Fluorine in PDB 6oaa: CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1

All present enzymatic activity of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1:
3.6.4.6;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 (pdb code 6oaa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1, PDB code: 6oaa:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:78.9 occ:1.00 F1 B:BEF902 0.0 78.9 1.0 BE B:BEF902 1.5 78.9 1.0 F3 B:BEF902 2.5 78.9 1.0 F2 B:BEF902 2.6 78.9 1.0 O3B B:ADP904 2.8 1.0 1.0 CB B:THR262 3.1 77.9 1.0 OD1 B:ASP314 3.1 86.5 1.0 OD2 B:ASP314 3.2 86.5 1.0 OG1 B:THR262 3.5 77.9 1.0 CG B:ASP314 3.6 86.5 1.0 CA B:THR262 3.8 77.9 1.0 O B:ALA356 4.0 91.4 1.0 CG2 B:THR262 4.1 77.9 1.0 N B:THR262 4.2 77.9 1.0 PB B:ADP904 4.3 1.0 1.0 OE1 B:GLU315 4.5 82.2 1.0 CB B:ALA356 4.7 91.4 1.0 CG B:GLU315 4.7 82.2 1.0 O B:PRO257 4.9 87.2 1.0 O2B B:ADP904 4.9 1.0 1.0 C B:LYS261 5.0 82.0 1.0

Fluorine binding site 2 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:78.9 occ:1.00 F2 B:BEF902 0.0 78.9 1.0 BE B:BEF902 1.6 78.9 1.0 OE1 B:GLU315 2.4 82.2 1.0 F3 B:BEF902 2.5 78.9 1.0 F1 B:BEF902 2.6 78.9 1.0 OD2 B:ASP314 3.3 86.5 1.0 CD B:GLU315 3.5 82.2 1.0 CG B:GLU315 3.8 82.2 1.0 NH2 C:ARG372 3.9 65.0 1.0 O C:LEU339 4.0 64.1 1.0 CG B:ASP314 4.1 86.5 1.0 OD1 B:ASP314 4.1 86.5 1.0 O3B B:ADP904 4.3 1.0 1.0 C C:LEU339 4.3 64.1 1.0 O C:ASP343 4.5 68.6 1.0 CA C:THR340 4.5 65.6 1.0 CB C:LEU339 4.5 64.1 1.0 N C:THR340 4.5 65.6 1.0 OE2 B:GLU315 4.6 82.2 1.0 OG1 B:THR262 4.7 77.9 1.0 CB C:THR340 4.8 65.6 1.0 CB B:THR262 4.8 77.9 1.0

Fluorine binding site 3 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:78.9 occ:1.00 F3 B:BEF902 0.0 78.9 1.0 BE B:BEF902 1.5 78.9 1.0 F2 B:BEF902 2.5 78.9 1.0 F1 B:BEF902 2.5 78.9 1.0 CG B:GLU315 3.3 82.2 1.0 OE1 B:GLU315 3.5 82.2 1.0 OD1 B:ASP314 3.7 86.5 1.0 O B:ALA356 3.7 91.4 1.0 O3B B:ADP904 3.9 1.0 1.0 CD B:GLU315 3.9 82.2 1.0 OD2 B:ASP314 4.3 86.5 1.0 CG B:ASP314 4.3 86.5 1.0 CB B:GLU315 4.6 82.2 1.0 CB B:PRO257 4.7 87.2 1.0 C B:ALA356 4.8 91.4 1.0 NH2 C:ARG372 4.9 65.0 1.0 O B:PRO257 4.9 87.2 1.0 CD2 C:LEU339 5.0 64.1 1.0

Fluorine binding site 4 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F903 b:71.0 occ:1.00 F1 B:BEF903 0.0 71.0 1.0 BE B:BEF903 1.5 71.0 1.0 O3B B:ADP901 2.4 76.2 1.0 F3 B:BEF903 2.5 71.0 1.0 F2 B:BEF903 2.6 71.0 1.0 NH1 C:ARG648 2.7 52.4 1.0 OE2 B:GLU588 2.7 66.5 1.0 NH2 C:ARG648 3.4 52.4 1.0 CZ C:ARG648 3.4 52.4 1.0 CD B:GLU588 3.6 66.5 1.0 PB B:ADP901 3.7 76.2 1.0 O2B B:ADP901 4.1 76.2 1.0 OE1 B:GLU588 4.1 66.5 1.0 OD2 B:ASP587 4.3 66.2 1.0 CB C:LEU615 4.4 56.5 1.0 CG2 B:THR535 4.5 78.7 1.0 CG B:GLU588 4.5 66.5 1.0 O1B B:ADP901 4.6 76.2 1.0 O C:LEU615 4.6 56.5 1.0 NE C:ARG648 4.7 52.4 1.0 NZ B:LYS534 4.8 80.5 1.0 O3A B:ADP901 4.9 76.2 1.0 CD1 C:LEU615 5.0 56.5 1.0

Fluorine binding site 5 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F903 b:71.0 occ:1.00 F2 B:BEF903 0.0 71.0 1.0 BE B:BEF903 1.6 71.0 1.0 F3 B:BEF903 2.5 71.0 1.0 F1 B:BEF903 2.6 71.0 1.0 OD2 B:ASP587 2.8 66.2 1.0 OD1 B:ASP587 3.0 66.2 1.0 CG B:ASP587 3.2 66.2 1.0 NH1 C:ARG648 3.3 52.4 1.0 CG2 B:THR535 3.3 78.7 1.0 O3B B:ADP901 3.5 76.2 1.0 CB B:THR535 3.8 78.7 1.0 OG1 B:THR535 4.0 78.7 1.0 OE2 B:GLU588 4.0 66.5 1.0 O C:LEU615 4.4 56.5 1.0 CD B:GLU588 4.4 66.5 1.0 CG B:GLU588 4.5 66.5 1.0 CZ C:ARG648 4.6 52.4 1.0 PB B:ADP901 4.6 76.2 1.0 CG2 C:THR616 4.6 55.6 1.0 CB B:ASP587 4.6 66.2 1.0 O2B B:ADP901 4.7 76.2 1.0 CA C:GLY620 4.8 62.1 1.0 N C:GLY620 5.0 62.1 1.0

Fluorine binding site 6 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F903 b:71.0 occ:1.00 F3 B:BEF903 0.0 71.0 1.0 BE B:BEF903 1.5 71.0 1.0 OD2 B:ASP587 2.4 66.2 1.0 F2 B:BEF903 2.5 71.0 1.0 F1 B:BEF903 2.5 71.0 1.0 CD B:GLU588 3.1 66.5 1.0 OE2 B:GLU588 3.2 66.5 1.0 CG2 B:THR535 3.3 78.7 1.0 OE1 B:GLU588 3.4 66.5 1.0 CG B:ASP587 3.5 66.2 1.0 CG B:GLU588 3.6 66.5 1.0 OD1 B:ASP587 3.9 66.2 1.0 NZ B:LYS534 3.9 80.5 1.0 O B:ALA632 4.0 72.1 1.0 O3B B:ADP901 4.1 76.2 1.0 N B:GLU588 4.2 66.5 1.0 C B:ALA632 4.4 72.1 1.0 O2B B:ADP901 4.5 76.2 1.0 CB B:THR535 4.5 78.7 1.0 CB B:ALA632 4.6 72.1 1.0 CA B:GLU588 4.6 66.5 1.0 CB B:GLU588 4.7 66.5 1.0 CA B:THR633 4.7 80.0 1.0 CB B:ASP587 4.7 66.2 1.0 N B:THR633 4.8 80.0 1.0 NH1 C:ARG648 4.8 52.4 1.0 C B:ASP587 4.9 66.2 1.0 PB B:ADP901 5.0 76.2 1.0 CA B:ASP587 5.0 66.2 1.0

Fluorine binding site 7 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F901 b:53.4 occ:1.00 F1 C:BEF901 0.0 53.4 1.0 BE C:BEF901 1.5 53.4 1.0 O2B C:ADP903 2.3 1.0 1.0 F3 C:BEF901 2.5 53.4 1.0 F2 C:BEF901 2.6 53.4 1.0 O3B C:ADP903 2.9 1.0 1.0 NH1 D:ARG372 2.9 42.1 1.0 OG1 C:THR262 3.0 56.1 1.0 PB C:ADP903 3.0 1.0 1.0 CG2 C:THR262 3.3 56.1 1.0 OD2 D:ASP343 3.6 50.6 1.0 CB C:THR262 3.7 56.1 1.0 O3A C:ADP903 3.8 1.0 1.0 CZ D:ARG372 4.0 42.1 1.0 OE2 C:GLU315 4.1 48.5 1.0 OD1 D:ASP343 4.1 50.6 1.0 O2A C:ADP903 4.1 1.0 1.0 CG D:ASP343 4.2 50.6 1.0 NH2 D:ARG372 4.2 42.1 1.0 O1B C:ADP903 4.4 1.0 1.0 NZ C:LYS261 4.5 49.9 1.0 PA C:ADP903 4.6 1.0 1.0 NE D:ARG369 4.8 48.3 1.0

Fluorine binding site 8 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F901 b:53.4 occ:1.00 F2 C:BEF901 0.0 53.4 1.0 BE C:BEF901 1.6 53.4 1.0 F3 C:BEF901 2.5 53.4 1.0 F1 C:BEF901 2.6 53.4 1.0 OE2 C:GLU315 2.8 48.5 1.0 O3B C:ADP903 3.0 1.0 1.0 O2B C:ADP903 3.0 1.0 1.0 CG2 C:THR262 3.3 56.1 1.0 CE C:LYS261 3.4 49.9 1.0 PB C:ADP903 3.4 1.0 1.0 NZ C:LYS261 3.6 49.9 1.0 CD C:GLU315 3.9 48.5 1.0 O1B C:ADP903 4.0 1.0 1.0 CG C:LYS261 4.0 49.9 1.0 CD C:LYS261 4.1 49.9 1.0 OG1 C:THR262 4.3 56.1 1.0 CB C:THR262 4.4 56.1 1.0 OE1 C:GLU315 4.5 48.5 1.0 O3A C:ADP903 4.9 1.0 1.0 OD1 C:ASP314 4.9 52.2 1.0

Fluorine binding site 9 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F901 b:53.4 occ:1.00 F3 C:BEF901 0.0 53.4 1.0 BE C:BEF901 1.5 53.4 1.0 F2 C:BEF901 2.5 53.4 1.0 F1 C:BEF901 2.5 53.4 1.0 O2B C:ADP903 2.6 1.0 1.0 NZ C:LYS261 3.1 49.9 1.0 CE C:LYS261 3.6 49.9 1.0 PB C:ADP903 3.9 1.0 1.0 NH2 D:ARG372 3.9 42.1 1.0 CB C:PRO257 3.9 42.0 1.0 NH1 D:ARG372 4.0 42.1 1.0 CA C:PRO257 4.1 42.0 1.0 O3B C:ADP903 4.3 1.0 1.0 N C:GLY258 4.4 42.7 1.0 CZ D:ARG372 4.5 42.1 1.0 O1B C:ADP903 4.6 1.0 1.0 OE2 C:GLU315 4.6 48.5 1.0 C C:PRO257 4.7 42.0 1.0 CB D:ALA366 4.8 36.4 1.0 ND2 C:ASN358 4.9 44.0 1.0 OG1 C:THR262 4.9 56.1 1.0 CD C:LYS261 4.9 49.9 1.0 NE D:ARG369 5.0 48.3 1.0

Fluorine binding site 10 out of 18 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F902 b:65.2 occ:1.00 F1 C:BEF902 0.0 65.2 1.0 BE C:BEF902 1.5 65.2 1.0 F3 C:BEF902 2.5 65.2 1.0 F2 C:BEF902 2.6 65.2 1.0 CB C:THR535 2.6 60.8 1.0 CG2 C:THR535 2.8 60.8 1.0 OG1 C:THR535 2.8 60.8 1.0 OD2 C:ASP587 3.2 46.5 1.0 OE1 C:GLU588 3.6 54.8 1.0 OD1 C:ASP587 3.7 46.5 1.0 CG C:ASP587 3.8 46.5 1.0 NH1 D:ARG648 4.0 63.7 1.0 CA C:THR535 4.1 60.8 1.0 O D:GLY620 4.1 58.3 1.0 CA D:GLY620 4.1 58.3 1.0 O3B C:ADP904 4.3 60.1 1.0 C D:GLY620 4.4 58.3 1.0 O C:THR535 4.4 60.8 1.0 N D:GLY620 4.5 58.3 1.0 CD C:GLU588 4.6 54.8 1.0 C C:THR535 4.6 60.8 1.0 O D:LEU615 4.7 57.5 1.0 OG1 D:THR616 4.7 54.9 1.0 CB D:THR616 4.8 54.9 1.0 CA D:THR616 4.8 54.9 1.0 CG C:GLU588 4.8 54.8 1.0 OD2 D:ASP619 5.0 61.2 1.0

E.C.Twomey, Z.Ji, T.E.Wales, N.O.Bodnar, S.B.Ficarro, J.A.Marto, J.R.Engen, T.A.Rapoport. Substrate Processing By the CDC48 Atpase Complex Is Initiated By Ubiquitin Unfolding. Science V. 365 2019.
ISSN: ESSN 1095-9203
PubMed: 31249135
DOI: 10.1126/SCIENCE.AAX1033