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

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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 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 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 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 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

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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

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