Magnesium in PDB 7qo4: 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Enzymatic activity of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
All present enzymatic activity of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs):
3.4.19.12;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
(pdb code 7qo4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs), PDB code: 7qo4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7qo4
Go back to
Magnesium Binding Sites List in 7qo4
Magnesium binding site 1 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg502
b:0.0
occ:1.00
|
OE1
|
H:GLU310
|
2.0
|
0.0
|
1.0
|
CB
|
H:ASN356
|
3.0
|
0.0
|
1.0
|
CD
|
H:GLU310
|
3.1
|
0.0
|
1.0
|
OE2
|
H:GLU310
|
3.4
|
0.0
|
1.0
|
O1G
|
H:ATP501
|
3.7
|
0.0
|
1.0
|
ND2
|
H:ASN356
|
3.9
|
0.0
|
1.0
|
N
|
H:ASN356
|
3.9
|
0.0
|
1.0
|
CG
|
H:ASN356
|
3.9
|
0.0
|
1.0
|
OD2
|
H:ASP312
|
4.0
|
0.0
|
1.0
|
CA
|
H:ASN356
|
4.0
|
0.0
|
1.0
|
CG
|
H:GLU310
|
4.4
|
0.0
|
1.0
|
CA
|
H:GLU310
|
4.5
|
0.0
|
1.0
|
PG
|
H:ATP501
|
4.7
|
0.0
|
1.0
|
CB
|
H:GLU310
|
4.7
|
0.0
|
1.0
|
CD1
|
I:LEU310
|
4.8
|
0.0
|
1.0
|
CG
|
H:ASP312
|
4.8
|
0.0
|
1.0
|
O3G
|
H:ATP501
|
4.8
|
0.0
|
1.0
|
CD2
|
I:LEU307
|
4.9
|
0.0
|
1.0
|
N
|
H:GLU310
|
4.9
|
0.0
|
1.0
|
O
|
H:ALA354
|
4.9
|
0.0
|
1.0
|
C
|
H:THR355
|
4.9
|
0.0
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7qo4
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Magnesium Binding Sites List in 7qo4
Magnesium binding site 2 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg502
b:0.0
occ:1.00
|
O3B
|
I:ATP501
|
2.5
|
0.0
|
1.0
|
O2G
|
I:ATP501
|
2.8
|
0.0
|
1.0
|
NH1
|
J:ARG306
|
3.1
|
0.0
|
1.0
|
PG
|
I:ATP501
|
3.1
|
0.0
|
1.0
|
O2B
|
I:ATP501
|
3.3
|
0.0
|
1.0
|
CZ
|
J:ARG306
|
3.4
|
0.0
|
1.0
|
O1G
|
I:ATP501
|
3.5
|
0.0
|
1.0
|
PB
|
I:ATP501
|
3.5
|
0.0
|
1.0
|
NH2
|
J:ARG306
|
3.6
|
0.0
|
1.0
|
NE
|
J:ARG306
|
4.2
|
0.0
|
1.0
|
OG1
|
I:THR230
|
4.2
|
0.0
|
1.0
|
O1B
|
I:ATP501
|
4.5
|
0.0
|
1.0
|
O3G
|
I:ATP501
|
4.5
|
0.0
|
1.0
|
CB
|
I:PRO225
|
4.6
|
0.0
|
1.0
|
OE2
|
I:GLU283
|
4.7
|
0.0
|
1.0
|
O3A
|
I:ATP501
|
4.8
|
0.0
|
1.0
|
O2A
|
I:ATP501
|
4.9
|
0.0
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7qo4
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Magnesium Binding Sites List in 7qo4
Magnesium binding site 3 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg502
b:0.0
occ:1.00
|
OE1
|
K:GLU273
|
2.2
|
0.0
|
1.0
|
CD
|
K:GLU273
|
2.9
|
0.0
|
1.0
|
CG
|
K:GLU273
|
2.9
|
0.0
|
1.0
|
O2G
|
K:ATP501
|
3.1
|
0.0
|
1.0
|
OG1
|
K:THR220
|
3.4
|
0.0
|
1.0
|
OD1
|
K:ASN319
|
3.9
|
0.0
|
1.0
|
O
|
K:ASP272
|
3.9
|
0.0
|
1.0
|
OE2
|
K:GLU273
|
4.0
|
0.0
|
1.0
|
O1G
|
K:ATP501
|
4.0
|
0.0
|
1.0
|
PG
|
K:ATP501
|
4.1
|
0.0
|
1.0
|
CB
|
K:ALA317
|
4.1
|
0.0
|
1.0
|
CB
|
K:GLU273
|
4.4
|
0.0
|
1.0
|
O2B
|
K:ATP501
|
4.6
|
0.0
|
1.0
|
C
|
K:ASP272
|
4.6
|
0.0
|
1.0
|
O3B
|
K:ATP501
|
4.8
|
0.0
|
1.0
|
CB
|
K:THR220
|
4.8
|
0.0
|
1.0
|
CG
|
K:ASN319
|
4.9
|
0.0
|
1.0
|
CA
|
K:GLU273
|
4.9
|
0.0
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7qo4
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Magnesium Binding Sites List in 7qo4
Magnesium binding site 4 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg502
b:0.0
occ:1.00
|
O1G
|
L:ATP501
|
2.2
|
0.0
|
1.0
|
CG2
|
L:THR229
|
2.8
|
0.0
|
1.0
|
O3B
|
L:ATP501
|
2.9
|
0.0
|
1.0
|
NH2
|
M:ARG342
|
3.1
|
0.0
|
1.0
|
OG1
|
L:THR229
|
3.1
|
0.0
|
1.0
|
PG
|
L:ATP501
|
3.2
|
0.0
|
1.0
|
CB
|
L:THR229
|
3.4
|
0.0
|
1.0
|
CG
|
M:ASP313
|
3.5
|
0.0
|
1.0
|
OD2
|
M:ASP313
|
3.5
|
0.0
|
1.0
|
CB
|
M:ASP313
|
3.8
|
0.0
|
1.0
|
O1A
|
L:ATP501
|
3.9
|
0.0
|
1.0
|
OD1
|
M:ASP313
|
4.0
|
0.0
|
1.0
|
O2G
|
L:ATP501
|
4.1
|
0.0
|
1.0
|
CZ
|
M:ARG342
|
4.3
|
0.0
|
1.0
|
PB
|
L:ATP501
|
4.3
|
0.0
|
1.0
|
O3G
|
L:ATP501
|
4.3
|
0.0
|
1.0
|
O3A
|
L:ATP501
|
4.5
|
0.0
|
1.0
|
PA
|
L:ATP501
|
4.6
|
0.0
|
1.0
|
OE1
|
L:GLU282
|
4.7
|
0.0
|
1.0
|
O2B
|
L:ATP501
|
4.8
|
0.0
|
1.0
|
CA
|
M:ASP313
|
4.8
|
0.0
|
1.0
|
NH1
|
M:ARG342
|
4.8
|
0.0
|
1.0
|
CA
|
L:THR229
|
4.8
|
0.0
|
1.0
|
O
|
M:LEU309
|
4.9
|
0.0
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7qo4
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Magnesium Binding Sites List in 7qo4
Magnesium binding site 5 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg502
b:0.0
occ:1.00
|
OG1
|
M:THR229
|
2.4
|
0.0
|
1.0
|
OD1
|
M:ASP281
|
2.6
|
0.0
|
1.0
|
O1G
|
M:ATP501
|
2.9
|
0.0
|
1.0
|
O2G
|
M:ATP501
|
2.9
|
0.0
|
1.0
|
O2B
|
M:ATP501
|
3.0
|
0.0
|
1.0
|
PG
|
M:ATP501
|
3.3
|
0.0
|
1.0
|
CG
|
M:ASP281
|
3.5
|
0.0
|
1.0
|
OD1
|
H:ASP341
|
3.6
|
0.0
|
1.0
|
CB
|
M:THR229
|
3.7
|
0.0
|
1.0
|
OD2
|
M:ASP281
|
3.7
|
0.0
|
1.0
|
CG2
|
M:THR229
|
3.9
|
0.0
|
1.0
|
O3B
|
M:ATP501
|
4.0
|
0.0
|
1.0
|
PB
|
M:ATP501
|
4.0
|
0.0
|
1.0
|
CG
|
H:ASP341
|
4.2
|
0.0
|
1.0
|
CB
|
M:ALA326
|
4.6
|
0.0
|
1.0
|
CA
|
M:THR229
|
4.7
|
0.0
|
1.0
|
O3G
|
M:ATP501
|
4.8
|
0.0
|
1.0
|
O3A
|
M:ATP501
|
4.8
|
0.0
|
1.0
|
OD2
|
H:ASP341
|
4.8
|
0.0
|
1.0
|
N
|
M:THR229
|
4.9
|
0.0
|
1.0
|
CB
|
H:ASP341
|
4.9
|
0.0
|
1.0
|
CB
|
M:ASP281
|
4.9
|
0.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7qo4
Go back to
Magnesium Binding Sites List in 7qo4
Magnesium binding site 6 out
of 6 in the 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of 26S Proteasome Wt-UBP6-Ubvs Complex in the Si State (Atpases, RPN1, UBP6, and Ubvs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg503
b:0.0
occ:1.00
|
O2A
|
J:ADP501
|
2.4
|
0.0
|
1.0
|
O3B
|
J:ADP501
|
2.9
|
0.0
|
1.0
|
PA
|
J:ADP501
|
3.6
|
0.0
|
1.0
|
CB
|
J:PRO191
|
3.7
|
0.0
|
1.0
|
O3A
|
J:ADP501
|
3.8
|
0.0
|
1.0
|
PB
|
J:ADP501
|
4.0
|
0.0
|
1.0
|
C
|
J:PRO191
|
4.2
|
0.0
|
1.0
|
CA
|
J:PRO191
|
4.3
|
0.0
|
1.0
|
N
|
J:GLY192
|
4.3
|
0.0
|
1.0
|
O5'
|
J:ADP501
|
4.5
|
0.0
|
1.0
|
O
|
J:PRO191
|
4.5
|
0.0
|
1.0
|
O1A
|
J:ADP501
|
4.8
|
0.0
|
1.0
|
C5'
|
J:ADP501
|
4.8
|
0.0
|
1.0
|
CG
|
J:PRO191
|
4.9
|
0.0
|
1.0
|
O1B
|
J:ADP501
|
5.0
|
0.0
|
1.0
|
CA
|
J:GLY192
|
5.0
|
0.0
|
1.0
|
|
Reference:
K.Y.S.Hung,
S.Klumpe,
M.R.Eisele,
S.Elsasser,
G.Tian,
S.Sun,
J.A.Moroco,
T.C.Cheng,
T.Joshi,
T.Seibel,
D.Van Dalen,
X.H.Feng,
Y.Lu,
H.Ovaa,
J.R.Engen,
B.H.Lee,
T.Rudack,
E.Sakata,
D.Finley.
Allosteric Control of UBP6 and the Proteasome Via A Bidirectional Switch. Nat Commun V. 13 838 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-28186-Y
Page generated: Thu Oct 3 05:10:15 2024
|