALA202
|
4.3
|
18.6
|
1.0
|
|
C
|
A:LYS201
|
4.3
|
19.3
|
1.0
|
|
CB
|
A:LYS201
|
4.3
|
22.7
|
1.0
|
|
HE3
|
A:MET177
|
4.4
|
24.5
|
0.5
|
|
N
|
A:LYS201
|
4.4
|
17.7
|
1.0
|
|
OD2
|
A:ASP199
|
4.4
|
26.5
|
1.0
|
|
NH1
|
A:ARG266
|
4.4
|
19.5
|
1.0
|
|
HD1
|
A:TYR198
|
4.5
|
18.9
|
1.0
|
|
HD2
|
A:HIS263
|
4.5
|
26.1
|
1.0
|
|
HB3
|
A:ALA202
|
4.5
|
19.2
|
1.0
|
|
CA
|
A:LYS201
|
4.5
|
20.0
|
1.0
|
|
HB3
|
A:ASP199
|
4.5
|
22.7
|
1.0
|
|
CE1
|
A:HIS263
|
4.6
|
28.9
|
1.0
|
|
HB3
|
A:LYS201
|
4.6
|
23.0
|
1.0
|
|
NE2
|
A:HIS263
|
4.7
|
25.5
|
1.0
|
|
HH11
|
A:ARG266
|
4.7
|
19.4
|
1.0
|
|
O
|
A:HOH420
|
4.7
|
34.9
|
1.0
|
|
HA
|
A:ASP199
|
4.7
|
20.4
|
1.0
|
|
CG
|
A:TYR198
|
4.7
|
18.2
|
1.0
|
|
OE1
|
A:GLU191
|
4.7
|
19.8
|
1.0
|
|
HE1
|
A:MET177
|
4.8
|
31.6
|
0.5
|
|
HE3
|
A:MET177
|
4.8
|
31.6
|
0.5
|
|
N
|
A:TYR198
|
4.8
|
19.2
|
1.0
|
|
HB1
|
A:ALA202
|
4.9
|
19.2
|
1.0
|
|
O
|
A:TYR198
|
4.9
|
19.9
|
1.0
|
|
N
|
A:GLY200
|
4.9
|
21.2
|
1.0
|
|
HE2
|
A:MET177
|
4.9
|
24.5
|
0.5
|
|
CA
|
A:HIS263
|
4.9
|
25.7
|
1.0
|
|
O
|
A:HIS197
|
4.9
|
21.6
|
1.0
|
|
HE2
|
A:MET177
|
5.0
|
31.6
|
0.5
|
|
Magnesium binding site 2 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 2 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:32.4
occ:1.00
|
H
|
A:PHE168
|
2.2
|
21.5
|
1.0
|
|
HA
|
A:PHE166
|
2.6
|
21.4
|
1.0
|
|
HB2
|
A:PHE168
|
2.7
|
22.1
|
1.0
|
|
O
|
A:ASP165
|
2.7
|
22.1
|
1.0
|
|
O
|
A:HIS136
|
2.8
|
17.4
|
1.0
|
|
H
|
A:ALA169
|
2.9
|
19.4
|
1.0
|
|
N
|
A:PHE168
|
2.9
|
21.1
|
1.0
|
|
N
|
A:ALA169
|
3.3
|
19.1
|
1.0
|
|
CA
|
A:PHE166
|
3.3
|
21.4
|
1.0
|
|
C
|
A:PHE166
|
3.4
|
21.5
|
1.0
|
|
HB3
|
A:ASP138
|
3.4
|
24.7
|
1.0
|
|
HD2
|
A:PHE168
|
3.4
|
33.0
|
1.0
|
|
HB2
|
A:ALA169
|
3.5
|
20.7
|
1.0
|
|
CB
|
A:PHE168
|
3.5
|
22.2
|
1.0
|
|
CA
|
A:PHE168
|
3.5
|
19.0
|
1.0
|
|
CE1
|
A:HIS136
|
3.5
|
19.4
|
1.0
|
|
N
|
A:GLY167
|
3.5
|
24.6
|
1.0
|
|
H
|
A:GLY167
|
3.5
|
23.4
|
1.0
|
|
HB2
|
A:ASP138
|
3.6
|
24.7
|
1.0
|
|
HE1
|
A:HIS136
|
3.6
|
18.9
|
1.0
|
|
C
|
A:PHE168
|
3.6
|
19.3
|
1.0
|
|
ND1
|
A:HIS136
|
3.7
|
18.3
|
1.0
|
|
C
|
A:ASP165
|
3.7
|
22.2
|
1.0
|
|
O
|
A:PHE166
|
3.8
|
23.5
|
1.0
|
|
HD1
|
A:HIS136
|
3.8
|
18.2
|
0.0
|
|
C
|
A:HIS136
|
3.9
|
17.8
|
1.0
|
|
N
|
A:PHE166
|
3.9
|
21.6
|
1.0
|
|
NE2
|
A:HIS136
|
3.9
|
18.0
|
1.0
|
|
CB
|
A:ASP138
|
3.9
|
24.4
|
1.0
|
|
C
|
A:GLY167
|
4.0
|
24.4
|
1.0
|
|
H
|
A:ASP138
|
4.0
|
22.2
|
1.0
|
|
CA
|
A:ALA169
|
4.1
|
20.0
|
1.0
|
|
CD2
|
A:PHE168
|
4.1
|
35.8
|
1.0
|
|
CG
|
A:HIS136
|
4.1
|
18.6
|
1.0
|
|
HB3
|
A:PHE168
|
4.2
|
21.9
|
1.0
|
|
CB
|
A:ALA169
|
4.2
|
21.0
|
1.0
|
|
HA
|
A:ALA169
|
4.2
|
20.2
|
1.0
|
|
HA
|
A:HIS136
|
4.2
|
18.4
|
1.0
|
|
HE2
|
A:HIS136
|
4.2
|
18.3
|
0.0
|
|
CD2
|
A:HIS136
|
4.3
|
19.8
|
1.0
|
|
CG
|
A:PHE168
|
4.3
|
24.7
|
1.0
|
|
N
|
A:ASP138
|
4.3
|
22.3
|
1.0
|
|
CA
|
A:GLY167
|
4.3
|
23.1
|
1.0
|
|
HB3
|
A:ASP165
|
4.4
|
28.2
|
0.5
|
|
HA
|
A:PHE168
|
4.4
|
20.1
|
1.0
|
|
HB3
|
A:ALA169
|
4.4
|
20.7
|
1.0
|
|
HB2
|
A:ARG137
|
4.5
|
18.4
|
1.0
|
|
O
|
A:PHE168
|
4.5
|
19.7
|
1.0
|
|
CA
|
A:HIS136
|
4.6
|
18.4
|
1.0
|
|
OD1
|
A:ASP165
|
4.6
|
17.9
|
0.5
|
|
CB
|
A:PHE166
|
4.6
|
20.7
|
1.0
|
|
CA
|
A:ASP138
|
4.7
|
22.9
|
1.0
|
|
HB3
|
A:PHE166
|
4.8
|
21.2
|
1.0
|
|
HA3
|
A:GLY167
|
4.8
|
23.7
|
1.0
|
|
H
|
A:PHE166
|
4.8
|
21.7
|
1.0
|
|
N
|
A:ARG137
|
4.8
|
19.5
|
1.0
|
|
HB3
|
A:ASP165
|
4.9
|
21.1
|
0.5
|
|
C
|
A:ARG137
|
4.9
|
21.8
|
1.0
|
|
HD2
|
A:HIS136
|
4.9
|
19.1
|
1.0
|
|
CG
|
A:ASP165
|
5.0
|
21.9
|
0.5
|
|
HB1
|
A:ALA169
|
5.0
|
20.7
|
1.0
|
|
CB
|
A:HIS136
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 3 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:35.1
occ:1.00
|
H
|
B:ASP199
|
2.1
|
22.6
|
1.0
|
|
OE2
|
B:GLU191
|
2.7
|
24.1
|
1.0
|
|
HB2
|
B:TYR198
|
2.8
|
18.3
|
1.0
|
|
OD1
|
B:ASP199
|
2.9
|
26.1
|
1.0
|
|
HA
|
B:TYR198
|
2.9
|
19.0
|
1.0
|
|
N
|
B:ASP199
|
3.0
|
23.2
|
1.0
|
|
HG3
|
B:GLU191
|
3.1
|
23.7
|
1.0
|
|
HB2
|
B:HIS263
|
3.1
|
31.3
|
1.0
|
|
H
|
B:ALA202
|
3.2
|
19.1
|
1.0
|
|
HB2
|
B:LYS201
|
3.3
|
23.5
|
1.0
|
|
HB3
|
B:HIS263
|
3.3
|
31.2
|
1.0
|
|
HB2
|
B:ALA202
|
3.3
|
21.2
|
1.0
|
|
CA
|
B:TYR198
|
3.5
|
17.5
|
1.0
|
|
CB
|
B:TYR198
|
3.5
|
18.7
|
1.0
|
|
HH12
|
B:ARG266
|
3.5
|
24.1
|
1.0
|
|
CB
|
B:HIS263
|
3.5
|
31.0
|
1.0
|
|
CD
|
B:GLU191
|
3.6
|
24.8
|
1.0
|
|
N
|
B:ALA202
|
3.6
|
19.0
|
1.0
|
|
CG
|
B:HIS263
|
3.7
|
34.4
|
1.0
|
|
C
|
B:TYR198
|
3.7
|
20.5
|
1.0
|
|
O
|
B:ASP199
|
3.7
|
21.9
|
1.0
|
|
CG
|
B:GLU191
|
3.7
|
23.0
|
1.0
|
|
CG
|
B:ASP199
|
3.8
|
26.6
|
1.0
|
|
HB3
|
B:TYR198
|
3.8
|
18.3
|
1.0
|
|
H
|
B:LYS201
|
3.9
|
22.7
|
1.0
|
|
CA
|
B:ASP199
|
3.9
|
23.5
|
1.0
|
|
HG2
|
B:GLU191
|
4.0
|
23.7
|
1.0
|
|
C
|
B:ASP199
|
4.0
|
21.6
|
1.0
|
|
CD2
|
B:HIS263
|
4.1
|
33.7
|
1.0
|
|
ND1
|
B:HIS263
|
4.1
|
36.7
|
1.0
|
|
CB
|
B:ALA202
|
4.1
|
22.1
|
1.0
|
|
HA
|
B:ALA202
|
4.2
|
20.0
|
1.0
|
|
CB
|
B:LYS201
|
4.2
|
23.0
|
1.0
|
|
C
|
B:LYS201
|
4.2
|
19.2
|
1.0
|
|
CA
|
B:ALA202
|
4.2
|
18.9
|
1.0
|
|
HD2
|
B:HIS263
|
4.3
|
34.2
|
1.0
|
|
HD1
|
B:HIS263
|
4.3
|
36.6
|
0.0
|
|
NH1
|
B:ARG266
|
4.3
|
23.7
|
1.0
|
|
HE3
|
B:MET177
|
4.3
|
25.6
|
0.5
|
|
N
|
B:LYS201
|
4.3
|
22.8
|
1.0
|
|
CB
|
B:ASP199
|
4.4
|
23.5
|
1.0
|
|
OD2
|
B:ASP199
|
4.5
|
32.5
|
1.0
|
|
CA
|
B:LYS201
|
4.5
|
22.1
|
1.0
|
|
HB3
|
B:LYS201
|
4.5
|
23.5
|
1.0
|
|
HD1
|
B:TYR198
|
4.5
|
19.3
|
1.0
|
|
HB3
|
B:ALA202
|
4.5
|
21.3
|
1.0
|
|
HH11
|
B:ARG266
|
4.6
|
24.2
|
1.0
|
|
HB3
|
B:ASP199
|
4.7
|
24.2
|
1.0
|
|
NE2
|
B:HIS263
|
4.7
|
35.1
|
1.0
|
|
OE1
|
B:GLU191
|
4.7
|
25.7
|
1.0
|
|
CE1
|
B:HIS263
|
4.7
|
34.8
|
1.0
|
|
CG
|
B:TYR198
|
4.8
|
17.7
|
1.0
|
|
HA
|
B:ASP199
|
4.8
|
23.0
|
1.0
|
|
HE2
|
B:MET177
|
4.8
|
30.0
|
0.5
|
|
N
|
B:TYR198
|
4.9
|
21.1
|
1.0
|
|
HB1
|
B:ALA202
|
4.9
|
21.2
|
1.0
|
|
HE2
|
B:MET177
|
4.9
|
25.6
|
0.5
|
|
O
|
B:TYR198
|
4.9
|
20.4
|
1.0
|
|
O
|
B:HIS197
|
4.9
|
23.2
|
1.0
|
|
HD2
|
B:LYS201
|
5.0
|
30.2
|
1.0
|
|
N
|
B:GLY200
|
5.0
|
21.6
|
1.0
|
|
CA
|
B:HIS263
|
5.0
|
29.2
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 4 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:30.4
occ:1.00
|
H
|
B:PHE168
|
2.1
|
18.3
|
1.0
|
|
HB2
|
B:PHE168
|
2.5
|
20.6
|
0.5
|
|
HB2
|
B:PHE168
|
2.7
|
21.0
|
0.5
|
|
HA
|
B:PHE166
|
2.7
|
18.8
|
1.0
|
|
O
|
B:HIS136
|
2.8
|
17.1
|
1.0
|
|
O
|
B:ASP165
|
2.8
|
19.1
|
0.5
|
|
O
|
B:ASP165
|
2.8
|
19.9
|
0.5
|
|
N
|
B:PHE168
|
2.9
|
17.3
|
1.0
|
|
H
|
B:ALA169
|
2.9
|
17.7
|
1.0
|
|
N
|
B:ALA169
|
3.3
|
17.5
|
1.0
|
|
HB3
|
B:ASP138
|
3.3
|
22.4
|
1.0
|
|
CB
|
B:PHE168
|
3.3
|
20.4
|
0.5
|
|
HB2
|
B:ASP138
|
3.4
|
22.5
|
1.0
|
|
C
|
B:PHE166
|
3.4
|
18.9
|
1.0
|
|
CA
|
B:PHE166
|
3.4
|
18.6
|
1.0
|
|
CA
|
B:PHE168
|
3.4
|
18.6
|
0.5
|
|
CA
|
B:PHE168
|
3.4
|
18.7
|
0.5
|
|
CB
|
B:PHE168
|
3.4
|
20.9
|
0.5
|
|
HD2
|
B:PHE168
|
3.5
|
25.3
|
0.5
|
|
HB2
|
B:ALA169
|
3.5
|
17.9
|
1.0
|
|
N
|
B:GLY167
|
3.5
|
18.9
|
1.0
|
|
H
|
B:GLY167
|
3.5
|
19.1
|
1.0
|
|
C
|
B:PHE168
|
3.6
|
18.5
|
1.0
|
|
CE1
|
B:HIS136
|
3.6
|
16.8
|
1.0
|
|
O
|
B:HOH470
|
3.7
|
50.9
|
1.0
|
|
HE1
|
B:HIS136
|
3.7
|
16.7
|
1.0
|
|
C
|
B:ASP165
|
3.7
|
18.4
|
0.5
|
|
C
|
B:ASP165
|
3.7
|
19.2
|
0.5
|
|
ND1
|
B:HIS136
|
3.7
|
15.9
|
1.0
|
|
C
|
B:HIS136
|
3.8
|
16.4
|
1.0
|
|
CB
|
B:ASP138
|
3.8
|
22.0
|
1.0
|
|
HD1
|
B:HIS136
|
3.8
|
15.9
|
0.0
|
|
O
|
B:PHE166
|
3.8
|
18.4
|
1.0
|
|
H
|
B:ASP138
|
4.0
|
19.0
|
1.0
|
|
N
|
B:PHE166
|
4.0
|
19.1
|
1.0
|
|
C
|
B:GLY167
|
4.0
|
19.9
|
1.0
|
|
HB3
|
B:PHE168
|
4.0
|
20.5
|
0.5
|
|
NE2
|
B:HIS136
|
4.1
|
17.1
|
1.0
|
|
HB3
|
B:PHE168
|
4.1
|
20.9
|
0.5
|
|
CA
|
B:ALA169
|
4.1
|
17.2
|
1.0
|
|
HA
|
B:ALA169
|
4.2
|
17.5
|
1.0
|
|
CD2
|
B:PHE168
|
4.2
|
25.1
|
0.5
|
|
CG
|
B:PHE168
|
4.2
|
22.9
|
0.5
|
|
CB
|
B:ALA169
|
4.2
|
18.2
|
1.0
|
|
N
|
B:ASP138
|
4.2
|
18.7
|
1.0
|
|
CG
|
B:HIS136
|
4.3
|
16.9
|
1.0
|
|
HA
|
B:HIS136
|
4.3
|
16.6
|
1.0
|
|
CG
|
B:PHE168
|
4.3
|
23.6
|
0.5
|
|
CA
|
B:GLY167
|
4.3
|
19.7
|
1.0
|
|
HB2
|
B:ARG137
|
4.4
|
18.0
|
1.0
|
|
HB3
|
B:ASP165
|
4.4
|
21.3
|
0.5
|
|
HA
|
B:PHE168
|
4.4
|
18.6
|
0.5
|
|
HA
|
B:PHE168
|
4.4
|
18.8
|
0.5
|
|
HD2
|
B:PHE168
|
4.4
|
23.0
|
0.5
|
|
HE2
|
B:HIS136
|
4.4
|
17.2
|
0.0
|
|
CD2
|
B:HIS136
|
4.4
|
17.3
|
1.0
|
|
O
|
B:PHE168
|
4.5
|
20.4
|
1.0
|
|
HB3
|
B:ALA169
|
4.5
|
17.9
|
1.0
|
|
CA
|
B:HIS136
|
4.6
|
16.7
|
1.0
|
|
CA
|
B:ASP138
|
4.6
|
19.4
|
1.0
|
|
CD2
|
B:PHE168
|
4.6
|
22.1
|
0.5
|
|
OD1
|
B:ASP165
|
4.7
|
14.8
|
0.5
|
|
CB
|
B:PHE166
|
4.7
|
18.7
|
1.0
|
|
C
|
B:ARG137
|
4.8
|
19.7
|
1.0
|
|
N
|
B:ARG137
|
4.8
|
17.6
|
1.0
|
|
HA3
|
B:GLY167
|
4.8
|
19.6
|
1.0
|
|
HB3
|
B:PHE166
|
4.8
|
18.6
|
1.0
|
|
H
|
B:PHE166
|
4.9
|
18.9
|
1.0
|
|
HB3
|
B:ASP165
|
4.9
|
18.6
|
0.5
|
|
HB1
|
B:ALA169
|
5.0
|
17.9
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 5 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg303
b:34.4
occ:1.00
|
H
|
C:ASP199
|
2.0
|
24.6
|
1.0
|
|
OE2
|
C:GLU191
|
2.7
|
23.9
|
1.0
|
|
HB2
|
C:TYR198
|
2.7
|
19.6
|
1.0
|
|
HA
|
C:TYR198
|
2.9
|
20.9
|
1.0
|
|
N
|
C:ASP199
|
2.9
|
24.2
|
1.0
|
|
OD1
|
C:ASP199
|
3.0
|
24.9
|
1.0
|
|
HG3
|
C:GLU191
|
3.1
|
24.3
|
1.0
|
|
HB2
|
C:HIS263
|
3.1
|
32.6
|
1.0
|
|
H
|
C:ALA202
|
3.2
|
20.8
|
1.0
|
|
HB2
|
C:ALA202
|
3.3
|
21.4
|
1.0
|
|
HB3
|
C:HIS263
|
3.3
|
32.5
|
1.0
|
|
HB2
|
C:LYS201
|
3.3
|
25.0
|
1.0
|
|
CB
|
C:TYR198
|
3.4
|
19.7
|
1.0
|
|
CA
|
C:TYR198
|
3.5
|
19.6
|
1.0
|
|
HH12
|
C:ARG266
|
3.5
|
24.3
|
1.0
|
|
CB
|
C:HIS263
|
3.6
|
32.9
|
1.0
|
|
CD
|
C:GLU191
|
3.6
|
25.0
|
1.0
|
|
N
|
C:ALA202
|
3.6
|
21.0
|
1.0
|
|
C
|
C:TYR198
|
3.7
|
25.0
|
1.0
|
|
CG
|
C:HIS263
|
3.7
|
35.4
|
1.0
|
|
O
|
C:ASP199
|
3.7
|
20.2
|
1.0
|
|
CG
|
C:GLU191
|
3.7
|
23.6
|
1.0
|
|
HB3
|
C:TYR198
|
3.7
|
19.5
|
1.0
|
|
CG
|
C:ASP199
|
3.8
|
28.4
|
1.0
|
|
CA
|
C:ASP199
|
3.9
|
25.3
|
1.0
|
|
H
|
C:LYS201
|
3.9
|
22.5
|
1.0
|
|
HG2
|
C:GLU191
|
4.0
|
24.3
|
1.0
|
|
C
|
C:ASP199
|
4.0
|
22.9
|
1.0
|
|
CD2
|
C:HIS263
|
4.1
|
39.1
|
1.0
|
|
CB
|
C:ALA202
|
4.1
|
21.8
|
1.0
|
|
HA
|
C:ALA202
|
4.1
|
21.2
|
1.0
|
|
ND1
|
C:HIS263
|
4.1
|
40.5
|
1.0
|
|
CB
|
C:LYS201
|
4.2
|
24.8
|
1.0
|
|
C
|
C:LYS201
|
4.2
|
20.3
|
1.0
|
|
CA
|
C:ALA202
|
4.2
|
20.5
|
1.0
|
|
NH1
|
C:ARG266
|
4.3
|
24.5
|
1.0
|
|
HD2
|
C:HIS263
|
4.3
|
38.2
|
1.0
|
|
HD1
|
C:HIS263
|
4.3
|
40.4
|
0.0
|
|
N
|
C:LYS201
|
4.3
|
22.0
|
1.0
|
|
HE3
|
C:MET177
|
4.4
|
28.6
|
0.5
|
|
CB
|
C:ASP199
|
4.4
|
24.8
|
1.0
|
|
CA
|
C:LYS201
|
4.5
|
23.3
|
1.0
|
|
HH11
|
C:ARG266
|
4.5
|
24.3
|
1.0
|
|
HB3
|
C:ALA202
|
4.5
|
21.5
|
1.0
|
|
HD1
|
C:TYR198
|
4.5
|
19.7
|
1.0
|
|
OD2
|
C:ASP199
|
4.6
|
33.3
|
1.0
|
|
HB3
|
C:LYS201
|
4.6
|
25.0
|
1.0
|
|
OE1
|
C:GLU191
|
4.7
|
25.9
|
1.0
|
|
HB3
|
C:ASP199
|
4.7
|
25.7
|
1.0
|
|
CG
|
C:TYR198
|
4.7
|
18.8
|
1.0
|
|
NE2
|
C:HIS263
|
4.8
|
39.1
|
1.0
|
|
HA
|
C:ASP199
|
4.8
|
24.5
|
1.0
|
|
CE1
|
C:HIS263
|
4.8
|
38.5
|
1.0
|
|
HB1
|
C:ALA202
|
4.8
|
21.5
|
1.0
|
|
N
|
C:TYR198
|
4.8
|
21.3
|
1.0
|
|
HE2
|
C:MET177
|
4.9
|
32.1
|
0.5
|
|
O
|
C:TYR198
|
4.9
|
21.1
|
1.0
|
|
O
|
C:HIS197
|
4.9
|
23.6
|
1.0
|
|
HE2
|
C:MET177
|
4.9
|
28.6
|
0.5
|
|
N
|
C:GLY200
|
5.0
|
24.8
|
1.0
|
|
O
|
C:LYS201
|
5.0
|
20.7
|
1.0
|
|
HD2
|
C:LYS201
|
5.0
|
31.9
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 6 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg304
b:30.9
occ:1.00
|
H
|
C:PHE168
|
2.1
|
19.5
|
1.0
|
|
HB2
|
C:PHE168
|
2.5
|
21.8
|
0.5
|
|
HB2
|
C:PHE168
|
2.6
|
19.2
|
0.5
|
|
HA
|
C:PHE166
|
2.7
|
19.2
|
1.0
|
|
O
|
C:ASP165
|
2.8
|
20.5
|
0.5
|
|
O
|
C:ASP165
|
2.8
|
19.9
|
0.5
|
|
O
|
C:HIS136
|
2.8
|
17.7
|
1.0
|
|
N
|
C:PHE168
|
2.9
|
19.1
|
1.0
|
|
H
|
C:ALA169
|
2.9
|
18.1
|
1.0
|
|
N
|
C:ALA169
|
3.3
|
17.6
|
1.0
|
|
CB
|
C:PHE168
|
3.3
|
21.6
|
0.5
|
|
HB3
|
C:ASP138
|
3.3
|
22.6
|
1.0
|
|
CA
|
C:PHE168
|
3.4
|
19.2
|
0.5
|
|
CB
|
C:PHE168
|
3.4
|
19.5
|
0.5
|
|
HB2
|
C:ASP138
|
3.4
|
22.6
|
1.0
|
|
C
|
C:PHE166
|
3.4
|
19.9
|
1.0
|
|
CA
|
C:PHE168
|
3.4
|
18.2
|
0.5
|
|
CA
|
C:PHE166
|
3.4
|
18.7
|
1.0
|
|
HD2
|
C:PHE168
|
3.5
|
20.3
|
0.5
|
|
N
|
C:GLY167
|
3.5
|
20.7
|
1.0
|
|
HB2
|
C:ALA169
|
3.5
|
17.8
|
1.0
|
|
H
|
C:GLY167
|
3.5
|
20.6
|
1.0
|
|
C
|
C:PHE168
|
3.6
|
19.2
|
1.0
|
|
CE1
|
C:HIS136
|
3.6
|
15.7
|
1.0
|
|
HE1
|
C:HIS136
|
3.7
|
16.3
|
1.0
|
|
C
|
C:ASP165
|
3.7
|
20.1
|
0.5
|
|
C
|
C:ASP165
|
3.7
|
19.4
|
0.5
|
|
ND1
|
C:HIS136
|
3.7
|
17.1
|
1.0
|
|
CB
|
C:ASP138
|
3.8
|
22.4
|
1.0
|
|
HD1
|
C:HIS136
|
3.8
|
17.0
|
0.0
|
|
O
|
C:PHE166
|
3.8
|
19.3
|
1.0
|
|
C
|
C:HIS136
|
3.9
|
16.4
|
1.0
|
|
N
|
C:PHE166
|
4.0
|
19.2
|
1.0
|
|
C
|
C:GLY167
|
4.0
|
21.6
|
1.0
|
|
HB3
|
C:PHE168
|
4.0
|
21.7
|
0.5
|
|
H
|
C:ASP138
|
4.0
|
18.4
|
1.0
|
|
HB3
|
C:PHE168
|
4.1
|
19.2
|
0.5
|
|
NE2
|
C:HIS136
|
4.1
|
16.5
|
1.0
|
|
CG
|
C:PHE168
|
4.1
|
24.9
|
0.5
|
|
CA
|
C:ALA169
|
4.2
|
18.1
|
1.0
|
|
CD2
|
C:PHE168
|
4.2
|
20.1
|
0.5
|
|
HA
|
C:ALA169
|
4.2
|
17.9
|
1.0
|
|
CB
|
C:ALA169
|
4.2
|
17.6
|
1.0
|
|
N
|
C:ASP138
|
4.2
|
17.6
|
1.0
|
|
CG
|
C:PHE168
|
4.3
|
19.5
|
0.5
|
|
CA
|
C:GLY167
|
4.3
|
21.3
|
1.0
|
|
CG
|
C:HIS136
|
4.3
|
17.0
|
1.0
|
|
HA
|
C:HIS136
|
4.3
|
16.8
|
1.0
|
|
HA
|
C:PHE168
|
4.4
|
19.6
|
0.5
|
|
HA
|
C:PHE168
|
4.4
|
18.8
|
0.5
|
|
HB2
|
C:ARG137
|
4.4
|
17.3
|
1.0
|
|
HB3
|
C:ASP165
|
4.4
|
22.4
|
0.5
|
|
HD2
|
C:PHE168
|
4.4
|
25.2
|
0.5
|
|
HE2
|
C:HIS136
|
4.4
|
16.4
|
0.0
|
|
CD2
|
C:HIS136
|
4.5
|
16.8
|
1.0
|
|
O
|
C:PHE168
|
4.5
|
18.2
|
1.0
|
|
HB3
|
C:ALA169
|
4.5
|
17.8
|
1.0
|
|
OD1
|
C:ASP165
|
4.6
|
14.3
|
0.5
|
|
CD2
|
C:PHE168
|
4.6
|
24.3
|
0.5
|
|
CA
|
C:HIS136
|
4.6
|
16.2
|
1.0
|
|
CA
|
C:ASP138
|
4.6
|
19.7
|
1.0
|
|
CB
|
C:PHE166
|
4.7
|
19.1
|
1.0
|
|
HA3
|
C:GLY167
|
4.7
|
21.2
|
1.0
|
|
C
|
C:ARG137
|
4.8
|
19.0
|
1.0
|
|
N
|
C:ARG137
|
4.8
|
16.3
|
1.0
|
|
H
|
C:PHE166
|
4.8
|
19.4
|
1.0
|
|
HB3
|
C:ASP165
|
4.8
|
20.3
|
0.5
|
|
HB3
|
C:PHE166
|
4.9
|
18.9
|
1.0
|
|
CG
|
C:ASP165
|
4.9
|
22.0
|
0.5
|
|
CG
|
C:ASP138
|
5.0
|
26.5
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 7 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:30.1
occ:1.00
|
H
|
D:ASP199
|
2.0
|
19.4
|
1.0
|
|
OE2
|
D:GLU191
|
2.7
|
20.1
|
1.0
|
|
HB2
|
D:TYR198
|
2.8
|
19.4
|
1.0
|
|
N
|
D:ASP199
|
2.9
|
19.0
|
1.0
|
|
HA
|
D:TYR198
|
2.9
|
20.0
|
1.0
|
|
OD1
|
D:ASP199
|
2.9
|
23.3
|
1.0
|
|
HG3
|
D:GLU191
|
3.0
|
20.5
|
1.0
|
|
HB2
|
D:HIS263
|
3.0
|
25.6
|
1.0
|
|
HB2
|
D:ALA202
|
3.3
|
18.2
|
1.0
|
|
HB3
|
D:HIS263
|
3.3
|
25.5
|
1.0
|
|
H
|
D:ALA202
|
3.3
|
18.2
|
1.0
|
|
HB2
|
D:LYS201
|
3.4
|
24.1
|
1.0
|
|
CA
|
D:TYR198
|
3.5
|
20.0
|
1.0
|
|
CB
|
D:TYR198
|
3.5
|
19.9
|
1.0
|
|
CB
|
D:HIS263
|
3.5
|
26.5
|
1.0
|
|
CD
|
D:GLU191
|
3.6
|
21.1
|
1.0
|
|
CG
|
D:HIS263
|
3.6
|
27.8
|
1.0
|
|
HH12
|
D:ARG266
|
3.6
|
19.5
|
1.0
|
|
C
|
D:TYR198
|
3.6
|
19.8
|
1.0
|
|
O
|
D:ASP199
|
3.7
|
20.4
|
1.0
|
|
CG
|
D:GLU191
|
3.7
|
20.3
|
1.0
|
|
CG
|
D:ASP199
|
3.7
|
28.0
|
1.0
|
|
N
|
D:ALA202
|
3.7
|
17.0
|
1.0
|
|
HB3
|
D:TYR198
|
3.8
|
19.4
|
1.0
|
|
CA
|
D:ASP199
|
3.8
|
19.4
|
1.0
|
|
ND1
|
D:HIS263
|
3.9
|
31.2
|
1.0
|
|
C
|
D:ASP199
|
4.0
|
20.0
|
1.0
|
|
HG2
|
D:GLU191
|
4.0
|
20.5
|
1.0
|
|
HD1
|
D:HIS263
|
4.0
|
31.5
|
0.0
|
|
H
|
D:LYS201
|
4.0
|
19.2
|
1.0
|
|
CB
|
D:ALA202
|
4.1
|
18.3
|
1.0
|
|
CD2
|
D:HIS263
|
4.1
|
31.2
|
1.0
|
|
HA
|
D:ALA202
|
4.2
|
18.5
|
1.0
|
|
CA
|
D:ALA202
|
4.3
|
18.2
|
1.0
|
|
CB
|
D:ASP199
|
4.3
|
22.5
|
1.0
|
|
C
|
D:LYS201
|
4.3
|
21.4
|
1.0
|
|
CB
|
D:LYS201
|
4.3
|
23.7
|
1.0
|
|
HE3
|
D:MET177
|
4.3
|
23.4
|
0.5
|
|
HD2
|
D:HIS263
|
4.4
|
30.4
|
1.0
|
|
NH1
|
D:ARG266
|
4.4
|
19.4
|
1.0
|
|
OD2
|
D:ASP199
|
4.4
|
26.1
|
1.0
|
|
N
|
D:LYS201
|
4.4
|
19.2
|
1.0
|
|
HD2
|
D:TYR198
|
4.5
|
18.2
|
1.0
|
|
HB3
|
D:ALA202
|
4.5
|
18.2
|
1.0
|
|
HB3
|
D:ASP199
|
4.6
|
22.9
|
1.0
|
|
CA
|
D:LYS201
|
4.6
|
20.1
|
1.0
|
|
CE1
|
D:HIS263
|
4.6
|
33.4
|
1.0
|
|
O
|
D:HOH424
|
4.6
|
35.3
|
1.0
|
|
HB3
|
D:LYS201
|
4.6
|
24.2
|
1.0
|
|
NE2
|
D:HIS263
|
4.7
|
31.0
|
1.0
|
|
HH11
|
D:ARG266
|
4.7
|
19.5
|
1.0
|
|
HA
|
D:ASP199
|
4.7
|
20.0
|
1.0
|
|
OE1
|
D:GLU191
|
4.7
|
20.1
|
1.0
|
|
CG
|
D:TYR198
|
4.7
|
17.7
|
1.0
|
|
HE2
|
D:MET177
|
4.7
|
28.8
|
0.5
|
|
HB1
|
D:ALA202
|
4.8
|
18.2
|
1.0
|
|
N
|
D:TYR198
|
4.8
|
19.9
|
1.0
|
|
O
|
D:TYR198
|
4.9
|
20.9
|
1.0
|
|
HE1
|
D:MET177
|
4.9
|
28.8
|
0.5
|
|
HE2
|
D:MET177
|
4.9
|
23.4
|
0.5
|
|
O
|
D:HIS197
|
4.9
|
21.8
|
1.0
|
|
N
|
D:GLY200
|
4.9
|
21.8
|
1.0
|
|
CA
|
D:HIS263
|
4.9
|
21.7
|
1.0
|
|
CB
|
D:GLU191
|
5.0
|
20.5
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 8p5i
Go back to
Magnesium Binding Sites List in 8p5i
Magnesium binding site 8 out
of 8 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg303
b:33.2
occ:1.00
|
H
|
D:PHE168
|
2.2
|
22.5
|
1.0
|
|
HA
|
D:PHE166
|
2.6
|
23.5
|
1.0
|
|
HB2
|
D:PHE168
|
2.7
|
23.5
|
1.0
|
|
O
|
D:ASP165
|
2.7
|
21.8
|
1.0
|
|
O
|
D:HIS136
|
2.8
|
18.6
|
1.0
|
|
H
|
D:ALA169
|
2.9
|
20.0
|
1.0
|
|
N
|
D:PHE168
|
3.0
|
21.8
|
1.0
|
|
N
|
D:ALA169
|
3.2
|
19.9
|
1.0
|
|
C
|
D:PHE166
|
3.4
|
24.2
|
1.0
|
|
CA
|
D:PHE166
|
3.4
|
23.2
|
1.0
|
|
HD2
|
D:PHE168
|
3.4
|
33.0
|
1.0
|
|
HB3
|
D:ASP138
|
3.4
|
25.7
|
1.0
|
|
HB2
|
D:ALA169
|
3.4
|
20.1
|
1.0
|
|
CB
|
D:PHE168
|
3.5
|
23.5
|
1.0
|
|
CA
|
D:PHE168
|
3.5
|
20.8
|
1.0
|
|
N
|
D:GLY167
|
3.5
|
24.4
|
1.0
|
|
H
|
D:GLY167
|
3.5
|
24.6
|
1.0
|
|
CE1
|
D:HIS136
|
3.5
|
18.7
|
1.0
|
|
C
|
D:PHE168
|
3.6
|
19.6
|
1.0
|
|
HE1
|
D:HIS136
|
3.6
|
19.2
|
1.0
|
|
HB2
|
D:ASP138
|
3.6
|
25.7
|
1.0
|
|
ND1
|
D:HIS136
|
3.7
|
18.9
|
1.0
|
|
C
|
D:ASP165
|
3.7
|
22.2
|
1.0
|
|
O
|
D:PHE166
|
3.8
|
24.7
|
1.0
|
|
HD1
|
D:HIS136
|
3.8
|
18.8
|
0.0
|
|
C
|
D:HIS136
|
3.9
|
19.0
|
1.0
|
|
N
|
D:PHE166
|
3.9
|
23.9
|
1.0
|
|
NE2
|
D:HIS136
|
4.0
|
20.3
|
1.0
|
|
CB
|
D:ASP138
|
4.0
|
25.4
|
1.0
|
|
H
|
D:ASP138
|
4.0
|
21.8
|
1.0
|
|
C
|
D:GLY167
|
4.0
|
25.3
|
1.0
|
|
CA
|
D:ALA169
|
4.1
|
20.1
|
1.0
|
|
CD2
|
D:PHE168
|
4.1
|
35.4
|
1.0
|
|
HA
|
D:ALA169
|
4.1
|
20.6
|
1.0
|
|
CB
|
D:ALA169
|
4.1
|
20.1
|
1.0
|
|
HB3
|
D:PHE168
|
4.2
|
23.4
|
1.0
|
|
CG
|
D:HIS136
|
4.2
|
18.7
|
1.0
|
|
HA
|
D:HIS136
|
4.2
|
18.8
|
1.0
|
|
CG
|
D:PHE168
|
4.3
|
26.1
|
1.0
|
|
CA
|
D:GLY167
|
4.3
|
25.4
|
1.0
|
|
N
|
D:ASP138
|
4.3
|
21.6
|
1.0
|
|
HE2
|
D:HIS136
|
4.3
|
20.3
|
0.0
|
|
CD2
|
D:HIS136
|
4.3
|
21.2
|
1.0
|
|
HB3
|
D:ALA169
|
4.4
|
20.1
|
1.0
|
|
HA
|
D:PHE168
|
4.4
|
21.2
|
1.0
|
|
HB2
|
D:ARG137
|
4.4
|
19.8
|
1.0
|
|
O
|
D:PHE168
|
4.5
|
21.4
|
1.0
|
|
OD1
|
D:ASP165
|
4.5
|
17.0
|
0.5
|
|
CA
|
D:HIS136
|
4.6
|
18.4
|
1.0
|
|
HB3
|
D:ASP165
|
4.6
|
27.5
|
0.5
|
|
CB
|
D:PHE166
|
4.6
|
22.9
|
1.0
|
|
CA
|
D:ASP138
|
4.7
|
23.9
|
1.0
|
|
HA3
|
D:GLY167
|
4.7
|
25.1
|
1.0
|
|
HB3
|
D:PHE166
|
4.8
|
23.0
|
1.0
|
|
H
|
D:PHE166
|
4.8
|
23.3
|
1.0
|
|
N
|
D:ARG137
|
4.8
|
18.2
|
1.0
|
|
HB3
|
D:ASP165
|
4.8
|
21.6
|
0.5
|
|
C
|
D:ARG137
|
4.9
|
20.9
|
1.0
|
|
CG
|
D:ASP165
|
4.9
|
23.0
|
0.5
|
|
HD2
|
D:HIS136
|
4.9
|
20.4
|
1.0
|
|
HB1
|
D:ALA169
|
5.0
|
20.1
|
1.0
|
|
CB
|
D:HIS136
|
5.0
|
19.5
|
1.0
|
|
Reference:
T.Battista,
M.S.Semrau,
G.Lolli,
P.Storici.
Crystal Structures of ULK1 in Complex with Kcgs Compounds To Be Published.
Page generated: Fri Aug 15 12:10:40 2025
|
