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Magnesium in PDB 8ub4: CDC48-SHP1 Unfolding Native Substrate, Consensus Structure

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure:
3.6.4.6;

Other elements in 8ub4:

The structure of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure (pdb code 8ub4). 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-SHP1 Unfolding Native Substrate, Consensus Structure, PDB code: 8ub4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8ub4

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Magnesium binding site 1 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:166.3
occ:1.00
 OG1 A:THR262 1.8 177.3 1.0
F1 A:08T901 1.9 157.5 1.0
O2B A:08T901 2.6 172.1 1.0
CB A:THR262 3.0 177.5 1.0
HB A:THR262 3.0 179.5 1.0
H A:THR262 3.2 175.8 1.0
BE A:08T901 3.4 156.3 1.0
PB A:08T901 3.7 158.1 1.0
HG21 A:THR262 3.8 181.7 1.0
N A:THR262 3.8 174.2 1.0
O3B A:08T901 3.9 154.7 1.0
OD1 B:ASP343 3.9 152.1 1.0
HB2 A:LYS261 3.9 173.3 1.0
CA A:THR262 4.0 177.4 1.0
CG2 A:THR262 4.0 182.4 1.0
HH12 B:ARG369 4.3 152.7 1.0
F2 A:08T901 4.3 161.9 1.0
O3A A:08T901 4.3 157.7 1.0
HA A:THR262 4.3 179.1 1.0
F3 A:08T901 4.3 155.5 1.0
O2A A:08T901 4.4 165.1 1.0
HG23 A:THR262 4.4 182.1 1.0
HH12 B:ARG372 4.4 142.0 1.0
OD2 A:ASP314 4.6 182.1 1.0
HG22 A:THR262 4.7 181.8 1.0
OD1 A:ASP314 4.8 180.3 1.0
CB A:LYS261 4.8 172.1 1.0
PA A:08T901 4.9 170.7 1.0
NH1 B:ARG369 4.9 148.8 1.0
CG B:ASP343 5.0 151.2 1.0
C A:LYS261 5.0 176.1 1.0

Magnesium binding site 2 out of 8 in 8ub4

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Magnesium binding site 2 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:112.5
occ:1.00
 OG1 A:THR535 1.8 123.9 1.0
F1 A:08T903 1.9 122.8 1.0
O2B A:08T903 3.1 125.4 1.0
CB A:THR535 3.1 122.0 1.0
HB A:THR535 3.2 122.7 1.0
BE A:08T903 3.4 124.7 1.0
H A:THR535 3.5 119.5 1.0
HH22 B:ARG648 3.7 117.3 1.0
HG21 A:THR535 3.8 124.4 1.0
O1A A:08T903 3.9 125.0 1.0
CG2 A:THR535 4.0 125.7 1.0
N A:THR535 4.0 117.3 1.0
CA A:THR535 4.1 118.2 1.0
PB A:08T903 4.1 119.7 1.0
OD2 A:ASP587 4.1 146.9 1.0
F3 A:08T903 4.2 126.5 1.0
O3B A:08T903 4.2 121.1 1.0
OD1 A:ASP587 4.2 140.8 1.0
F2 A:08T903 4.2 132.5 1.0
HB2 A:LYS534 4.4 116.7 1.0
HA A:THR535 4.4 119.7 1.0
HG23 A:THR535 4.4 123.6 1.0
OE2 A:GLU588 4.4 140.8 1.0
NH2 B:ARG648 4.5 116.9 1.0
HH12 B:ARG645 4.5 122.0 1.0
HH12 B:ARG648 4.5 116.8 1.0
HE2 A:LYS534 4.6 119.3 1.0
CG A:ASP587 4.6 143.2 1.0
O3A A:08T903 4.7 117.0 1.0
PA A:08T903 4.8 124.5 1.0
HG22 A:THR535 4.8 123.8 1.0
HH21 B:ARG648 4.9 114.5 1.0

Magnesium binding site 3 out of 8 in 8ub4

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Magnesium binding site 3 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:95.7
occ:1.00
 OG1 B:THR262 1.8 95.0 1.0
F1 B:08T901 1.9 98.8 1.0
O2B B:08T901 2.8 92.2 1.0
CB B:THR262 3.0 91.9 1.0
HB B:THR262 3.0 91.7 1.0
BE B:08T901 3.4 94.4 1.0
HG21 B:THR262 3.5 98.7 1.0
H B:THR262 3.6 88.8 1.0
CG2 B:THR262 3.8 100.6 1.0
PB B:08T901 3.9 87.0 1.0
HH22 C:ARG372 3.9 99.5 1.0
OD1 B:ASP314 4.0 111.8 1.0
HH21 C:ARG372 4.0 98.7 1.0
HA2 C:GLY344 4.0 105.6 1.0
OD2 B:ASP314 4.0 110.3 1.0
O C:ASP343 4.0 101.2 1.0
O3B B:08T901 4.1 85.2 1.0
CA B:THR262 4.1 87.0 1.0
F3 B:08T901 4.1 103.0 1.0
N B:THR262 4.1 87.6 1.0
O1A B:08T901 4.2 93.3 1.0
HG23 B:THR262 4.2 95.5 1.0
NH2 C:ARG372 4.3 100.7 1.0
F2 B:08T901 4.3 100.0 1.0
HA B:THR262 4.4 90.0 1.0
CG B:ASP314 4.4 112.2 1.0
HB2 B:LYS261 4.5 85.2 1.0
HG22 B:THR262 4.6 96.4 1.0
O3A B:08T901 4.6 89.0 1.0
HE2 B:LYS261 4.8 85.0 1.0
HH22 C:ARG369 4.9 97.2 1.0
PA B:08T901 4.9 91.5 1.0
CA C:GLY344 4.9 107.0 1.0

Magnesium binding site 4 out of 8 in 8ub4

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Magnesium binding site 4 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:97.1
occ:1.00
 F1 B:08T903 1.8 102.8 1.0
OG1 B:THR535 1.9 96.9 1.0
O2B B:08T903 1.9 99.7 1.0
PB B:08T903 3.0 90.4 1.0
BE B:08T903 3.0 99.1 1.0
CB B:THR535 3.0 90.9 1.0
HB B:THR535 3.1 89.8 1.0
H B:THR535 3.1 84.3 1.0
O3B B:08T903 3.4 96.0 1.0
O3A B:08T903 3.6 83.8 1.0
F3 B:08T903 3.7 102.9 1.0
N B:THR535 3.8 80.8 1.0
HG21 B:THR535 3.9 92.0 1.0
CG2 B:THR535 4.0 94.9 1.0
HB2 B:LYS534 4.0 83.6 1.0
CA B:THR535 4.0 81.8 1.0
HH22 C:ARG648 4.1 100.2 1.0
O1A B:08T903 4.1 98.1 1.0
F2 B:08T903 4.3 99.7 1.0
O1B B:08T903 4.3 94.3 1.0
PA B:08T903 4.3 93.5 1.0
HG23 B:THR535 4.4 92.1 1.0
HH21 C:ARG645 4.4 98.2 1.0
HA B:THR535 4.5 84.0 1.0
O C:ASP619 4.5 105.1 1.0
OD1 B:ASP587 4.6 107.6 1.0
NH2 C:ARG648 4.6 100.6 1.0
HH22 C:ARG645 4.7 99.6 1.0
O2A B:08T903 4.7 90.8 1.0
OD1 C:ASP619 4.7 104.6 1.0
NH2 C:ARG645 4.7 99.2 1.0
HG22 B:THR535 4.8 90.9 1.0
HD2 B:LYS534 4.9 80.0 1.0
OD2 B:ASP587 4.9 117.3 1.0
HH21 C:ARG648 4.9 99.7 1.0
HA2 C:GLY620 4.9 113.8 1.0
HH12 C:ARG648 4.9 97.2 1.0
CB B:LYS534 5.0 83.2 1.0

Magnesium binding site 5 out of 8 in 8ub4

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Magnesium binding site 5 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:102.5
occ:1.00
 OG1 C:THR262 1.8 96.9 1.0
F1 C:08T901 1.9 103.0 1.0
O2B C:08T901 2.2 96.9 1.0
CB C:THR262 2.9 90.2 1.0
HB C:THR262 2.9 89.8 1.0
H C:THR262 3.2 86.1 1.0
BE C:08T901 3.3 98.0 1.0
PB C:08T901 3.4 82.7 1.0
O3B C:08T901 3.7 91.9 1.0
HG21 C:THR262 3.8 95.8 1.0
N C:THR262 3.8 84.5 1.0
HH22 D:ARG372 3.9 96.5 1.0
CA C:THR262 3.9 82.0 1.0
CG2 C:THR262 3.9 96.8 1.0
HB2 C:LYS261 4.0 80.1 1.0
O3A C:08T901 4.1 87.2 1.0
O1A C:08T901 4.1 88.6 1.0
F2 C:08T901 4.2 110.5 1.0
HA C:THR262 4.3 83.5 1.0
OD2 C:ASP314 4.3 106.0 1.0
F3 C:08T901 4.3 97.2 1.0
OD1 C:ASP314 4.3 111.7 1.0
HG23 C:THR262 4.4 92.2 1.0
HH21 D:ARG372 4.4 95.5 1.0
NH2 D:ARG372 4.5 94.0 1.0
O D:ASP343 4.5 108.4 1.0
HA2 D:GLY344 4.5 106.8 1.0
PA C:08T901 4.6 97.0 1.0
HG22 C:THR262 4.7 92.9 1.0
O1B C:08T901 4.7 90.5 1.0
CG C:ASP314 4.7 109.5 1.0
C C:LYS261 4.9 85.0 1.0
HZ1 C:LYS261 5.0 82.6 1.0
CB C:LYS261 5.0 78.1 1.0

Magnesium binding site 6 out of 8 in 8ub4

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Magnesium binding site 6 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:97.5
occ:1.00
 OG1 C:THR535 1.8 92.5 1.0
O2B C:08T903 1.9 101.6 1.0
F1 C:08T903 1.9 101.5 1.0
CB C:THR535 3.0 89.9 1.0
HB C:THR535 3.0 89.0 1.0
PB C:08T903 3.2 87.6 1.0
BE C:08T903 3.3 100.3 1.0
H C:THR535 3.3 84.5 1.0
O3B C:08T903 3.7 96.3 1.0
HG21 C:THR535 3.7 92.6 1.0
O3A C:08T903 3.8 88.1 1.0
N C:THR535 3.9 81.8 1.0
CG2 C:THR535 3.9 93.5 1.0
CA C:THR535 4.0 83.0 1.0
HH22 D:ARG648 4.1 96.6 1.0
F3 C:08T903 4.2 101.5 1.0
HB2 C:LYS534 4.2 78.7 1.0
HH21 D:ARG645 4.3 100.7 1.0
F2 C:08T903 4.3 103.4 1.0
HH22 D:ARG645 4.3 101.2 1.0
O1A C:08T903 4.3 94.8 1.0
HG23 C:THR535 4.4 89.6 1.0
O1B C:08T903 4.4 82.8 1.0
HA C:THR535 4.4 84.0 1.0
HE2 C:LYS534 4.4 84.6 1.0
OD1 C:ASP587 4.4 105.4 1.0
OD2 C:ASP587 4.4 107.4 1.0
HH21 D:ARG648 4.5 95.8 1.0
O D:ASP619 4.5 108.5 1.0
NH2 D:ARG648 4.6 93.9 1.0
PA C:08T903 4.6 99.4 1.0
NH2 D:ARG645 4.6 102.8 1.0
HG22 C:THR535 4.7 91.6 1.0
HA2 D:GLY620 4.8 104.0 1.0
O2A C:08T903 4.9 98.0 1.0
CG C:ASP587 4.9 105.7 1.0
OE2 C:GLU588 5.0 115.0 1.0

Magnesium binding site 7 out of 8 in 8ub4

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Magnesium binding site 7 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:103.2
occ:1.00
 OG1 D:THR262 1.8 100.6 1.0
F1 D:08T901 1.9 113.0 1.0
O2B D:08T901 1.9 103.5 1.0
CB D:THR262 3.0 96.6 1.0
HB D:THR262 3.1 96.1 1.0
H D:THR262 3.1 92.5 1.0
BE D:08T901 3.2 110.2 1.0
PB D:08T901 3.3 95.4 1.0
O3B D:08T901 3.7 103.6 1.0
N D:THR262 3.7 89.1 1.0
HH22 E:ARG372 3.9 120.6 1.0
HG21 D:THR262 3.9 103.0 1.0
CA D:THR262 3.9 88.4 1.0
HB2 D:LYS261 4.0 88.7 1.0
CG2 D:THR262 4.0 107.1 1.0
F2 D:08T901 4.1 112.3 1.0
O3A D:08T901 4.2 94.8 1.0
HA D:THR262 4.2 90.5 1.0
O2A D:08T901 4.3 102.8 1.0
F3 D:08T901 4.3 117.2 1.0
O1B D:08T901 4.4 108.1 1.0
HE3 D:LYS261 4.4 88.8 1.0
HG23 D:THR262 4.4 100.9 1.0
NH2 E:ARG372 4.6 121.9 1.0
PA D:08T901 4.8 106.5 1.0
HG22 D:THR262 4.8 101.4 1.0
HH21 E:ARG372 4.8 117.1 1.0
C D:LYS261 4.8 92.7 1.0
CB D:LYS261 4.9 88.3 1.0
HA2 E:GLY344 4.9 137.6 1.0
O1A D:08T901 5.0 111.1 1.0

Magnesium binding site 8 out of 8 in 8ub4

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Magnesium binding site 8 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Consensus Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of CDC48-SHP1 Unfolding Native Substrate, Consensus Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:98.1
occ:1.00
 OG1 D:THR535 1.8 104.1 1.0
F1 D:08T903 1.9 111.7 1.0
O2B D:08T903 1.9 105.6 1.0
CB D:THR535 3.0 100.0 1.0
HB D:THR535 3.0 98.9 1.0
H D:THR535 3.1 96.5 1.0
PB D:08T903 3.2 102.1 1.0
BE D:08T903 3.2 111.3 1.0
O3B D:08T903 3.6 108.3 1.0
N D:THR535 3.8 95.0 1.0
O2A D:08T903 3.8 108.1 1.0
HG21 D:THR535 3.9 106.6 1.0
CG2 D:THR535 3.9 105.5 1.0
CA D:THR535 4.0 96.0 1.0
HH22 E:ARG648 4.0 113.0 1.0
HB2 D:LYS534 4.0 94.5 1.0
F3 D:08T903 4.0 114.7 1.0
O3A D:08T903 4.1 100.8 1.0
HG23 D:THR535 4.1 102.8 1.0
HE2 D:LYS534 4.2 97.2 1.0
F2 D:08T903 4.3 109.5 1.0
HA D:THR535 4.4 96.8 1.0
O1B D:08T903 4.4 106.9 1.0
PA D:08T903 4.4 107.2 1.0
HH21 E:ARG648 4.5 114.9 1.0
NH2 E:ARG648 4.5 112.5 1.0
OD2 D:ASP587 4.5 113.4 1.0
HH21 E:ARG645 4.5 112.4 1.0
O E:ASP619 4.7 121.0 1.0
O1A D:08T903 4.7 106.4 1.0
HA2 E:GLY620 4.7 119.4 1.0
HG22 D:THR535 4.8 100.2 1.0
OD1 D:ASP587 4.8 109.5 1.0
OE2 D:GLU588 4.8 116.9 1.0
CB D:LYS534 4.9 92.0 1.0
C D:LYS534 5.0 92.5 1.0
OD2 E:ASP619 5.0 124.3 1.0
NH2 E:ARG645 5.0 111.8 1.0

Reference:

I.Cooney, H.L.Schubert, K.Cedeno, O.N.Fisher, R.Carson, J.C.Price, C.P.Hill, P.S.Shen. Visualization of the CDC48 Aaa+ Atpase Protein Unfolding Pathway. Nat Commun V. 15 7505 2024.
ISSN: ESSN 2041-1723
PubMed: 39209885
DOI: 10.1038/S41467-024-51835-3
Page generated: Wed Nov 13 11:58:16 2024

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