Fluorine in PDB 6oab: CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2

All present enzymatic activity of CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2:
3.6.4.6;

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-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2 (pdb code 6oab). 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-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2, PDB code: 6oab:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F902 b:66.6 occ:1.00 F1 D:BEF902 0.0 66.6 1.0 BE D:BEF902 1.5 66.6 1.0 O3B D:ADP901 2.2 65.9 1.0 F3 D:BEF902 2.5 66.6 1.0 F2 D:BEF902 2.6 66.6 1.0 OD2 E:ASP343 2.8 81.6 1.0 OG1 D:THR262 3.2 61.9 1.0 NH2 E:ARG372 3.2 73.3 1.0 PB D:ADP901 3.7 65.9 1.0 O E:LEU339 3.7 73.3 1.0 CG E:ASP343 3.8 81.6 1.0 NH2 E:ARG369 3.9 71.6 1.0 CB E:ASP343 4.1 81.6 1.0 CG2 D:THR262 4.2 61.9 1.0 CB D:THR262 4.2 61.9 1.0 O3A D:ADP901 4.2 65.9 1.0 CZ E:ARG372 4.3 73.3 1.0 O1B D:ADP901 4.4 65.9 1.0 NH1 E:ARG372 4.6 73.3 1.0 O2B D:ADP901 4.7 65.9 1.0 C E:LEU339 4.7 73.3 1.0 O2A D:ADP901 4.9 65.9 1.0 OD1 E:ASP343 4.9 81.6 1.0

Fluorine binding site 2 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F902 b:66.6 occ:1.00 F2 D:BEF902 0.0 66.6 1.0 BE D:BEF902 1.6 66.6 1.0 F3 D:BEF902 2.5 66.6 1.0 F1 D:BEF902 2.6 66.6 1.0 OE1 D:GLU315 2.8 60.7 1.0 OD2 D:ASP314 3.0 57.9 1.0 CG2 D:THR262 3.3 61.9 1.0 OD2 E:ASP343 3.6 81.6 1.0 CG D:ASP314 3.8 57.9 1.0 CD D:GLU315 3.8 60.7 1.0 OD1 D:ASP314 3.8 57.9 1.0 O E:LEU339 4.0 73.3 1.0 OG1 D:THR262 4.1 61.9 1.0 O3B D:ADP901 4.1 65.9 1.0 CB D:THR262 4.2 61.9 1.0 OE2 D:GLU315 4.4 60.7 1.0 C E:LEU339 4.5 73.3 1.0 CB E:LEU339 4.6 73.3 1.0 CA E:THR340 4.7 71.4 1.0 CG D:GLU315 4.8 60.7 1.0 CG E:ASP343 4.8 81.6 1.0 N E:THR340 4.9 71.4 1.0 CB E:THR340 4.9 71.4 1.0

Fluorine binding site 3 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F902 b:66.6 occ:1.00 F3 D:BEF902 0.0 66.6 1.0 BE D:BEF902 1.5 66.6 1.0 O3B D:ADP901 2.3 65.9 1.0 F2 D:BEF902 2.5 66.6 1.0 F1 D:BEF902 2.5 66.6 1.0 CG2 D:THR262 3.5 61.9 1.0 PB D:ADP901 3.5 65.9 1.0 OG1 D:THR262 3.5 61.9 1.0 O2B D:ADP901 3.6 65.9 1.0 NZ D:LYS261 3.9 60.7 1.0 CG D:LYS261 4.1 60.7 1.0 CB D:THR262 4.1 61.9 1.0 OE1 D:GLU315 4.2 60.7 1.0 CD D:LYS261 4.3 60.7 1.0 O1B D:ADP901 4.5 65.9 1.0 O3A D:ADP901 4.6 65.9 1.0 CE D:LYS261 4.8 60.7 1.0 O2A D:ADP901 4.8 65.9 1.0 N D:THR262 4.9 61.9 1.0 OD1 D:ASP314 5.0 57.9 1.0

Fluorine binding site 4 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F903 b:68.9 occ:1.00 F1 D:BEF903 0.0 68.9 1.0 BE D:BEF903 1.5 68.9 1.0 F3 D:BEF903 2.5 68.9 1.0 F2 D:BEF903 2.6 68.9 1.0 O D:ALA632 3.4 63.7 1.0 CB D:ASP587 3.4 63.9 1.0 CG2 D:THR535 3.4 72.0 1.0 CB D:ALA632 3.4 63.7 1.0 OE2 D:GLU588 3.5 71.8 1.0 N D:GLU588 3.7 71.8 1.0 C D:ALA632 3.8 63.7 1.0 CE D:LYS534 4.0 71.4 1.0 O2B D:ADP904 4.1 77.5 1.0 CA D:ASP587 4.1 63.9 1.0 CA D:ALA632 4.2 63.7 1.0 CD D:GLU588 4.3 71.8 1.0 CG D:GLU588 4.3 71.8 1.0 C D:ASP587 4.3 63.9 1.0 CG D:LYS534 4.4 71.4 1.0 CG D:ASP587 4.5 63.9 1.0 CD D:LYS534 4.5 71.4 1.0 CA D:GLU588 4.5 71.8 1.0 N D:THR633 4.6 71.4 1.0 NZ D:LYS534 4.6 71.4 1.0 OD2 D:ASP587 4.6 63.9 1.0 O3B D:ADP904 4.7 77.5 1.0 CB D:THR535 4.9 72.0 1.0 CA D:THR633 4.9 71.4 1.0 CB D:GLU588 5.0 71.8 1.0

Fluorine binding site 5 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F903 b:68.9 occ:1.00 F2 D:BEF903 0.0 68.9 1.0 BE D:BEF903 1.6 68.9 1.0 OE2 D:GLU588 2.3 71.8 1.0 F3 D:BEF903 2.5 68.9 1.0 F1 D:BEF903 2.6 68.9 1.0 CE D:LYS534 3.3 71.4 1.0 NZ D:LYS534 3.3 71.4 1.0 O2B D:ADP904 3.4 77.5 1.0 CD D:GLU588 3.5 71.8 1.0 O3B D:ADP904 4.0 77.5 1.0 PB D:ADP904 4.1 77.5 1.0 CG D:GLU588 4.1 71.8 1.0 OE1 D:GLU588 4.5 71.8 1.0 CD D:LYS534 4.5 71.4 1.0 O1B D:ADP904 4.6 77.5 1.0 CD2 E:LEU615 4.6 71.0 1.0 CG E:LEU615 4.7 71.0 1.0 NH2 E:ARG648 4.9 81.9 1.0 CG2 D:THR535 4.9 72.0 1.0 NH2 E:ARG645 4.9 83.0 1.0 CG D:LYS534 5.0 71.4 1.0

Fluorine binding site 6 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F903 b:68.9 occ:1.00 F3 D:BEF903 0.0 68.9 1.0 BE D:BEF903 1.5 68.9 1.0 F2 D:BEF903 2.5 68.9 1.0 F1 D:BEF903 2.5 68.9 1.0 O3B D:ADP904 2.8 77.5 1.0 CG2 D:THR535 3.3 72.0 1.0 O2B D:ADP904 3.6 77.5 1.0 PB D:ADP904 3.7 77.5 1.0 NH2 E:ARG648 4.0 81.9 1.0 OE2 D:GLU588 4.1 71.8 1.0 OD2 D:ASP587 4.3 63.9 1.0 OG1 D:THR535 4.4 72.0 1.0 CB D:THR535 4.4 72.0 1.0 CB D:ASP587 4.4 63.9 1.0 CE D:LYS534 4.6 71.4 1.0 OG1 E:THR616 4.7 69.5 1.0 O1B D:ADP904 4.7 77.5 1.0 CG D:GLU588 4.7 71.8 1.0 CB E:THR616 4.8 69.5 1.0 CG D:ASP587 4.9 63.9 1.0 O3A D:ADP904 4.9 77.5 1.0 CD D:GLU588 4.9 71.8 1.0 CA E:THR616 5.0 69.5 1.0

Fluorine binding site 7 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:0.0 occ:1.00 F1 B:BEF902 0.0 0.0 1.0 BE B:BEF902 1.5 0.0 1.0 F3 B:BEF902 2.5 0.0 1.0 NH1 B:ARG372 2.5 0.2 1.0 F2 B:BEF902 2.6 0.0 1.0 O3B A:ADP902 2.6 0.2 1.0 OD2 B:ASP343 3.0 0.7 1.0 CZ B:ARG372 3.8 0.2 1.0 PB A:ADP902 3.9 0.2 1.0 CE2 B:PHE370 4.1 0.4 1.0 CZ B:PHE370 4.1 0.4 1.0 CG B:ASP343 4.2 0.7 1.0 O3A A:ADP902 4.2 0.2 1.0 NH2 B:ARG372 4.3 0.2 1.0 O2B A:ADP902 4.4 0.2 1.0 NE B:ARG369 4.6 1.0 1.0 NH1 B:ARG369 4.7 1.0 1.0 CB B:ASP343 4.8 0.7 1.0 NE B:ARG372 4.8 0.2 1.0

Fluorine binding site 8 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:0.0 occ:1.00 F2 B:BEF902 0.0 0.0 1.0 BE B:BEF902 1.6 0.0 1.0 O3B A:ADP902 2.1 0.2 1.0 O2B A:ADP902 2.3 0.2 1.0 F3 B:BEF902 2.5 0.0 1.0 F1 B:BEF902 2.6 0.0 1.0 PB A:ADP902 2.7 0.2 1.0 OD2 A:ASP314 3.0 0.0 1.0 O3A A:ADP902 3.6 0.2 1.0 CG A:GLU315 3.7 0.0 1.0 O1B A:ADP902 4.0 0.2 1.0 CG A:ASP314 4.1 0.0 1.0 CG2 A:THR262 4.1 0.1 1.0 CB A:ASP314 4.5 0.0 1.0 CD A:GLU315 4.5 0.0 1.0 CB A:GLU315 4.9 0.0 1.0 NH1 B:ARG372 4.9 0.2 1.0

Fluorine binding site 9 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F902 b:0.0 occ:1.00 F3 B:BEF902 0.0 0.0 1.0 O3B A:ADP902 1.2 0.2 1.0 BE B:BEF902 1.5 0.0 1.0 F2 B:BEF902 2.5 0.0 1.0 F1 B:BEF902 2.5 0.0 1.0 PB A:ADP902 2.6 0.2 1.0 NE B:ARG369 3.1 1.0 1.0 O1B A:ADP902 3.3 0.2 1.0 NH1 B:ARG369 3.3 1.0 1.0 CZ B:ARG369 3.3 1.0 1.0 O2B A:ADP902 3.5 0.2 1.0 O3A A:ADP902 3.7 0.2 1.0 NH1 B:ARG372 4.0 0.2 1.0 CD B:ARG369 4.0 1.0 1.0 CD A:GLU315 4.2 0.0 1.0 NH2 B:ARG369 4.2 1.0 1.0 CG A:GLU315 4.2 0.0 1.0 OE1 A:GLU315 4.3 0.0 1.0 OE2 A:GLU315 4.5 0.0 1.0 CE2 B:PHE370 4.6 0.4 1.0 NH2 B:ARG372 4.6 0.2 1.0 CZ B:ARG372 4.7 0.2 1.0

Fluorine binding site 10 out of 24 in the CDC48-NPL4 Complex Processing Poly-Ubiquitinated Substrate in the Presence of Adp-Befx, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F903 b:64.3 occ:1.00 F1 B:BEF903 0.0 64.3 1.0 O3B B:ADP905 1.3 1.0 1.0 BE B:BEF903 1.5 64.3 1.0 F3 B:BEF903 2.5 64.3 1.0 F2 B:BEF903 2.6 64.3 1.0 PB B:ADP905 2.6 1.0 1.0 OG1 B:THR262 2.9 55.9 1.0 O2B B:ADP905 3.1 1.0 1.0 O3A B:ADP905 3.6 1.0 1.0 O1B B:ADP905 3.7 1.0 1.0 OE1 B:GLU315 3.8 68.1 1.0 NH2 C:ARG372 3.9 54.3 1.0 O C:LEU339 3.9 56.9 1.0 CB B:THR262 4.1 55.9 1.0 OD2 B:ASP314 4.1 65.3 1.0 CG2 B:THR262 4.2 55.9 1.0 O C:ASP343 4.2 56.9 1.0 CD B:GLU315 4.7 68.1 1.0 OD1 B:ASP314 4.7 65.3 1.0 NH2 C:ARG369 4.8 57.0 1.0 C C:LEU339 4.8 56.9 1.0 CG B:ASP314 4.8 65.3 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