Fluorine 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:

Magnesium (Mg) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 24 binding sites of Fluorine where determined in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore, PDB code: 6omb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 6omb

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Fluorine binding site 1 out of 24 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 Fluorine with other atoms in the F 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:F902

b:61.3
occ:1.00
F1 A:BEF902 0.0 61.3 1.0
BE A:BEF902 1.5 61.3 1.0
MG A:MG903 2.4 52.1 1.0
F3 A:BEF902 2.5 61.3 1.0
F2 A:BEF902 2.5 61.3 1.0
O3B A:ADP901 2.6 61.3 1.0
O1B A:ADP901 2.6 61.3 1.0
PB A:ADP901 3.2 61.3 1.0
OG1 A:THR535 3.7 59.4 1.0
NH2 B:ARG648 3.8 51.4 1.0
NZ A:LYS534 4.0 58.2 1.0
OD1 A:ASN634 4.1 59.0 1.0
ND2 A:ASN634 4.2 59.0 1.0
O3A A:ADP901 4.2 61.3 1.0
OE2 A:GLU588 4.3 59.4 1.0
O2B A:ADP901 4.4 61.3 1.0
CE A:LYS534 4.4 58.2 1.0
CG A:ASN634 4.6 59.0 1.0
NH1 B:ARG648 4.6 51.4 1.0
CZ B:ARG648 4.7 51.4 1.0
O1A A:ADP901 4.7 61.3 1.0
CB A:THR535 5.0 59.4 1.0

Fluorine binding site 2 out of 24 in 6omb

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Fluorine binding site 2 out of 24 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 Fluorine with other atoms in the F 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:F902

b:61.3
occ:1.00
F2 A:BEF902 0.0 61.3 1.0
BE A:BEF902 1.5 61.3 1.0
OD1 A:ASN634 2.3 59.0 1.0
NZ A:LYS534 2.4 58.2 1.0
O1B A:ADP901 2.5 61.3 1.0
F1 A:BEF902 2.5 61.3 1.0
F3 A:BEF902 2.6 61.3 1.0
CG A:ASN634 3.2 59.0 1.0
CE A:LYS534 3.3 58.2 1.0
CA A:PRO530 3.4 57.2 1.0
PB A:ADP901 3.6 61.3 1.0
ND2 A:ASN634 3.6 59.0 1.0
CB A:PRO530 3.7 57.2 1.0
O3B A:ADP901 3.8 61.3 1.0
O2B A:ADP901 4.0 61.3 1.0
N A:GLY531 4.1 62.7 1.0
N A:PRO530 4.2 57.2 1.0
O A:PRO529 4.3 58.7 1.0
C A:PRO530 4.3 57.2 1.0
CB A:ASN634 4.5 59.0 1.0
C A:PRO529 4.6 58.7 1.0
CD A:LYS534 4.7 58.2 1.0
MG A:MG903 4.7 52.1 1.0
CA A:ASN634 4.8 59.0 1.0
O3A A:ADP901 4.9 61.3 1.0
CG A:PRO530 5.0 57.2 1.0

Fluorine binding site 3 out of 24 in 6omb

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Fluorine binding site 3 out of 24 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 Fluorine with other atoms in the F 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
A:F902

b:61.3
occ:1.00
F3 A:BEF902 0.0 61.3 1.0
BE A:BEF902 1.5 61.3 1.0
O1B A:ADP901 2.4 61.3 1.0
F1 A:BEF902 2.5 61.3 1.0
F2 A:BEF902 2.6 61.3 1.0
NH1 B:ARG648 3.0 51.4 1.0
CB A:PRO530 3.4 57.2 1.0
OD1 A:ASN634 3.4 59.0 1.0
NE B:ARG645 3.5 54.4 1.0
NH2 B:ARG648 3.7 51.4 1.0
CD B:ARG645 3.7 54.4 1.0
CZ B:ARG648 3.8 51.4 1.0
CA A:PRO530 3.8 57.2 1.0
CZ B:ARG645 3.8 54.4 1.0
N A:GLY531 3.9 62.7 1.0
PB A:ADP901 3.9 61.3 1.0
O3B A:ADP901 4.2 61.3 1.0
C A:PRO530 4.3 57.2 1.0
NH1 B:ARG645 4.3 54.4 1.0
NH2 B:ARG645 4.3 54.4 1.0
CG A:ASN634 4.3 59.0 1.0
ND2 A:ASN634 4.4 59.0 1.0
O3A A:ADP901 4.5 61.3 1.0
NZ A:LYS534 4.8 58.2 1.0
MG A:MG903 4.8 52.1 1.0
CG A:PRO530 4.9 57.2 1.0
CA A:GLY531 4.9 62.7 1.0
O2B A:ADP901 5.0 61.3 1.0
O B:ALA642 5.0 47.9 1.0

Fluorine binding site 4 out of 24 in 6omb

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Fluorine binding site 4 out of 24 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 Fluorine with other atoms in the F 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
A:F905

b:89.7
occ:1.00
F1 A:BEF905 0.0 89.7 1.0
BE A:BEF905 1.5 89.7 1.0
F3 A:BEF905 2.5 89.7 1.0
F2 A:BEF905 2.5 89.7 1.0
O3B A:ADP904 2.6 89.7 1.0
O1B A:ADP904 2.6 89.7 1.0
MG A:MG906 2.8 85.0 1.0
PB A:ADP904 3.1 89.7 1.0
CD A:LYS261 3.6 98.4 1.0
CG A:LYS261 3.7 98.4 1.0
O2B A:ADP904 3.8 89.7 1.0
OG1 A:THR262 4.2 96.0 1.0
O3A A:ADP904 4.5 89.7 1.0
N A:GLY258 4.5 85.3 1.0
OD1 A:ASN358 4.5 94.5 1.0
ND2 A:ASN358 4.5 94.5 1.0
NZ A:LYS261 4.7 98.4 1.0
CE A:LYS261 4.7 98.4 1.0
CG A:ASN358 4.9 94.5 1.0
NH2 B:ARG372 5.0 68.2 1.0

Fluorine binding site 5 out of 24 in 6omb

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Fluorine binding site 5 out of 24 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 Fluorine with other atoms in the F 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
A:F905

b:89.7
occ:1.00
F2 A:BEF905 0.0 89.7 1.0
BE A:BEF905 1.5 89.7 1.0
O1B A:ADP904 2.5 89.7 1.0
F1 A:BEF905 2.5 89.7 1.0
F3 A:BEF905 2.6 89.7 1.0
NZ A:LYS261 3.0 98.4 1.0
N A:GLY258 3.0 85.3 1.0
CA A:PRO257 3.3 85.3 1.0
O A:PRO256 3.3 86.8 1.0
CD A:LYS261 3.5 98.4 1.0
C A:PRO257 3.6 85.3 1.0
CG A:LYS261 3.6 98.4 1.0
N A:THR259 3.7 86.2 1.0
CE A:LYS261 3.8 98.4 1.0
PB A:ADP904 3.9 89.7 1.0
CA A:GLY258 4.0 85.3 1.0
C A:PRO256 4.2 86.8 1.0
N A:PRO257 4.2 85.3 1.0
O2B A:ADP904 4.3 89.7 1.0
OG1 A:THR259 4.3 86.2 1.0
C A:GLY258 4.3 85.3 1.0
O3B A:ADP904 4.3 89.7 1.0
CB A:PRO257 4.4 85.3 1.0
CB A:THR259 4.5 86.2 1.0
OD1 A:ASN358 4.5 94.5 1.0
CA A:THR259 4.6 86.2 1.0
O A:PRO257 4.7 85.3 1.0
N A:GLY260 4.8 92.4 1.0
O3A A:ADP904 5.0 89.7 1.0

Fluorine binding site 6 out of 24 in 6omb

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Fluorine binding site 6 out of 24 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 Fluorine with other atoms in the F 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
A:F905

b:89.7
occ:1.00
F3 A:BEF905 0.0 89.7 1.0
BE A:BEF905 1.5 89.7 1.0
O1B A:ADP904 2.4 89.7 1.0
N A:GLY258 2.5 85.3 1.0
F1 A:BEF905 2.5 89.7 1.0
F2 A:BEF905 2.6 89.7 1.0
C A:PRO257 3.3 85.3 1.0
CA A:PRO257 3.3 85.3 1.0
NE B:ARG369 3.3 70.4 1.0
CA A:GLY258 3.4 85.3 1.0
CZ B:ARG369 3.6 70.4 1.0
CB A:PRO257 3.6 85.3 1.0
PB A:ADP904 3.7 89.7 1.0
CD B:ARG369 3.7 70.4 1.0
O3B A:ADP904 3.7 89.7 1.0
NH2 B:ARG369 4.0 70.4 1.0
NH1 B:ARG369 4.1 70.4 1.0
O3A A:ADP904 4.3 89.7 1.0
OD1 A:ASN358 4.4 94.5 1.0
O A:PRO257 4.4 85.3 1.0
C A:GLY258 4.5 85.3 1.0
N A:THR259 4.6 86.2 1.0
N A:PRO257 4.7 85.3 1.0
NH2 B:ARG372 4.8 68.2 1.0
MG A:MG906 4.8 85.0 1.0
NH1 B:ARG372 4.8 68.2 1.0
O2B A:ADP904 4.9 89.7 1.0
O A:PRO256 5.0 86.8 1.0

Fluorine binding site 7 out of 24 in 6omb

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Fluorine binding site 7 out of 24 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 Fluorine with other atoms in the F 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
B:F904

b:43.3
occ:1.00
F1 B:BEF904 0.0 43.3 1.0
BE B:BEF904 1.5 43.3 1.0
MG B:MG905 2.1 31.4 1.0
F3 B:BEF904 2.5 43.3 1.0
F2 B:BEF904 2.5 43.3 1.0
O1B B:ADP903 2.6 43.3 1.0
O3B B:ADP903 2.9 43.3 1.0
PB B:ADP903 3.4 43.3 1.0
OG1 B:THR262 3.4 41.7 1.0
NH2 C:ARG372 4.1 41.5 1.0
O3A B:ADP903 4.3 43.3 1.0
ND2 B:ASN358 4.4 43.8 1.0
O2B B:ADP903 4.5 43.3 1.0
CG B:LYS261 4.6 40.6 1.0
CD B:LYS261 4.7 40.6 1.0
CB B:THR262 4.7 41.7 1.0
OE1 B:GLU315 4.9 47.8 1.0

Fluorine binding site 8 out of 24 in 6omb

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Fluorine binding site 8 out of 24 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 Fluorine with other atoms in the F 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
B:F904

b:43.3
occ:1.00
F2 B:BEF904 0.0 43.3 1.0
BE B:BEF904 1.5 43.3 1.0
O1B B:ADP903 2.5 43.3 1.0
F1 B:BEF904 2.5 43.3 1.0
F3 B:BEF904 2.6 43.3 1.0
ND2 B:ASN358 3.2 43.8 1.0
NZ B:LYS261 3.3 40.6 1.0
PB B:ADP903 3.3 43.3 1.0
CA B:PRO257 3.4 39.9 1.0
O3B B:ADP903 3.4 43.3 1.0
N B:GLY258 3.5 39.1 1.0
CD B:LYS261 3.5 40.6 1.0
O2B B:ADP903 3.7 43.3 1.0
CG B:LYS261 3.7 40.6 1.0
O B:PRO256 3.9 43.5 1.0
CE B:LYS261 4.0 40.6 1.0
C B:PRO257 4.0 39.9 1.0
CB B:PRO257 4.1 39.9 1.0
N B:PRO257 4.3 39.9 1.0
MG B:MG905 4.4 31.4 1.0
CG B:ASN358 4.5 43.8 1.0
C B:PRO256 4.5 43.5 1.0
CA B:GLY258 4.7 39.1 1.0
O3A B:ADP903 4.8 43.3 1.0
N B:THR259 4.8 38.3 1.0

Fluorine binding site 9 out of 24 in 6omb

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Fluorine binding site 9 out of 24 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 Fluorine with other atoms in the F binding site number 9 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:F904

b:43.3
occ:1.00
F3 B:BEF904 0.0 43.3 1.0
BE B:BEF904 1.5 43.3 1.0
O1B B:ADP903 2.4 43.3 1.0
F1 B:BEF904 2.5 43.3 1.0
F2 B:BEF904 2.6 43.3 1.0
CB B:PRO257 3.3 39.9 1.0
CA B:PRO257 3.5 39.9 1.0
N B:GLY258 3.6 39.1 1.0
NE C:ARG369 3.6 39.6 1.0
NH1 C:ARG372 3.7 41.5 1.0
ND2 B:ASN358 3.8 43.8 1.0
PB B:ADP903 4.0 43.3 1.0
C B:PRO257 4.0 39.9 1.0
NH2 C:ARG372 4.0 41.5 1.0
CZ C:ARG369 4.1 39.6 1.0
CD C:ARG369 4.2 39.6 1.0
NH2 C:ARG369 4.3 39.6 1.0
CZ C:ARG372 4.4 41.5 1.0
O3B B:ADP903 4.4 43.3 1.0
MG B:MG905 4.6 31.4 1.0
CA B:GLY258 4.6 39.1 1.0
O3A B:ADP903 4.7 43.3 1.0
CG B:ASN358 4.7 43.8 1.0
OD1 B:ASN358 4.8 43.8 1.0
CB C:ALA366 4.8 39.1 1.0
CG B:PRO257 4.8 39.9 1.0
O2B B:ADP903 4.8 43.3 1.0
N B:PRO257 4.9 39.9 1.0
NH1 C:ARG369 5.0 39.6 1.0

Fluorine binding site 10 out of 24 in 6omb

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Fluorine binding site 10 out of 24 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 Fluorine with other atoms in the F binding site number 10 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:F901

b:36.0
occ:1.00
F1 C:BEF901 0.0 36.0 1.0
BE C:BEF901 1.5 36.0 1.0
MG B:MG902 2.5 30.5 1.0
O3B B:ADP901 2.5 36.0 1.0
F3 C:BEF901 2.5 36.0 1.0
F2 C:BEF901 2.5 36.0 1.0
O1B B:ADP901 2.6 36.0 1.0
PB B:ADP901 3.2 36.0 1.0
NH2 C:ARG648 3.6 37.7 1.0
OE2 B:GLU588 3.7 41.2 1.0
OG1 B:THR535 4.0 37.2 1.0
O2B B:ADP901 4.1 36.0 1.0
O3A B:ADP901 4.3 36.0 1.0
NH2 C:ARG645 4.6 39.3 1.0
CZ C:ARG648 4.7 37.7 1.0
NH1 C:ARG648 4.8 37.7 1.0
CE B:LYS534 4.9 38.0 1.0
CD B:GLU588 4.9 41.2 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: Sun Dec 13 13:02:26 2020

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