Magnesium in PDB 7lmy: Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6:
3.6.4.6;
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
(pdb code 7lmy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6, PDB code: 7lmy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 1 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg904
b:2.9
occ:1.00
|
OG1
|
A:THR252
|
2.0
|
5.0
|
1.0
|
O3G
|
A:ATP901
|
2.4
|
14.8
|
1.0
|
O2B
|
A:ATP901
|
2.9
|
14.8
|
1.0
|
O3B
|
A:ATP901
|
3.2
|
14.8
|
1.0
|
CB
|
A:THR252
|
3.2
|
5.0
|
1.0
|
PG
|
A:ATP901
|
3.5
|
14.8
|
1.0
|
O1A
|
A:ATP901
|
3.7
|
14.8
|
1.0
|
PB
|
A:ATP901
|
3.7
|
14.8
|
1.0
|
OD2
|
A:ASP304
|
3.8
|
4.1
|
1.0
|
OD1
|
A:ASP304
|
3.9
|
4.1
|
1.0
|
CG2
|
A:THR252
|
4.0
|
5.0
|
1.0
|
CG
|
A:ASP304
|
4.2
|
4.1
|
1.0
|
N
|
A:THR252
|
4.3
|
5.0
|
1.0
|
CA
|
A:THR252
|
4.3
|
5.0
|
1.0
|
O2G
|
A:ATP901
|
4.3
|
14.8
|
1.0
|
O3A
|
A:ATP901
|
4.4
|
14.8
|
1.0
|
O1G
|
A:ATP901
|
4.6
|
14.8
|
1.0
|
PA
|
A:ATP901
|
4.6
|
14.8
|
1.0
|
CG
|
A:GLU305
|
4.9
|
6.9
|
1.0
|
O1B
|
A:ATP901
|
4.9
|
14.8
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 2 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg905
b:17.8
occ:1.00
|
O2G
|
A:ATP902
|
2.2
|
14.8
|
1.0
|
O1A
|
A:ATP902
|
2.3
|
14.8
|
1.0
|
OG1
|
A:THR525
|
3.2
|
7.0
|
1.0
|
O1B
|
A:ATP902
|
3.4
|
14.8
|
1.0
|
PG
|
A:ATP902
|
3.6
|
14.8
|
1.0
|
PA
|
A:ATP902
|
3.7
|
14.8
|
1.0
|
OD2
|
A:ASP577
|
3.7
|
12.3
|
1.0
|
NH2
|
F:ARG635
|
3.8
|
6.5
|
1.0
|
CB
|
A:THR525
|
3.9
|
7.0
|
1.0
|
O3A
|
A:ATP902
|
4.0
|
14.8
|
1.0
|
PB
|
A:ATP902
|
4.0
|
14.8
|
1.0
|
O3B
|
A:ATP902
|
4.1
|
14.8
|
1.0
|
O1G
|
A:ATP902
|
4.3
|
14.8
|
1.0
|
CG2
|
A:THR525
|
4.4
|
7.0
|
1.0
|
O2A
|
A:ATP902
|
4.6
|
14.8
|
1.0
|
O3G
|
A:ATP902
|
4.6
|
14.8
|
1.0
|
O5'
|
A:ATP902
|
4.7
|
14.8
|
1.0
|
C5'
|
A:ATP902
|
4.7
|
14.8
|
1.0
|
CG
|
A:ASP577
|
4.7
|
12.3
|
1.0
|
CZ
|
F:ARG635
|
4.9
|
6.5
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 3 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg904
b:3.8
occ:1.00
|
OG1
|
B:THR252
|
2.0
|
6.4
|
1.0
|
O3G
|
B:ATP901
|
2.4
|
14.8
|
1.0
|
O2B
|
B:ATP901
|
2.9
|
14.8
|
1.0
|
CB
|
B:THR252
|
3.2
|
6.4
|
1.0
|
O3B
|
B:ATP901
|
3.2
|
14.8
|
1.0
|
PG
|
B:ATP901
|
3.5
|
14.8
|
1.0
|
O1A
|
B:ATP901
|
3.7
|
14.8
|
1.0
|
PB
|
B:ATP901
|
3.7
|
14.8
|
1.0
|
OD2
|
B:ASP304
|
3.8
|
5.2
|
1.0
|
OD1
|
B:ASP304
|
3.8
|
5.2
|
1.0
|
CG2
|
B:THR252
|
4.0
|
6.4
|
1.0
|
CG
|
B:ASP304
|
4.2
|
5.2
|
1.0
|
N
|
B:THR252
|
4.3
|
6.4
|
1.0
|
CA
|
B:THR252
|
4.3
|
6.4
|
1.0
|
O2G
|
B:ATP901
|
4.3
|
14.8
|
1.0
|
O3A
|
B:ATP901
|
4.4
|
14.8
|
1.0
|
O1G
|
B:ATP901
|
4.6
|
14.8
|
1.0
|
PA
|
B:ATP901
|
4.6
|
14.8
|
1.0
|
CG
|
B:GLU305
|
4.9
|
6.4
|
1.0
|
O1B
|
B:ATP901
|
4.9
|
14.8
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 4 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg905
b:19.2
occ:1.00
|
O2G
|
B:ATP902
|
2.1
|
14.8
|
1.0
|
O1A
|
B:ATP902
|
2.3
|
14.8
|
1.0
|
OG1
|
B:THR525
|
3.2
|
14.8
|
1.0
|
O1B
|
B:ATP902
|
3.4
|
14.8
|
1.0
|
PG
|
B:ATP902
|
3.6
|
14.8
|
1.0
|
PA
|
B:ATP902
|
3.6
|
14.8
|
1.0
|
OD2
|
B:ASP577
|
3.7
|
12.9
|
1.0
|
NH2
|
A:ARG635
|
3.8
|
9.3
|
1.0
|
CB
|
B:THR525
|
3.9
|
14.8
|
1.0
|
O3A
|
B:ATP902
|
4.0
|
14.8
|
1.0
|
PB
|
B:ATP902
|
4.0
|
14.8
|
1.0
|
O3B
|
B:ATP902
|
4.0
|
14.8
|
1.0
|
O1G
|
B:ATP902
|
4.3
|
14.8
|
1.0
|
CG2
|
B:THR525
|
4.4
|
14.8
|
1.0
|
O2A
|
B:ATP902
|
4.5
|
14.8
|
1.0
|
O3G
|
B:ATP902
|
4.6
|
14.8
|
1.0
|
O5'
|
B:ATP902
|
4.7
|
14.8
|
1.0
|
C5'
|
B:ATP902
|
4.7
|
14.8
|
1.0
|
CG
|
B:ASP577
|
4.8
|
12.9
|
1.0
|
CZ
|
A:ARG635
|
4.9
|
9.3
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 5 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg904
b:4.0
occ:1.00
|
OG1
|
C:THR252
|
2.0
|
6.4
|
1.0
|
O3G
|
C:ATP901
|
2.4
|
14.8
|
1.0
|
O2B
|
C:ATP901
|
2.9
|
14.8
|
1.0
|
O3B
|
C:ATP901
|
3.2
|
14.8
|
1.0
|
CB
|
C:THR252
|
3.2
|
6.4
|
1.0
|
PG
|
C:ATP901
|
3.4
|
14.8
|
1.0
|
O1A
|
C:ATP901
|
3.7
|
14.8
|
1.0
|
PB
|
C:ATP901
|
3.7
|
14.8
|
1.0
|
OD2
|
C:ASP304
|
3.8
|
4.7
|
1.0
|
OD1
|
C:ASP304
|
3.9
|
4.7
|
1.0
|
CG2
|
C:THR252
|
4.0
|
6.4
|
1.0
|
CG
|
C:ASP304
|
4.2
|
4.7
|
1.0
|
O2G
|
C:ATP901
|
4.3
|
14.8
|
1.0
|
N
|
C:THR252
|
4.3
|
6.4
|
1.0
|
CA
|
C:THR252
|
4.3
|
6.4
|
1.0
|
O3A
|
C:ATP901
|
4.4
|
14.8
|
1.0
|
O1G
|
C:ATP901
|
4.6
|
14.8
|
1.0
|
PA
|
C:ATP901
|
4.6
|
14.8
|
1.0
|
CG
|
C:GLU305
|
4.9
|
5.6
|
1.0
|
O1B
|
C:ATP901
|
4.9
|
14.8
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 6 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg905
b:17.2
occ:1.00
|
O2G
|
C:ATP902
|
2.1
|
28.4
|
1.0
|
O1A
|
C:ATP902
|
2.3
|
28.4
|
1.0
|
OG1
|
C:THR525
|
3.1
|
14.8
|
1.0
|
O1B
|
C:ATP902
|
3.4
|
28.4
|
1.0
|
PG
|
C:ATP902
|
3.6
|
28.4
|
1.0
|
PA
|
C:ATP902
|
3.6
|
28.4
|
1.0
|
OD2
|
C:ASP577
|
3.7
|
11.8
|
1.0
|
NH2
|
B:ARG635
|
3.8
|
7.5
|
1.0
|
CB
|
C:THR525
|
3.8
|
14.8
|
1.0
|
O3A
|
C:ATP902
|
4.0
|
28.4
|
1.0
|
PB
|
C:ATP902
|
4.0
|
28.4
|
1.0
|
O3B
|
C:ATP902
|
4.0
|
28.4
|
1.0
|
O1G
|
C:ATP902
|
4.3
|
28.4
|
1.0
|
CG2
|
C:THR525
|
4.4
|
14.8
|
1.0
|
O2A
|
C:ATP902
|
4.5
|
28.4
|
1.0
|
O3G
|
C:ATP902
|
4.6
|
28.4
|
1.0
|
O5'
|
C:ATP902
|
4.7
|
28.4
|
1.0
|
C5'
|
C:ATP902
|
4.7
|
28.4
|
1.0
|
CG
|
C:ASP577
|
4.7
|
11.8
|
1.0
|
CZ
|
B:ARG635
|
4.9
|
7.5
|
1.0
|
NH1
|
B:ARG635
|
5.0
|
7.5
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 7 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg904
b:3.4
occ:1.00
|
OG1
|
D:THR252
|
2.0
|
3.4
|
1.0
|
O3G
|
D:ATP901
|
2.4
|
14.8
|
1.0
|
O2B
|
D:ATP901
|
2.9
|
14.8
|
1.0
|
O3B
|
D:ATP901
|
3.2
|
14.8
|
1.0
|
CB
|
D:THR252
|
3.2
|
3.4
|
1.0
|
PG
|
D:ATP901
|
3.4
|
14.8
|
1.0
|
O1A
|
D:ATP901
|
3.7
|
14.8
|
1.0
|
PB
|
D:ATP901
|
3.7
|
14.8
|
1.0
|
OD2
|
D:ASP304
|
3.9
|
5.3
|
1.0
|
OD1
|
D:ASP304
|
3.9
|
5.3
|
1.0
|
CG2
|
D:THR252
|
4.0
|
3.4
|
1.0
|
CG
|
D:ASP304
|
4.2
|
5.3
|
1.0
|
O2G
|
D:ATP901
|
4.3
|
14.8
|
1.0
|
N
|
D:THR252
|
4.3
|
3.4
|
1.0
|
CA
|
D:THR252
|
4.3
|
3.4
|
1.0
|
O3A
|
D:ATP901
|
4.4
|
14.8
|
1.0
|
O1G
|
D:ATP901
|
4.5
|
14.8
|
1.0
|
PA
|
D:ATP901
|
4.6
|
14.8
|
1.0
|
CG
|
D:GLU305
|
4.9
|
5.9
|
1.0
|
O1B
|
D:ATP901
|
4.9
|
14.8
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 8 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg905
b:18.6
occ:1.00
|
O2G
|
D:ATP902
|
2.2
|
14.8
|
1.0
|
O1A
|
D:ATP902
|
2.3
|
14.8
|
1.0
|
OG1
|
D:THR525
|
3.1
|
6.6
|
1.0
|
O1B
|
D:ATP902
|
3.4
|
14.8
|
1.0
|
PG
|
D:ATP902
|
3.6
|
14.8
|
1.0
|
PA
|
D:ATP902
|
3.6
|
14.8
|
1.0
|
OD2
|
D:ASP577
|
3.7
|
12.0
|
1.0
|
NH2
|
C:ARG635
|
3.8
|
6.9
|
1.0
|
CB
|
D:THR525
|
3.8
|
6.6
|
1.0
|
O3A
|
D:ATP902
|
4.0
|
14.8
|
1.0
|
PB
|
D:ATP902
|
4.0
|
14.8
|
1.0
|
O3B
|
D:ATP902
|
4.0
|
14.8
|
1.0
|
O1G
|
D:ATP902
|
4.3
|
14.8
|
1.0
|
CG2
|
D:THR525
|
4.4
|
6.6
|
1.0
|
O2A
|
D:ATP902
|
4.5
|
14.8
|
1.0
|
O3G
|
D:ATP902
|
4.6
|
14.8
|
1.0
|
O5'
|
D:ATP902
|
4.7
|
14.8
|
1.0
|
C5'
|
D:ATP902
|
4.7
|
14.8
|
1.0
|
CG
|
D:ASP577
|
4.7
|
12.0
|
1.0
|
CZ
|
C:ARG635
|
4.9
|
6.9
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 9 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg904
b:3.0
occ:1.00
|
OG1
|
E:THR252
|
2.0
|
7.5
|
1.0
|
O3G
|
E:ATP901
|
2.4
|
14.8
|
1.0
|
O2B
|
E:ATP901
|
2.9
|
14.8
|
1.0
|
CB
|
E:THR252
|
3.2
|
7.5
|
1.0
|
O3B
|
E:ATP901
|
3.2
|
14.8
|
1.0
|
PG
|
E:ATP901
|
3.5
|
14.8
|
1.0
|
O1A
|
E:ATP901
|
3.7
|
14.8
|
1.0
|
PB
|
E:ATP901
|
3.7
|
14.8
|
1.0
|
OD2
|
E:ASP304
|
3.8
|
4.6
|
1.0
|
OD1
|
E:ASP304
|
3.9
|
4.6
|
1.0
|
CG2
|
E:THR252
|
4.0
|
7.5
|
1.0
|
CG
|
E:ASP304
|
4.2
|
4.6
|
1.0
|
N
|
E:THR252
|
4.3
|
7.5
|
1.0
|
CA
|
E:THR252
|
4.3
|
7.5
|
1.0
|
O2G
|
E:ATP901
|
4.3
|
14.8
|
1.0
|
O3A
|
E:ATP901
|
4.4
|
14.8
|
1.0
|
O1G
|
E:ATP901
|
4.6
|
14.8
|
1.0
|
PA
|
E:ATP901
|
4.6
|
14.8
|
1.0
|
CG
|
E:GLU305
|
4.9
|
6.9
|
1.0
|
O1B
|
E:ATP901
|
4.9
|
14.8
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 7lmy
Go back to
Magnesium Binding Sites List in 7lmy
Magnesium binding site 10 out
of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg905
b:18.5
occ:1.00
|
O2G
|
E:ATP902
|
2.2
|
14.8
|
1.0
|
O1A
|
E:ATP902
|
2.3
|
14.8
|
1.0
|
OG1
|
E:THR525
|
3.1
|
5.1
|
1.0
|
O1B
|
E:ATP902
|
3.4
|
14.8
|
1.0
|
PG
|
E:ATP902
|
3.6
|
14.8
|
1.0
|
PA
|
E:ATP902
|
3.6
|
14.8
|
1.0
|
OD2
|
E:ASP577
|
3.7
|
12.5
|
1.0
|
NH2
|
D:ARG635
|
3.8
|
9.6
|
1.0
|
CB
|
E:THR525
|
3.8
|
5.1
|
1.0
|
O3A
|
E:ATP902
|
4.0
|
14.8
|
1.0
|
PB
|
E:ATP902
|
4.0
|
14.8
|
1.0
|
O3B
|
E:ATP902
|
4.0
|
14.8
|
1.0
|
O1G
|
E:ATP902
|
4.3
|
14.8
|
1.0
|
CG2
|
E:THR525
|
4.4
|
5.1
|
1.0
|
O2A
|
E:ATP902
|
4.5
|
14.8
|
1.0
|
O3G
|
E:ATP902
|
4.6
|
14.8
|
1.0
|
O5'
|
E:ATP902
|
4.7
|
14.8
|
1.0
|
C5'
|
E:ATP902
|
4.7
|
14.8
|
1.0
|
CG
|
E:ASP577
|
4.7
|
12.5
|
1.0
|
CZ
|
D:ARG635
|
4.9
|
9.6
|
1.0
|
|
Reference:
M.Pan,
Y.Yu,
H.Ai,
Q.Zheng,
Y.Xie,
L.Liu,
M.Zhao.
Mechanistic Insight Into Substrate Processing and Allosteric Inhibition of Human P97. Nat.Struct.Mol.Biol. V. 28 614 2021.
ISSN: ESSN 1545-9985
PubMed: 34262183
DOI: 10.1038/S41594-021-00617-2
Page generated: Wed Oct 2 23:26:04 2024
|