Fluorine in PDB 8u9c: CDC48-SHP1 Unfolding Native Substrate, Class 5

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 5

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 5:
3.6.4.6;

Other elements in 8u9c:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 5 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-SHP1 Unfolding Native Substrate, Class 5 (pdb code 8u9c). 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-SHP1 Unfolding Native Substrate, Class 5, PDB code: 8u9c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 8u9c

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Fluorine binding site 1 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:140.4
occ:1.00
 F1 A:08T901 0.0 140.4 1.0
BE A:08T901 1.5 140.4 1.0
MG A:MG902 2.0 136.7 1.0
F3 A:08T901 2.5 140.4 1.0
O2B A:08T901 2.5 131.5 1.0
F2 A:08T901 2.6 140.4 1.0
O3B A:08T901 2.6 131.5 1.0
PB A:08T901 3.0 131.5 1.0
OG1 A:THR262 3.5 128.3 1.0
CG A:LYS261 3.8 132.3 1.0
OD1 A:ASN358 3.9 164.6 1.0
CD A:LYS261 3.9 132.3 1.0
NH2 B:ARG372 4.1 133.3 1.0
O3A A:08T901 4.2 131.5 1.0
O1B A:08T901 4.2 131.5 1.0
OE2 A:GLU315 4.4 178.3 1.0
NZ A:LYS261 4.4 132.3 1.0
NH1 B:ARG369 4.7 142.1 1.0
CB A:THR262 4.7 128.3 1.0
CE A:LYS261 4.8 132.3 1.0
CG A:ASN358 4.8 164.6 1.0
NH2 B:ARG369 4.9 142.1 1.0
N A:GLY258 4.9 117.5 1.0
ND2 A:ASN358 4.9 164.6 1.0
N A:THR262 5.0 128.3 1.0

Fluorine binding site 2 out of 24 in 8u9c

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Fluorine binding site 2 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:140.4
occ:1.00
 F2 A:08T901 0.0 140.4 1.0
BE A:08T901 1.6 140.4 1.0
OD1 A:ASN358 2.3 164.6 1.0
NZ A:LYS261 2.5 132.3 1.0
F3 A:08T901 2.5 140.4 1.0
F1 A:08T901 2.6 140.4 1.0
O3B A:08T901 2.6 131.5 1.0
CA A:PRO257 3.2 118.7 1.0
CD A:LYS261 3.3 132.3 1.0
CE A:LYS261 3.3 132.3 1.0
CG A:ASN358 3.5 164.6 1.0
PB A:08T901 3.6 131.5 1.0
N A:GLY258 3.7 117.5 1.0
CB A:PRO257 3.8 118.7 1.0
CG A:LYS261 3.8 132.3 1.0
O2B A:08T901 3.9 131.5 1.0
O1B A:08T901 3.9 131.5 1.0
C A:PRO257 4.0 118.7 1.0
N A:PRO257 4.2 118.7 1.0
ND2 A:ASN358 4.2 164.6 1.0
O A:PRO256 4.2 117.8 1.0
MG A:MG902 4.4 136.7 1.0
CB A:ASN358 4.5 164.6 1.0
C A:PRO256 4.5 117.8 1.0
OE2 A:GLU315 4.8 178.3 1.0
CA A:ASN358 4.8 164.6 1.0
NH1 B:ARG369 4.9 142.1 1.0
CA A:GLY258 4.9 117.5 1.0
O3A A:08T901 5.0 131.5 1.0

Fluorine binding site 3 out of 24 in 8u9c

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Fluorine binding site 3 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:140.4
occ:1.00
 F3 A:08T901 0.0 140.4 1.0
BE A:08T901 1.5 140.4 1.0
F2 A:08T901 2.5 140.4 1.0
F1 A:08T901 2.5 140.4 1.0
O3B A:08T901 2.6 131.5 1.0
NH2 B:ARG372 3.2 133.3 1.0
NH1 B:ARG369 3.3 142.1 1.0
CB A:PRO257 3.4 118.7 1.0
NH1 B:ARG372 3.6 133.3 1.0
OD1 A:ASN358 3.6 164.6 1.0
CA A:PRO257 3.7 118.7 1.0
N A:GLY258 3.8 117.5 1.0
NH2 B:ARG369 3.8 142.1 1.0
CZ B:ARG372 3.9 133.3 1.0
CZ B:ARG369 3.9 142.1 1.0
PB A:08T901 4.0 131.5 1.0
MG A:MG902 4.1 136.7 1.0
C A:PRO257 4.2 118.7 1.0
CG A:ASN358 4.3 164.6 1.0
ND2 A:ASN358 4.3 164.6 1.0
O2B A:08T901 4.3 131.5 1.0
O3A A:08T901 4.7 131.5 1.0
CG A:PRO257 4.8 118.7 1.0
CA A:GLY258 4.9 117.5 1.0
NZ A:LYS261 4.9 132.3 1.0
CB B:ALA366 5.0 138.0 1.0
O1B A:08T901 5.0 131.5 1.0

Fluorine binding site 4 out of 24 in 8u9c

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Fluorine binding site 4 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:110.9
occ:1.00
 F1 A:08T903 0.0 110.9 1.0
BE A:08T903 1.5 110.9 1.0
MG A:MG904 2.0 114.5 1.0
O1A A:08T903 2.5 117.4 1.0
F3 A:08T903 2.5 110.9 1.0
F2 A:08T903 2.6 110.9 1.0
O3B A:08T903 2.6 117.4 1.0
O2B A:08T903 2.9 117.4 1.0
PB A:08T903 3.0 117.4 1.0
O3A A:08T903 3.3 117.4 1.0
OG1 A:THR535 3.4 110.5 1.0
PA A:08T903 3.5 117.4 1.0
NH2 B:ARG648 3.7 120.9 1.0
CB A:THR535 4.2 110.5 1.0
O2A A:08T903 4.3 117.4 1.0
NH1 B:ARG648 4.5 120.9 1.0
CZ B:ARG648 4.5 120.9 1.0
O1B A:08T903 4.5 117.4 1.0
O5' A:08T903 4.7 117.4 1.0
NH2 B:ARG645 4.7 120.0 1.0
CZ B:ARG645 4.8 120.0 1.0
N A:THR535 5.0 110.5 1.0
NE B:ARG645 5.0 120.0 1.0
N A:GLY531 5.0 110.6 1.0

Fluorine binding site 5 out of 24 in 8u9c

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Fluorine binding site 5 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:110.9
occ:1.00
 F2 A:08T903 0.0 110.9 1.0
BE A:08T903 1.6 110.9 1.0
F3 A:08T903 2.5 110.9 1.0
F1 A:08T903 2.6 110.9 1.0
O3B A:08T903 2.6 117.4 1.0
O2B A:08T903 3.5 117.4 1.0
PB A:08T903 3.6 117.4 1.0
NH2 B:ARG648 4.0 120.9 1.0
MG A:MG904 4.0 114.5 1.0
OD1 A:ASN634 4.0 139.6 1.0
NH1 B:ARG648 4.2 120.9 1.0
OE2 A:GLU588 4.3 151.2 1.0
CA A:PRO530 4.4 113.1 1.0
CZ B:ARG648 4.6 120.9 1.0
NZ A:LYS534 4.6 109.5 1.0
CE A:LYS534 4.6 109.5 1.0
CB A:PRO530 4.6 113.1 1.0
CB A:ASN634 4.6 139.6 1.0
O1B A:08T903 4.6 117.4 1.0
N A:GLY531 4.7 110.6 1.0
CG A:ASN634 4.7 139.6 1.0
O3A A:08T903 4.7 117.4 1.0
O1A A:08T903 4.9 117.4 1.0

Fluorine binding site 6 out of 24 in 8u9c

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Fluorine binding site 6 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:110.9
occ:1.00
 F3 A:08T903 0.0 110.9 1.0
BE A:08T903 1.5 110.9 1.0
NH1 B:ARG648 2.4 120.9 1.0
F2 A:08T903 2.5 110.9 1.0
F1 A:08T903 2.5 110.9 1.0
O3B A:08T903 2.6 117.4 1.0
NH2 B:ARG648 2.9 120.9 1.0
CZ B:ARG648 3.0 120.9 1.0
NE B:ARG645 3.0 120.0 1.0
CZ B:ARG645 3.5 120.0 1.0
CD B:ARG645 3.5 120.0 1.0
NH2 B:ARG645 3.8 120.0 1.0
PB A:08T903 4.0 117.4 1.0
N A:GLY531 4.0 110.6 1.0
NH1 B:ARG645 4.2 120.0 1.0
O1A A:08T903 4.2 117.4 1.0
NE B:ARG648 4.2 120.9 1.0
O3A A:08T903 4.3 117.4 1.0
CB A:PRO530 4.3 113.1 1.0
MG A:MG904 4.4 114.5 1.0
CA A:PRO530 4.5 113.1 1.0
O2B A:08T903 4.6 117.4 1.0
CA A:GLY531 4.7 110.6 1.0
C A:PRO530 4.7 113.1 1.0
PA A:08T903 5.0 117.4 1.0
CG B:ARG645 5.0 120.0 1.0

Fluorine binding site 7 out of 24 in 8u9c

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Fluorine binding site 7 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:125.0
occ:1.00
 F1 B:08T901 0.0 125.0 1.0
BE B:08T901 1.5 125.0 1.0
MG B:MG902 2.1 123.1 1.0
F3 B:08T901 2.5 125.0 1.0
O2B B:08T901 2.5 121.4 1.0
F2 B:08T901 2.6 125.0 1.0
O3B B:08T901 2.6 121.4 1.0
PB B:08T901 3.0 121.4 1.0
OG1 B:THR262 3.1 112.0 1.0
NH2 C:ARG372 3.7 131.3 1.0
O3A B:08T901 4.0 121.4 1.0
CB B:THR262 4.3 112.0 1.0
O1B B:08T901 4.3 121.4 1.0
CG B:LYS261 4.4 109.4 1.0
NH2 C:ARG369 4.5 133.8 1.0
CD B:LYS261 4.7 109.4 1.0
O1A B:08T901 4.8 121.4 1.0
OD1 B:ASN358 4.9 122.0 1.0
CZ C:ARG372 4.9 131.3 1.0
N B:THR262 4.9 112.0 1.0
PA B:08T901 5.0 121.4 1.0

Fluorine binding site 8 out of 24 in 8u9c

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Fluorine binding site 8 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:125.0
occ:1.00
 F2 B:08T901 0.0 125.0 1.0
BE B:08T901 1.6 125.0 1.0
F3 B:08T901 2.5 125.0 1.0
F1 B:08T901 2.6 125.0 1.0
O3B B:08T901 2.6 121.4 1.0
OD1 B:ASN358 2.9 122.0 1.0
CA B:PRO257 3.3 107.7 1.0
ND2 B:ASN358 3.5 122.0 1.0
CG B:ASN358 3.5 122.0 1.0
NZ B:LYS261 3.6 109.4 1.0
PB B:08T901 3.6 121.4 1.0
CB B:PRO257 3.6 107.7 1.0
O2B B:08T901 3.8 121.4 1.0
N B:GLY258 3.8 109.3 1.0
CD B:LYS261 4.1 109.4 1.0
C B:PRO257 4.1 107.7 1.0
O1B B:08T901 4.2 121.4 1.0
N B:PRO257 4.3 107.7 1.0
MG B:MG902 4.4 123.1 1.0
CG B:LYS261 4.4 109.4 1.0
CE B:LYS261 4.4 109.4 1.0
O B:PRO256 4.6 108.0 1.0
NH2 C:ARG372 4.7 131.3 1.0
C B:PRO256 4.8 108.0 1.0
O3A B:08T901 4.9 121.4 1.0
CG B:PRO257 5.0 107.7 1.0
CB B:ASN358 5.0 122.0 1.0
NH2 C:ARG369 5.0 133.8 1.0

Fluorine binding site 9 out of 24 in 8u9c

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Fluorine binding site 9 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:125.0
occ:1.00
 F3 B:08T901 0.0 125.0 1.0
BE B:08T901 1.5 125.0 1.0
NH2 C:ARG372 2.4 131.3 1.0
F2 B:08T901 2.5 125.0 1.0
F1 B:08T901 2.5 125.0 1.0
O3B B:08T901 2.6 121.4 1.0
NH2 C:ARG369 2.9 133.8 1.0
NH1 C:ARG372 3.0 131.3 1.0
CZ C:ARG372 3.1 131.3 1.0
CZ C:ARG369 3.8 133.8 1.0
CB B:PRO257 3.9 107.7 1.0
NE C:ARG369 3.9 133.8 1.0
PB B:08T901 4.0 121.4 1.0
MG B:MG902 4.0 123.1 1.0
N B:GLY258 4.1 109.3 1.0
CA B:PRO257 4.3 107.7 1.0
O2B B:08T901 4.3 121.4 1.0
NE C:ARG372 4.4 131.3 1.0
ND2 B:ASN358 4.6 122.0 1.0
O3A B:08T901 4.6 121.4 1.0
C B:PRO257 4.7 107.7 1.0
NH1 C:ARG369 4.9 133.8 1.0
CA B:GLY258 5.0 109.3 1.0

Fluorine binding site 10 out of 24 in 8u9c

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Fluorine binding site 10 out of 24 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of CDC48-SHP1 Unfolding Native Substrate, Class 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F903

b:125.5
occ:1.00
 F1 B:08T903 0.0 125.5 1.0
BE B:08T903 1.5 125.5 1.0
MG B:MG904 2.2 123.6 1.0
F3 B:08T903 2.5 125.5 1.0
F2 B:08T903 2.6 125.5 1.0
O3B B:08T903 2.6 119.0 1.0
O2B B:08T903 2.7 119.0 1.0
PB B:08T903 3.0 119.0 1.0
O3A B:08T903 3.5 119.0 1.0
NH2 C:ARG648 3.6 114.1 1.0
OG1 B:THR535 3.6 113.8 1.0
OE2 B:GLU588 3.9 143.9 1.0
NH1 C:ARG648 4.3 114.1 1.0
CZ C:ARG648 4.4 114.1 1.0
O1B B:08T903 4.5 119.0 1.0
CE B:LYS534 4.6 117.4 1.0
PA B:08T903 4.9 119.0 1.0
N B:GLY531 4.9 116.7 1.0
O1A B:08T903 5.0 119.0 1.0
CB B:THR535 5.0 113.8 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 08:17:28 2024

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