Fluorine in PDB 8u7t: Substrate-Bound CDC48, Class 1

All present enzymatic activity of Substrate-Bound CDC48, Class 1:
3.6.4.6;

The structure of Substrate-Bound CDC48, Class 1 also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

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 Substrate-Bound CDC48, Class 1 (pdb code 8u7t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Substrate-Bound CDC48, Class 1, PDB code: 8u7t:
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 Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:115.3 occ:1.00 F1 A:08T1101 0.0 115.3 1.0 BE A:08T1101 1.5 115.3 1.0 MG A:MG1102 2.0 115.3 1.0 F3 A:08T1101 2.5 115.3 1.0 F2 A:08T1101 2.5 115.3 1.0 O3B A:08T1101 2.6 115.3 1.0 O1B A:08T1101 2.8 115.3 1.0 PB A:08T1101 3.2 115.3 1.0 OD1 A:ASN883 3.4 117.3 1.0 OE2 A:GLU837 3.5 117.8 1.0 ND2 A:ASN883 3.6 117.3 1.0 OG1 A:THR784 3.8 119.4 1.0 CG A:ASN883 3.9 117.3 1.0 O2B A:08T1101 4.1 115.3 1.0 CE A:LYS783 4.2 120.1 1.0 O3A A:08T1101 4.4 115.3 1.0 CD A:GLU837 4.7 117.8 1.0 NH2 B:ARG1419 4.7 101.4 1.0 NZ A:LYS783 4.8 120.1 1.0 O2A A:08T1101 5.0 115.3 1.0 NH1 B:ARG1419 5.0 101.4 1.0 CB A:THR784 5.0 119.4 1.0

Fluorine binding site 2 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:115.3 occ:1.00 F2 A:08T1101 0.0 115.3 1.0 BE A:08T1101 1.5 115.3 1.0 OD1 A:ASN883 2.3 117.3 1.0 O3B A:08T1101 2.5 115.3 1.0 F1 A:08T1101 2.5 115.3 1.0 F3 A:08T1101 2.6 115.3 1.0 CG A:ASN883 3.1 117.3 1.0 ND2 A:ASN883 3.3 117.3 1.0 CB A:PRO779 3.4 112.2 1.0 NH1 B:ARG1419 3.6 101.4 1.0 CA A:PRO779 3.6 112.2 1.0 NH1 B:ARG1416 3.9 105.8 1.0 PB A:08T1101 4.0 115.3 1.0 N A:GLY780 4.1 113.0 1.0 CG A:PRO779 4.3 112.2 1.0 C A:PRO779 4.4 112.2 1.0 OE2 A:GLU837 4.4 117.8 1.0 CZ B:ARG1419 4.4 101.4 1.0 O1B A:08T1101 4.5 115.3 1.0 NH2 B:ARG1419 4.5 101.4 1.0 MG A:MG1102 4.5 115.3 1.0 CB A:ASN883 4.5 117.3 1.0 O2B A:08T1101 4.6 115.3 1.0 N A:PRO779 4.7 112.2 1.0 CD B:ARG1416 4.8 105.8 1.0 CZ B:ARG1416 4.9 105.8 1.0 O3A A:08T1101 4.9 115.3 1.0

Fluorine binding site 3 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:115.3 occ:1.00 F3 A:08T1101 0.0 115.3 1.0 BE A:08T1101 1.5 115.3 1.0 O3B A:08T1101 2.4 115.3 1.0 F1 A:08T1101 2.5 115.3 1.0 F2 A:08T1101 2.6 115.3 1.0 NH1 B:ARG1416 2.8 105.8 1.0 NH2 B:ARG1419 3.3 101.4 1.0 NH1 B:ARG1419 3.3 101.4 1.0 PB A:08T1101 3.4 115.3 1.0 CZ B:ARG1419 3.5 101.4 1.0 MG A:MG1102 3.6 115.3 1.0 O1B A:08T1101 3.6 115.3 1.0 O3A A:08T1101 3.7 115.3 1.0 CZ B:ARG1416 3.8 105.8 1.0 O2A A:08T1101 3.8 115.3 1.0 OD2 B:ASP1390 4.2 107.8 1.0 NH2 B:ARG1416 4.3 105.8 1.0 NE B:ARG1419 4.4 101.4 1.0 PA A:08T1101 4.4 115.3 1.0 OG1 A:THR784 4.5 119.4 1.0 NE B:ARG1416 4.7 105.8 1.0 OD1 A:ASN883 4.7 117.3 1.0 O2B A:08T1101 4.7 115.3 1.0 N A:GLY780 4.8 113.0 1.0 OE2 A:GLU837 4.8 117.8 1.0 O B:ASP1390 5.0 107.8 1.0 CD B:ARG1416 5.0 105.8 1.0 ND2 A:ASN883 5.0 117.3 1.0

Fluorine binding site 4 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:161.5 occ:1.00 F1 A:08T1103 0.0 161.5 1.0 BE A:08T1103 1.5 161.5 1.0 MG A:MG1104 2.0 161.5 1.0 F3 A:08T1103 2.5 161.5 1.0 F2 A:08T1103 2.5 161.5 1.0 O3B A:08T1103 2.6 161.5 1.0 O2B A:08T1103 2.8 161.5 1.0 PB A:08T1103 3.2 161.5 1.0 OG1 A:THR511 3.4 170.0 1.0 CG A:LYS510 3.9 167.9 1.0 CD A:LYS510 4.1 167.9 1.0 NH2 B:ARG1147 4.2 141.4 1.0 O1B A:08T1103 4.2 161.5 1.0 O3A A:08T1103 4.3 161.5 1.0 NH2 B:ARG1150 4.4 133.4 1.0 CB A:THR511 4.4 170.0 1.0 O2A A:08T1103 4.6 161.5 1.0 N A:THR511 4.8 170.0 1.0 CZ B:ARG1147 4.9 141.4 1.0 NE B:ARG1147 4.9 141.4 1.0

Fluorine binding site 5 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:161.5 occ:1.00 F2 A:08T1103 0.0 161.5 1.0 BE A:08T1103 1.5 161.5 1.0 O3B A:08T1103 2.5 161.5 1.0 F1 A:08T1103 2.5 161.5 1.0 F3 A:08T1103 2.6 161.5 1.0 CD A:LYS510 3.2 167.9 1.0 CE A:LYS510 3.3 167.9 1.0 N A:GLY507 3.4 156.0 1.0 CG A:LYS510 3.5 167.9 1.0 PB A:08T1103 3.5 161.5 1.0 CA A:PRO506 3.6 153.3 1.0 O1B A:08T1103 3.7 161.5 1.0 O2B A:08T1103 3.9 161.5 1.0 C A:PRO506 4.0 153.3 1.0 CB A:PRO506 4.1 153.3 1.0 NZ A:LYS510 4.2 167.9 1.0 MG A:MG1104 4.3 161.5 1.0 CA A:GLY507 4.4 156.0 1.0 O A:PRO505 4.6 155.7 1.0 N A:PRO506 4.7 153.3 1.0 CB A:ASN607 4.7 161.3 1.0 O3A A:08T1103 4.9 161.5 1.0 N A:THR508 5.0 159.3 1.0 CB A:LYS510 5.0 167.9 1.0

Fluorine binding site 6 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:161.5 occ:1.00 F3 A:08T1103 0.0 161.5 1.0 BE A:08T1103 1.5 161.5 1.0 O3B A:08T1103 2.4 161.5 1.0 F1 A:08T1103 2.5 161.5 1.0 F2 A:08T1103 2.6 161.5 1.0 NE B:ARG1147 2.9 141.4 1.0 NH2 B:ARG1150 3.2 133.4 1.0 NH2 B:ARG1147 3.3 141.4 1.0 CZ B:ARG1147 3.4 141.4 1.0 N A:GLY507 3.8 156.0 1.0 CD B:ARG1147 3.8 141.4 1.0 PB A:08T1103 3.9 161.5 1.0 MG A:MG1104 4.1 161.5 1.0 CB A:PRO506 4.2 153.3 1.0 CZ B:ARG1150 4.3 133.4 1.0 CA A:PRO506 4.4 153.3 1.0 O2B A:08T1103 4.4 161.5 1.0 CA A:GLY507 4.5 156.0 1.0 C A:PRO506 4.5 153.3 1.0 NE B:ARG1150 4.6 133.4 1.0 O3A A:08T1103 4.6 161.5 1.0 NH1 B:ARG1147 4.6 141.4 1.0 OD2 B:ASP1121 4.6 141.7 1.0 O1B A:08T1103 4.8 161.5 1.0

Fluorine binding site 7 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1601 b:81.0 occ:1.00 F1 B:08T1601 0.0 81.0 1.0 BE B:08T1601 1.5 81.0 1.0 MG B:MG1602 2.0 81.0 1.0 O1B B:08T1601 2.4 81.0 1.0 F3 B:08T1601 2.5 81.0 1.0 F2 B:08T1601 2.5 81.0 1.0 O3B B:08T1601 2.6 81.0 1.0 OG1 B:THR1306 2.7 81.4 1.0 PB B:08T1601 3.0 81.0 1.0 NH2 C:ARG1981 3.6 79.9 1.0 O3A B:08T1601 3.7 81.0 1.0 CB B:THR1306 3.9 81.4 1.0 O2B B:08T1601 4.2 81.0 1.0 O C:ASP1952 4.5 86.0 1.0 CZ C:ARG1981 4.5 79.9 1.0 NH1 C:ARG1981 4.5 79.9 1.0 NH2 C:ARG1978 4.6 79.9 1.0 N B:THR1306 4.6 81.4 1.0 OD1 B:ASP1358 4.6 86.5 1.0 PA B:08T1601 4.7 81.0 1.0 OE2 B:GLU1359 4.7 88.8 1.0 O1A B:08T1601 4.8 81.0 1.0 CG2 B:THR1306 4.8 81.4 1.0 O2A B:08T1601 4.8 81.0 1.0 CA B:THR1306 4.9 81.4 1.0 OD2 C:ASP1952 4.9 86.0 1.0

Fluorine binding site 8 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1601 b:81.0 occ:1.00 F2 B:08T1601 0.0 81.0 1.0 BE B:08T1601 1.5 81.0 1.0 F1 B:08T1601 2.5 81.0 1.0 O3B B:08T1601 2.6 81.0 1.0 F3 B:08T1601 2.6 81.0 1.0 OE2 B:GLU1359 3.3 88.8 1.0 O1B B:08T1601 3.7 81.0 1.0 PB B:08T1601 3.7 81.0 1.0 ND2 B:ASN1405 3.9 88.6 1.0 O2B B:08T1601 4.2 81.0 1.0 CD B:GLU1359 4.3 88.8 1.0 CD B:LYS1305 4.4 81.2 1.0 MG B:MG1602 4.4 81.0 1.0 NZ B:LYS1305 4.4 81.2 1.0 NH2 C:ARG1981 4.6 79.9 1.0 NH1 C:ARG1981 4.6 79.9 1.0 CB B:ASN1405 4.6 88.6 1.0 CG B:ASN1405 4.7 88.6 1.0 OG1 B:THR1306 4.9 81.4 1.0 CA B:PRO1301 4.9 82.3 1.0 O3A B:08T1601 4.9 81.0 1.0 N B:ASN1405 5.0 88.6 1.0 CB B:PRO1301 5.0 82.3 1.0

Fluorine binding site 9 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1601 b:81.0 occ:1.00 F3 B:08T1601 0.0 81.0 1.0 BE B:08T1601 1.5 81.0 1.0 O3B B:08T1601 2.1 81.0 1.0 NH1 C:ARG1981 2.4 79.9 1.0 F1 B:08T1601 2.5 81.0 1.0 F2 B:08T1601 2.6 81.0 1.0 NH2 C:ARG1981 2.8 79.9 1.0 CZ C:ARG1981 3.0 79.9 1.0 NH2 C:ARG1978 3.1 79.9 1.0 NE C:ARG1978 3.4 79.9 1.0 PB B:08T1601 3.4 81.0 1.0 CZ C:ARG1978 3.7 79.9 1.0 MG B:MG1602 3.7 81.0 1.0 O3A B:08T1601 3.7 81.0 1.0 O1B B:08T1601 3.9 81.0 1.0 N B:GLY1302 4.3 81.8 1.0 NE C:ARG1981 4.3 79.9 1.0 O2B B:08T1601 4.5 81.0 1.0 CD C:ARG1978 4.6 79.9 1.0 OD2 C:ASP1952 4.6 86.0 1.0 CB B:PRO1301 4.7 82.3 1.0 OE2 B:GLU1359 4.8 88.8 1.0 CA B:PRO1301 4.9 82.3 1.0 O C:ASP1952 4.9 86.0 1.0 CA B:GLY1302 5.0 81.8 1.0

Fluorine binding site 10 out of 24 in the Substrate-Bound CDC48, Class 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Substrate-Bound CDC48, Class 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1603 b:88.3 occ:1.00 F1 B:08T1603 0.0 88.3 1.0 BE B:08T1603 1.5 88.3 1.0 MG B:MG1604 2.0 88.3 1.0 F3 B:08T1603 2.5 88.3 1.0 F2 B:08T1603 2.5 88.3 1.0 O3B B:08T1603 2.6 88.3 1.0 O1B B:08T1603 2.8 88.3 1.0 PB B:08T1603 3.2 88.3 1.0 OG1 B:THR1040 3.6 93.6 1.0 NH2 C:ARG1705 3.6 88.1 1.0 OE2 B:GLU1093 4.0 102.3 1.0 O3A B:08T1603 4.1 88.3 1.0 NH2 C:ARG1702 4.4 88.0 1.0 O2B B:08T1603 4.5 88.3 1.0 O2A B:08T1603 4.6 88.3 1.0 O C:ASP1676 4.6 93.6 1.0 CB B:THR1040 4.7 93.6 1.0 ND2 B:ASN1136 4.7 94.8 1.0 CD B:LYS1039 4.7 89.6 1.0 CZ C:ARG1705 4.8 88.1 1.0 PA B:08T1603 4.9 88.3 1.0 OD1 B:ASP1092 5.0 105.4 1.0

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