Magnesium in PDB 8u7t: Substrate-Bound CDC48, Class 1

Enzymatic activity of Substrate-Bound CDC48, Class 1

All present enzymatic activity of Substrate-Bound CDC48, Class 1:
3.6.4.6;

Other elements in 8u7t:

The structure of Substrate-Bound CDC48, Class 1 also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Substrate-Bound CDC48, Class 1 (pdb code 8u7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Substrate-Bound CDC48, Class 1, PDB code: 8u7t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8u7t

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Magnesium binding site 1 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:115.3
occ:1.00
 OG1 A:THR784 2.0 119.4 1.0
F1 A:08T1101 2.0 115.3 1.0
O1B A:08T1101 2.0 115.3 1.0
CB A:THR784 3.2 119.4 1.0
BE A:08T1101 3.2 115.3 1.0
PB A:08T1101 3.3 115.3 1.0
N A:THR784 3.3 119.4 1.0
F3 A:08T1101 3.6 115.3 1.0
O3B A:08T1101 3.6 115.3 1.0
CA A:THR784 3.7 119.4 1.0
CB A:LYS783 4.1 120.1 1.0
C A:LYS783 4.3 120.1 1.0
O3A A:08T1101 4.3 115.3 1.0
O2B A:08T1101 4.3 115.3 1.0
O2A A:08T1101 4.4 115.3 1.0
CG2 A:THR784 4.4 119.4 1.0
O1A A:08T1101 4.4 115.3 1.0
OE2 A:GLU837 4.4 117.8 1.0
F2 A:08T1101 4.5 115.3 1.0
CE A:LYS783 4.6 120.1 1.0
PA A:08T1101 4.6 115.3 1.0
CA A:LYS783 4.6 120.1 1.0
N A:LYS783 4.9 120.1 1.0

Magnesium binding site 2 out of 8 in 8u7t

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Magnesium binding site 2 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:161.5
occ:1.00
 OG1 A:THR511 2.0 170.0 1.0
F1 A:08T1103 2.0 161.5 1.0
O2B A:08T1103 2.0 161.5 1.0
CB A:THR511 2.7 170.0 1.0
O2A A:08T1103 3.0 161.5 1.0
PB A:08T1103 3.1 161.5 1.0
BE A:08T1103 3.2 161.5 1.0
O3B A:08T1103 3.3 161.5 1.0
CG2 A:THR511 3.7 170.0 1.0
O3A A:08T1103 3.7 161.5 1.0
CA A:THR511 3.9 170.0 1.0
N A:THR511 3.9 170.0 1.0
PA A:08T1103 4.0 161.5 1.0
F3 A:08T1103 4.1 161.5 1.0
NH2 B:ARG1147 4.1 141.4 1.0
F2 A:08T1103 4.3 161.5 1.0
O1B A:08T1103 4.4 161.5 1.0
CG A:LYS510 4.5 167.9 1.0
OD2 B:ASP1121 4.6 141.7 1.0
O5' A:08T1103 5.0 161.5 1.0

Magnesium binding site 3 out of 8 in 8u7t

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Magnesium binding site 3 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:81.0
occ:1.00
 OG1 B:THR1306 1.9 81.4 1.0
F1 B:08T1601 2.0 81.0 1.0
O1B B:08T1601 2.0 81.0 1.0
CB B:THR1306 2.5 81.4 1.0
PB B:08T1601 2.8 81.0 1.0
O3A B:08T1601 2.8 81.0 1.0
O2A B:08T1601 3.1 81.0 1.0
BE B:08T1601 3.2 81.0 1.0
O1A B:08T1601 3.2 81.0 1.0
PA B:08T1601 3.2 81.0 1.0
O3B B:08T1601 3.4 81.0 1.0
CG2 B:THR1306 3.5 81.4 1.0
CA B:THR1306 3.6 81.4 1.0
N B:THR1306 3.6 81.4 1.0
F3 B:08T1601 3.7 81.0 1.0
OD2 C:ASP1952 4.0 86.0 1.0
O2B B:08T1601 4.3 81.0 1.0
NH2 C:ARG1978 4.4 79.9 1.0
F2 B:08T1601 4.4 81.0 1.0
O C:ASP1952 4.4 86.0 1.0
NH2 C:ARG1981 4.5 79.9 1.0
C B:THR1306 4.6 81.4 1.0
O5' B:08T1601 4.7 81.0 1.0
N B:LEU1307 4.8 81.3 1.0
C B:LYS1305 4.9 81.2 1.0

Magnesium binding site 4 out of 8 in 8u7t

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Magnesium binding site 4 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1604

b:88.3
occ:1.00
 OG1 B:THR1040 2.0 93.6 1.0
F1 B:08T1603 2.0 88.3 1.0
O1B B:08T1603 2.0 88.3 1.0
CB B:THR1040 2.7 93.6 1.0
PB B:08T1603 3.0 88.3 1.0
O2A B:08T1603 3.1 88.3 1.0
BE B:08T1603 3.2 88.3 1.0
O3B B:08T1603 3.3 88.3 1.0
N B:THR1040 3.4 93.6 1.0
O3A B:08T1603 3.4 88.3 1.0
CA B:THR1040 3.6 93.6 1.0
PA B:08T1603 3.7 88.3 1.0
O1A B:08T1603 3.9 88.3 1.0
CG2 B:THR1040 3.9 93.6 1.0
F2 B:08T1603 4.1 88.3 1.0
F3 B:08T1603 4.3 88.3 1.0
O2B B:08T1603 4.4 88.3 1.0
O C:ASP1676 4.5 93.6 1.0
C B:LYS1039 4.6 89.6 1.0
CB B:LYS1039 4.6 89.6 1.0
C B:THR1040 4.8 93.6 1.0
OD1 B:ASP1092 4.8 105.4 1.0
NH2 C:ARG1705 5.0 88.1 1.0
CA B:LYS1039 5.0 89.6 1.0

Magnesium binding site 5 out of 8 in 8u7t

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Magnesium binding site 5 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2202

b:78.9
occ:1.00
 OG1 C:THR1868 2.0 78.5 1.0
F1 C:08T2201 2.0 78.9 1.0
O1B C:08T2201 2.0 78.9 1.0
PB C:08T2201 3.1 78.9 1.0
CB C:THR1868 3.2 78.5 1.0
BE C:08T2201 3.2 78.9 1.0
O3B C:08T2201 3.4 78.9 1.0
O3A C:08T2201 3.7 78.9 1.0
F2 C:08T2201 3.9 78.9 1.0
N C:THR1868 4.0 78.5 1.0
CG2 C:THR1868 4.1 78.5 1.0
CA C:THR1868 4.2 78.5 1.0
OD1 C:ASP1920 4.2 80.7 1.0
OD2 C:ASP1920 4.4 80.7 1.0
F3 C:08T2201 4.4 78.9 1.0
O2B C:08T2201 4.4 78.9 1.0
NH2 D:ARG2539 4.5 79.6 1.0
O D:ASP2510 4.5 84.2 1.0
PA C:08T2201 4.7 78.9 1.0
CG C:ASP1920 4.7 80.7 1.0
OE2 C:GLU1921 4.8 81.1 1.0
O1A C:08T2201 4.8 78.9 1.0
O2A C:08T2201 4.9 78.9 1.0

Magnesium binding site 6 out of 8 in 8u7t

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Magnesium binding site 6 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2204

b:83.5
occ:1.00
 OG1 C:THR1595 2.0 82.9 1.0
O1B C:08T2203 2.0 83.5 1.0
F1 C:08T2203 2.0 83.5 1.0
CB C:THR1595 3.0 82.9 1.0
PB C:08T2203 3.1 83.5 1.0
BE C:08T2203 3.2 83.5 1.0
O3B C:08T2203 3.4 83.5 1.0
N C:THR1595 3.6 82.9 1.0
O2A C:08T2203 3.8 83.5 1.0
O3A C:08T2203 3.9 83.5 1.0
CA C:THR1595 3.9 82.9 1.0
F2 C:08T2203 4.0 83.5 1.0
CG2 C:THR1595 4.1 82.9 1.0
PA C:08T2203 4.3 83.5 1.0
F3 C:08T2203 4.4 83.5 1.0
O2B C:08T2203 4.4 83.5 1.0
O1A C:08T2203 4.4 83.5 1.0
OD1 C:ASP1647 4.5 87.3 1.0
CB C:LYS1594 4.7 78.8 1.0
C C:LYS1594 4.7 78.8 1.0
OD2 C:ASP1647 4.8 87.3 1.0
OD2 D:ASP2234 4.8 89.4 1.0
O D:ASP2234 4.8 89.4 1.0
NH2 D:ARG2263 4.9 85.6 1.0

Magnesium binding site 7 out of 8 in 8u7t

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Magnesium binding site 7 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2802

b:94.3
occ:1.00
 OG1 D:THR2426 2.0 85.5 1.0
F1 D:08T2801 2.0 94.3 1.0
O2B D:08T2801 2.0 94.3 1.0
CB D:THR2426 2.8 85.5 1.0
PB D:08T2801 3.1 94.3 1.0
BE D:08T2801 3.2 94.3 1.0
O1A D:08T2801 3.2 94.3 1.0
O3B D:08T2801 3.5 94.3 1.0
O3A D:08T2801 3.6 94.3 1.0
F3 D:08T2801 3.8 94.3 1.0
N D:THR2426 3.8 85.5 1.0
CG2 D:THR2426 3.9 85.5 1.0
PA D:08T2801 3.9 94.3 1.0
CA D:THR2426 3.9 85.5 1.0
O2A D:08T2801 4.2 94.3 1.0
O E:ASP3081 4.3 101.8 1.0
O1B D:08T2801 4.4 94.3 1.0
F2 D:08T2801 4.5 94.3 1.0
NH2 E:ARG3110 4.7 98.1 1.0

Magnesium binding site 8 out of 8 in 8u7t

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Magnesium binding site 8 out of 8 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Substrate-Bound CDC48, Class 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2804

b:85.8
occ:1.00
 OG1 D:THR2153 2.0 88.0 1.0
F1 D:08T2803 2.0 85.8 1.0
O2B D:08T2803 2.0 85.8 1.0
CB D:THR2153 3.0 88.0 1.0
PB D:08T2803 3.1 85.8 1.0
BE D:08T2803 3.2 85.8 1.0
O3B D:08T2803 3.4 85.8 1.0
O3A D:08T2803 3.7 85.8 1.0
CG2 D:THR2153 3.9 88.0 1.0
N D:THR2153 4.1 88.0 1.0
CA D:THR2153 4.1 88.0 1.0
F2 D:08T2803 4.2 85.8 1.0
F3 D:08T2803 4.2 85.8 1.0
O2A D:08T2803 4.3 85.8 1.0
O1B D:08T2803 4.4 85.8 1.0
NH2 E:ARG2834 4.4 96.4 1.0
PA D:08T2803 4.5 85.8 1.0
O1A D:08T2803 4.6 85.8 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 11:58:11 2024

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