Magnesium in PDB 6omb: CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Enzymatic activity of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
All present enzymatic activity of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore:
3.6.4.6;
Other elements in 6omb:
The structure of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
(pdb code 6omb). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore, PDB code: 6omb:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 1 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg903
b:52.1
occ:1.00
|
OG1
|
A:THR535
|
2.0
|
59.4
|
1.0
|
F1
|
A:BEF902
|
2.4
|
61.3
|
1.0
|
O3B
|
A:ADP901
|
3.0
|
61.3
|
1.0
|
CB
|
A:THR535
|
3.4
|
59.4
|
1.0
|
CG2
|
A:THR535
|
3.9
|
59.4
|
1.0
|
BE
|
A:BEF902
|
3.9
|
61.3
|
1.0
|
OD2
|
A:ASP587
|
3.9
|
59.2
|
1.0
|
OD1
|
A:ASP587
|
4.0
|
59.2
|
1.0
|
CA
|
A:THR535
|
4.4
|
59.4
|
1.0
|
CG
|
A:ASP587
|
4.4
|
59.2
|
1.0
|
N
|
A:THR535
|
4.4
|
59.4
|
1.0
|
PB
|
A:ADP901
|
4.4
|
61.3
|
1.0
|
NH2
|
B:ARG648
|
4.5
|
51.4
|
1.0
|
O
|
B:ASP619
|
4.5
|
58.4
|
1.0
|
O1B
|
A:ADP901
|
4.6
|
61.3
|
1.0
|
OE2
|
A:GLU588
|
4.6
|
59.4
|
1.0
|
O1A
|
A:ADP901
|
4.7
|
61.3
|
1.0
|
F2
|
A:BEF902
|
4.7
|
61.3
|
1.0
|
F3
|
A:BEF902
|
4.8
|
61.3
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 2 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg906
b:85.0
occ:1.00
|
OG1
|
A:THR262
|
2.0
|
96.0
|
1.0
|
O3B
|
A:ADP904
|
2.2
|
89.7
|
1.0
|
F1
|
A:BEF905
|
2.8
|
89.7
|
1.0
|
CB
|
A:THR262
|
3.4
|
96.0
|
1.0
|
PB
|
A:ADP904
|
3.6
|
89.7
|
1.0
|
O2B
|
A:ADP904
|
4.1
|
89.7
|
1.0
|
CG2
|
A:THR262
|
4.1
|
96.0
|
1.0
|
BE
|
A:BEF905
|
4.1
|
89.7
|
1.0
|
O1B
|
A:ADP904
|
4.3
|
89.7
|
1.0
|
OD2
|
A:ASP314
|
4.3
|
0.8
|
1.0
|
CA
|
A:THR262
|
4.4
|
96.0
|
1.0
|
N
|
A:THR262
|
4.4
|
96.0
|
1.0
|
NH2
|
B:ARG372
|
4.6
|
68.2
|
1.0
|
OD1
|
A:ASP314
|
4.6
|
0.8
|
1.0
|
CG
|
A:LYS261
|
4.7
|
98.4
|
1.0
|
O3A
|
A:ADP904
|
4.8
|
89.7
|
1.0
|
F3
|
A:BEF905
|
4.8
|
89.7
|
1.0
|
CG
|
A:ASP314
|
4.9
|
0.8
|
1.0
|
O2A
|
A:ADP904
|
5.0
|
89.7
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 3 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg902
b:30.5
occ:1.00
|
OG1
|
B:THR535
|
2.0
|
37.2
|
1.0
|
O3B
|
B:ADP901
|
2.4
|
36.0
|
1.0
|
F1
|
C:BEF901
|
2.5
|
36.0
|
1.0
|
CB
|
B:THR535
|
3.3
|
37.2
|
1.0
|
OD2
|
B:ASP587
|
3.6
|
38.2
|
1.0
|
CG2
|
B:THR535
|
3.7
|
37.2
|
1.0
|
BE
|
C:BEF901
|
3.9
|
36.0
|
1.0
|
PB
|
B:ADP901
|
3.9
|
36.0
|
1.0
|
OD1
|
B:ASP587
|
4.1
|
38.2
|
1.0
|
O
|
C:ASP619
|
4.2
|
40.2
|
1.0
|
O1B
|
B:ADP901
|
4.2
|
36.0
|
1.0
|
CG
|
B:ASP587
|
4.3
|
38.2
|
1.0
|
NH2
|
C:ARG648
|
4.4
|
37.7
|
1.0
|
O1A
|
B:ADP901
|
4.4
|
36.0
|
1.0
|
CA
|
B:THR535
|
4.4
|
37.2
|
1.0
|
F3
|
C:BEF901
|
4.6
|
36.0
|
1.0
|
N
|
B:THR535
|
4.6
|
37.2
|
1.0
|
O3A
|
B:ADP901
|
4.6
|
36.0
|
1.0
|
OE2
|
B:GLU588
|
4.7
|
41.2
|
1.0
|
O2B
|
B:ADP901
|
4.9
|
36.0
|
1.0
|
PA
|
B:ADP901
|
5.0
|
36.0
|
1.0
|
F2
|
C:BEF901
|
5.0
|
36.0
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 4 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg905
b:31.4
occ:1.00
|
OG1
|
B:THR262
|
2.0
|
41.7
|
1.0
|
F1
|
B:BEF904
|
2.1
|
43.3
|
1.0
|
CB
|
B:THR262
|
3.3
|
41.7
|
1.0
|
O3B
|
B:ADP903
|
3.3
|
43.3
|
1.0
|
BE
|
B:BEF904
|
3.6
|
43.3
|
1.0
|
CG2
|
B:THR262
|
3.8
|
41.7
|
1.0
|
OD1
|
B:ASP314
|
3.8
|
50.2
|
1.0
|
OD2
|
B:ASP314
|
3.9
|
50.2
|
1.0
|
CG
|
B:ASP314
|
4.3
|
50.2
|
1.0
|
O1B
|
B:ADP903
|
4.3
|
43.3
|
1.0
|
O
|
C:ASP343
|
4.3
|
46.6
|
1.0
|
F2
|
B:BEF904
|
4.4
|
43.3
|
1.0
|
CA
|
B:THR262
|
4.4
|
41.7
|
1.0
|
PB
|
B:ADP903
|
4.5
|
43.3
|
1.0
|
NH2
|
C:ARG372
|
4.5
|
41.5
|
1.0
|
N
|
B:THR262
|
4.6
|
41.7
|
1.0
|
F3
|
B:BEF904
|
4.6
|
43.3
|
1.0
|
O1A
|
B:ADP903
|
4.9
|
43.3
|
1.0
|
CG
|
B:LYS261
|
5.0
|
40.6
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 5 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg904
b:34.1
occ:1.00
|
OG1
|
C:THR535
|
2.0
|
37.4
|
1.0
|
F1
|
C:BEF903
|
2.1
|
41.3
|
1.0
|
CB
|
C:THR535
|
3.4
|
37.4
|
1.0
|
O3B
|
C:ADP902
|
3.5
|
41.3
|
1.0
|
BE
|
C:BEF903
|
3.6
|
41.3
|
1.0
|
CG2
|
C:THR535
|
3.8
|
37.4
|
1.0
|
OD1
|
C:ASP587
|
4.0
|
39.7
|
1.0
|
OD2
|
C:ASP587
|
4.0
|
39.7
|
1.0
|
CA
|
C:THR535
|
4.3
|
37.4
|
1.0
|
N
|
C:THR535
|
4.4
|
37.4
|
1.0
|
CG
|
C:ASP587
|
4.4
|
39.7
|
1.0
|
O1B
|
C:ADP902
|
4.4
|
41.3
|
1.0
|
F3
|
C:BEF903
|
4.5
|
41.3
|
1.0
|
F2
|
C:BEF903
|
4.5
|
41.3
|
1.0
|
PB
|
C:ADP902
|
4.6
|
41.3
|
1.0
|
O
|
D:ASP619
|
4.6
|
39.0
|
1.0
|
NH2
|
D:ARG648
|
4.8
|
39.3
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 6 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg907
b:27.8
occ:1.00
|
OG1
|
C:THR262
|
2.0
|
38.4
|
1.0
|
F1
|
C:BEF906
|
2.2
|
38.8
|
1.0
|
O3B
|
C:ADP905
|
3.3
|
38.8
|
1.0
|
CB
|
C:THR262
|
3.4
|
38.4
|
1.0
|
OD2
|
C:ASP314
|
3.5
|
37.8
|
1.0
|
BE
|
C:BEF906
|
3.7
|
38.8
|
1.0
|
CG2
|
C:THR262
|
3.9
|
38.4
|
1.0
|
OD1
|
C:ASP314
|
4.0
|
37.8
|
1.0
|
CG
|
C:ASP314
|
4.2
|
37.8
|
1.0
|
O
|
D:ASP343
|
4.3
|
45.8
|
1.0
|
CA
|
C:THR262
|
4.4
|
38.4
|
1.0
|
O1B
|
C:ADP905
|
4.4
|
38.8
|
1.0
|
N
|
C:THR262
|
4.5
|
38.4
|
1.0
|
PB
|
C:ADP905
|
4.5
|
38.8
|
1.0
|
F2
|
C:BEF906
|
4.5
|
38.8
|
1.0
|
NH2
|
D:ARG372
|
4.6
|
39.8
|
1.0
|
CG
|
C:LYS261
|
4.6
|
34.5
|
1.0
|
F3
|
C:BEF906
|
4.7
|
38.8
|
1.0
|
O3A
|
C:ADP905
|
5.0
|
38.8
|
1.0
|
CD
|
C:LYS261
|
5.0
|
34.5
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 6omb
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Magnesium Binding Sites List in 6omb
Magnesium binding site 7 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg903
b:38.9
occ:1.00
|
OG1
|
D:THR535
|
2.0
|
46.7
|
1.0
|
F1
|
D:BEF902
|
2.1
|
51.7
|
1.0
|
O2B
|
D:ADP901
|
3.1
|
51.7
|
1.0
|
CB
|
D:THR535
|
3.4
|
46.7
|
1.0
|
BE
|
D:BEF902
|
3.4
|
51.7
|
1.0
|
F3
|
D:BEF902
|
3.6
|
51.7
|
1.0
|
CG2
|
D:THR535
|
3.8
|
46.7
|
1.0
|
OD2
|
D:ASP587
|
4.1
|
44.9
|
1.0
|
O3B
|
D:ADP901
|
4.2
|
51.7
|
1.0
|
O
|
E:ASP619
|
4.2
|
56.2
|
1.0
|
PB
|
D:ADP901
|
4.3
|
51.7
|
1.0
|
CA
|
D:THR535
|
4.4
|
46.7
|
1.0
|
N
|
D:THR535
|
4.4
|
46.7
|
1.0
|
OD1
|
D:ASP587
|
4.5
|
44.9
|
1.0
|
F2
|
D:BEF902
|
4.6
|
51.7
|
1.0
|
NH2
|
E:ARG648
|
4.6
|
54.1
|
1.0
|
CA
|
E:GLY620
|
4.7
|
53.7
|
1.0
|
OE2
|
D:GLU588
|
4.7
|
49.2
|
1.0
|
CG
|
D:ASP587
|
4.8
|
44.9
|
1.0
|
O2A
|
D:ADP901
|
5.0
|
51.7
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 6omb
Go back to
Magnesium Binding Sites List in 6omb
Magnesium binding site 8 out
of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg906
b:41.6
occ:1.00
|
OG1
|
D:THR262
|
2.0
|
46.8
|
1.0
|
O2B
|
D:ADP904
|
2.3
|
49.7
|
1.0
|
F1
|
D:BEF905
|
3.1
|
49.7
|
1.0
|
CB
|
D:THR262
|
3.4
|
46.8
|
1.0
|
PB
|
D:ADP904
|
3.5
|
49.7
|
1.0
|
OD1
|
D:ASP314
|
3.7
|
42.8
|
1.0
|
O3B
|
D:ADP904
|
3.9
|
49.7
|
1.0
|
CG2
|
D:THR262
|
4.0
|
46.8
|
1.0
|
BE
|
D:BEF905
|
4.0
|
49.7
|
1.0
|
O1B
|
D:ADP904
|
4.2
|
49.7
|
1.0
|
N
|
D:THR262
|
4.3
|
46.8
|
1.0
|
CA
|
D:THR262
|
4.4
|
46.8
|
1.0
|
OD2
|
D:ASP314
|
4.4
|
42.8
|
1.0
|
CG
|
D:ASP314
|
4.5
|
42.8
|
1.0
|
CG
|
D:LYS261
|
4.5
|
42.9
|
1.0
|
F3
|
D:BEF905
|
4.6
|
49.7
|
1.0
|
O3A
|
D:ADP904
|
4.7
|
49.7
|
1.0
|
NH2
|
E:ARG372
|
4.8
|
57.3
|
1.0
|
O2A
|
D:ADP904
|
4.9
|
49.7
|
1.0
|
CD
|
D:LYS261
|
4.9
|
42.9
|
1.0
|
|
Reference:
I.Cooney,
H.Han,
M.G.Stewart,
R.H.Carson,
D.T.Hansen,
J.H.Iwasa,
J.C.Price,
C.P.Hill,
P.S.Shen.
Structure of the CDC48 Segregase in the Act of Unfolding An Authentic Substrate. Science V. 365 502 2019.
ISSN: ESSN 1095-9203
PubMed: 31249134
DOI: 10.1126/SCIENCE.AAX0486
Page generated: Tue Oct 1 13:26:38 2024
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