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:

Fluorine (F) 24 atoms

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 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 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 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 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 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 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 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

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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: Mon Dec 14 23:43:55 2020

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