Magnesium in PDB 7ln4: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3):
3.6.4.6;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
(pdb code 7ln4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3), PDB code: 7ln4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 1 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg903
b:34.8
occ:1.00
|
O3G
|
B:ATP901
|
2.1
|
31.7
|
1.0
|
CG2
|
B:THR525
|
3.0
|
44.7
|
1.0
|
O1B
|
B:ATP901
|
3.0
|
31.7
|
1.0
|
PG
|
B:ATP901
|
3.1
|
31.7
|
1.0
|
O1G
|
B:ATP901
|
3.2
|
31.7
|
1.0
|
CB
|
B:THR525
|
3.2
|
44.7
|
1.0
|
OD2
|
A:ASP609
|
3.3
|
48.9
|
1.0
|
O3B
|
B:ATP901
|
3.6
|
31.7
|
1.0
|
PB
|
B:ATP901
|
3.8
|
31.7
|
1.0
|
O1A
|
B:ATP901
|
3.9
|
31.7
|
1.0
|
NH2
|
A:ARG638
|
4.0
|
24.9
|
1.0
|
OD1
|
B:ASP577
|
4.1
|
28.2
|
1.0
|
OG1
|
B:THR525
|
4.2
|
44.7
|
1.0
|
OD2
|
B:ASP577
|
4.2
|
28.2
|
1.0
|
N
|
B:THR525
|
4.2
|
44.7
|
1.0
|
CG
|
A:ASP609
|
4.4
|
48.9
|
1.0
|
CA
|
B:THR525
|
4.4
|
44.7
|
1.0
|
O2G
|
B:ATP901
|
4.4
|
31.7
|
1.0
|
O3A
|
B:ATP901
|
4.4
|
31.7
|
1.0
|
NE2
|
B:GLN578
|
4.5
|
22.1
|
1.0
|
CG
|
B:ASP577
|
4.6
|
28.2
|
1.0
|
PA
|
B:ATP901
|
4.6
|
31.7
|
1.0
|
OD1
|
A:ASP609
|
4.9
|
48.9
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 2 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg903
b:20.8
occ:1.00
|
OG1
|
C:THR525
|
2.1
|
31.7
|
1.0
|
O1G
|
C:ATP902
|
2.1
|
31.7
|
1.0
|
O1B
|
C:ATP902
|
2.2
|
31.7
|
1.0
|
CB
|
C:THR525
|
3.3
|
31.7
|
1.0
|
PB
|
C:ATP902
|
3.3
|
31.7
|
1.0
|
PG
|
C:ATP902
|
3.3
|
31.7
|
1.0
|
O3B
|
C:ATP902
|
3.4
|
31.7
|
1.0
|
NH2
|
B:ARG638
|
4.0
|
31.7
|
1.0
|
OD1
|
C:ASP577
|
4.1
|
41.5
|
1.0
|
O1A
|
C:ATP902
|
4.1
|
31.7
|
1.0
|
CG2
|
C:THR525
|
4.1
|
31.7
|
1.0
|
O3A
|
C:ATP902
|
4.1
|
31.7
|
1.0
|
N
|
C:THR525
|
4.2
|
31.7
|
1.0
|
O2G
|
C:ATP902
|
4.2
|
31.7
|
1.0
|
CA
|
C:THR525
|
4.3
|
31.7
|
1.0
|
OD2
|
C:ASP577
|
4.3
|
41.5
|
1.0
|
NE2
|
C:GLN578
|
4.4
|
31.7
|
1.0
|
O3G
|
C:ATP902
|
4.4
|
31.7
|
1.0
|
O2B
|
C:ATP902
|
4.5
|
31.7
|
1.0
|
O
|
B:ASP609
|
4.5
|
27.4
|
1.0
|
CG
|
C:ASP577
|
4.6
|
41.5
|
1.0
|
PA
|
C:ATP902
|
4.7
|
31.7
|
1.0
|
NH1
|
B:ARG635
|
4.8
|
31.7
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 3 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg904
b:29.7
occ:1.00
|
OG1
|
C:THR252
|
2.3
|
13.3
|
1.0
|
O3G
|
C:ATP901
|
2.4
|
31.7
|
1.0
|
O2B
|
C:ATP901
|
2.7
|
31.7
|
1.0
|
O3B
|
C:ATP901
|
2.8
|
31.7
|
1.0
|
PG
|
C:ATP901
|
3.2
|
31.7
|
1.0
|
PB
|
C:ATP901
|
3.3
|
31.7
|
1.0
|
CB
|
C:THR252
|
3.5
|
13.3
|
1.0
|
O1A
|
C:ATP901
|
3.5
|
31.7
|
1.0
|
OD2
|
C:ASP304
|
3.9
|
33.6
|
1.0
|
OD1
|
C:ASP304
|
4.0
|
33.6
|
1.0
|
O3A
|
C:ATP901
|
4.1
|
31.7
|
1.0
|
O2G
|
C:ATP901
|
4.1
|
31.7
|
1.0
|
N
|
C:THR252
|
4.3
|
13.3
|
1.0
|
PA
|
C:ATP901
|
4.3
|
31.7
|
1.0
|
OE2
|
C:GLU305
|
4.4
|
39.5
|
1.0
|
CG
|
C:ASP304
|
4.4
|
33.6
|
1.0
|
O1G
|
C:ATP901
|
4.4
|
31.7
|
1.0
|
CG2
|
C:THR252
|
4.4
|
13.3
|
1.0
|
CA
|
C:THR252
|
4.5
|
13.3
|
1.0
|
OD2
|
B:ASP333
|
4.5
|
36.9
|
1.0
|
NH2
|
B:ARG362
|
4.6
|
31.7
|
1.0
|
O1B
|
C:ATP901
|
4.6
|
31.7
|
1.0
|
NH1
|
B:ARG359
|
4.8
|
31.7
|
1.0
|
O2A
|
C:ATP901
|
5.0
|
31.7
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 4 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg903
b:25.0
occ:1.00
|
OG1
|
D:THR525
|
2.0
|
31.7
|
1.0
|
O2G
|
D:ATP902
|
2.1
|
31.7
|
1.0
|
O1B
|
D:ATP902
|
2.6
|
31.7
|
1.0
|
CB
|
D:THR525
|
3.2
|
31.7
|
1.0
|
PG
|
D:ATP902
|
3.5
|
31.7
|
1.0
|
PB
|
D:ATP902
|
3.7
|
31.7
|
1.0
|
O3B
|
D:ATP902
|
3.7
|
31.7
|
1.0
|
O1A
|
D:ATP902
|
3.8
|
31.7
|
1.0
|
OD1
|
D:ASP577
|
3.9
|
31.7
|
1.0
|
CG2
|
D:THR525
|
3.9
|
31.7
|
1.0
|
OD2
|
D:ASP577
|
4.1
|
31.7
|
1.0
|
O
|
C:ASP609
|
4.1
|
3.7
|
1.0
|
NH2
|
C:ARG638
|
4.2
|
31.7
|
1.0
|
O3A
|
D:ATP902
|
4.2
|
31.7
|
1.0
|
NE2
|
D:GLN578
|
4.3
|
31.7
|
1.0
|
O1G
|
D:ATP902
|
4.3
|
31.7
|
1.0
|
CA
|
D:THR525
|
4.4
|
31.7
|
1.0
|
CG
|
D:ASP577
|
4.4
|
31.7
|
1.0
|
N
|
D:THR525
|
4.4
|
31.7
|
1.0
|
O3G
|
D:ATP902
|
4.5
|
31.7
|
1.0
|
PA
|
D:ATP902
|
4.6
|
31.7
|
1.0
|
NH1
|
C:ARG635
|
4.7
|
31.7
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 5 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg904
b:29.1
occ:1.00
|
OG1
|
D:THR252
|
2.0
|
31.7
|
1.0
|
O3G
|
D:ATP901
|
2.1
|
31.7
|
1.0
|
O2B
|
D:ATP901
|
2.3
|
31.7
|
1.0
|
CB
|
D:THR252
|
3.3
|
31.7
|
1.0
|
PG
|
D:ATP901
|
3.4
|
31.7
|
1.0
|
PB
|
D:ATP901
|
3.5
|
31.7
|
1.0
|
O3B
|
D:ATP901
|
3.5
|
31.7
|
1.0
|
O1A
|
D:ATP901
|
3.6
|
31.7
|
1.0
|
NH2
|
C:ARG362
|
3.9
|
31.7
|
1.0
|
OD2
|
D:ASP304
|
4.1
|
34.1
|
1.0
|
OD1
|
D:ASP304
|
4.1
|
34.1
|
1.0
|
CG2
|
D:THR252
|
4.1
|
31.7
|
1.0
|
O2G
|
D:ATP901
|
4.1
|
31.7
|
1.0
|
N
|
D:THR252
|
4.2
|
31.7
|
1.0
|
O3A
|
D:ATP901
|
4.2
|
31.7
|
1.0
|
OE2
|
D:GLU305
|
4.2
|
30.0
|
1.0
|
CA
|
D:THR252
|
4.3
|
31.7
|
1.0
|
O1G
|
D:ATP901
|
4.5
|
31.7
|
1.0
|
PA
|
D:ATP901
|
4.5
|
31.7
|
1.0
|
CG
|
D:ASP304
|
4.5
|
34.1
|
1.0
|
O
|
C:ASP333
|
4.6
|
39.7
|
1.0
|
O1B
|
D:ATP901
|
4.7
|
31.7
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 6 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg903
b:24.8
occ:1.00
|
OG1
|
E:THR525
|
2.1
|
31.7
|
1.0
|
O1G
|
E:ATP902
|
2.3
|
31.7
|
1.0
|
O1B
|
E:ATP902
|
2.8
|
31.7
|
1.0
|
CB
|
E:THR525
|
3.4
|
31.7
|
1.0
|
OD1
|
E:ASP577
|
3.6
|
7.0
|
1.0
|
PG
|
E:ATP902
|
3.6
|
31.7
|
1.0
|
PB
|
E:ATP902
|
3.9
|
31.7
|
1.0
|
O3B
|
E:ATP902
|
3.9
|
31.7
|
1.0
|
NE2
|
E:GLN578
|
3.9
|
31.7
|
1.0
|
O1A
|
E:ATP902
|
4.0
|
31.7
|
1.0
|
CG2
|
E:THR525
|
4.0
|
31.7
|
1.0
|
OD2
|
E:ASP577
|
4.0
|
7.0
|
1.0
|
NH2
|
D:ARG638
|
4.2
|
31.7
|
1.0
|
CG
|
E:ASP577
|
4.2
|
7.0
|
1.0
|
O
|
D:ASP609
|
4.3
|
3.4
|
1.0
|
O3G
|
E:ATP902
|
4.5
|
31.7
|
1.0
|
CA
|
E:THR525
|
4.5
|
31.7
|
1.0
|
O3A
|
E:ATP902
|
4.5
|
31.7
|
1.0
|
N
|
E:THR525
|
4.5
|
31.7
|
1.0
|
O2G
|
E:ATP902
|
4.7
|
31.7
|
1.0
|
PA
|
E:ATP902
|
4.8
|
31.7
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 7 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg904
b:19.4
occ:1.00
|
OG1
|
E:THR252
|
2.1
|
31.7
|
1.0
|
O3G
|
E:ATP901
|
2.3
|
31.7
|
1.0
|
O2B
|
E:ATP901
|
2.4
|
31.7
|
1.0
|
CB
|
E:THR252
|
3.2
|
31.7
|
1.0
|
PG
|
E:ATP901
|
3.6
|
31.7
|
1.0
|
PB
|
E:ATP901
|
3.6
|
31.7
|
1.0
|
O1A
|
E:ATP901
|
3.6
|
31.7
|
1.0
|
O3B
|
E:ATP901
|
3.7
|
31.7
|
1.0
|
CG2
|
E:THR252
|
4.0
|
31.7
|
1.0
|
NH2
|
D:ARG362
|
4.0
|
31.7
|
1.0
|
OD2
|
E:ASP304
|
4.0
|
31.5
|
1.0
|
OD1
|
E:ASP304
|
4.1
|
31.5
|
1.0
|
O3A
|
E:ATP901
|
4.3
|
31.7
|
1.0
|
CA
|
E:THR252
|
4.3
|
31.7
|
1.0
|
N
|
E:THR252
|
4.3
|
31.7
|
1.0
|
CG
|
E:ASP304
|
4.5
|
31.5
|
1.0
|
O
|
D:ASP333
|
4.5
|
45.1
|
1.0
|
NH2
|
D:ARG359
|
4.5
|
31.7
|
1.0
|
O2G
|
E:ATP901
|
4.5
|
31.7
|
1.0
|
O1G
|
E:ATP901
|
4.5
|
31.7
|
1.0
|
PA
|
E:ATP901
|
4.6
|
31.7
|
1.0
|
OE2
|
E:GLU305
|
4.7
|
12.6
|
1.0
|
O1B
|
E:ATP901
|
4.8
|
31.7
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7ln4
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Magnesium Binding Sites List in 7ln4
Magnesium binding site 8 out
of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)
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 NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg903
b:31.1
occ:1.00
|
OG1
|
F:THR252
|
2.3
|
56.5
|
1.0
|
O2G
|
F:ATP901
|
2.4
|
59.6
|
1.0
|
O3B
|
F:ATP901
|
2.7
|
59.6
|
1.0
|
O2B
|
F:ATP901
|
2.8
|
59.6
|
1.0
|
PG
|
F:ATP901
|
3.0
|
59.6
|
1.0
|
O1A
|
F:ATP901
|
3.2
|
59.6
|
1.0
|
O3G
|
F:ATP901
|
3.3
|
59.6
|
1.0
|
PB
|
F:ATP901
|
3.4
|
59.6
|
1.0
|
CB
|
F:THR252
|
3.5
|
56.5
|
1.0
|
OD2
|
F:ASP304
|
3.5
|
51.4
|
1.0
|
OD1
|
F:ASP304
|
3.6
|
51.4
|
1.0
|
O3A
|
F:ATP901
|
3.9
|
59.6
|
1.0
|
CG
|
F:ASP304
|
4.0
|
51.4
|
1.0
|
PA
|
F:ATP901
|
4.0
|
59.6
|
1.0
|
N
|
F:THR252
|
4.2
|
56.5
|
1.0
|
O2A
|
F:ATP901
|
4.4
|
59.6
|
1.0
|
O1G
|
F:ATP901
|
4.4
|
59.6
|
1.0
|
CG2
|
F:THR252
|
4.4
|
56.5
|
1.0
|
CA
|
F:THR252
|
4.4
|
56.5
|
1.0
|
O1B
|
F:ATP901
|
4.7
|
59.6
|
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 23:28:13 2024
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