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Fluorine in PDB 6bmf: VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P

Other elements in 6bmf:

The structure of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P (pdb code 6bmf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P, PDB code: 6bmf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6bmf

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Fluorine binding site 1 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:37.8
occ:1.00
 F1 A:BEF502 0.0 37.8 1.0
BE A:BEF502 1.5 37.8 1.0
MG A:MG503 2.0 37.8 1.0
O2B A:ADP501 2.5 37.8 1.0
O3B A:ADP501 2.6 37.8 1.0
F2 A:BEF502 2.6 37.8 1.0
F3 A:BEF502 2.6 37.8 1.0
PB A:ADP501 3.0 37.8 1.0
O1B A:ADP501 3.3 37.8 1.0
OG A:SER180 3.8 16.1 1.0
CE A:LYS179 4.0 12.8 1.0
OD1 A:ASN277 4.2 13.2 1.0
NZ A:LYS179 4.2 12.8 1.0
O3A A:ADP501 4.4 37.8 1.0
ND2 A:ASN277 4.5 13.2 1.0
CG A:ASN277 4.8 13.2 1.0
CB A:SER180 4.8 16.1 1.0
N A:GLY176 4.8 11.2 1.0
CB A:LYS179 4.8 12.8 1.0
N A:SER180 4.8 16.1 1.0
O2A A:ADP501 4.9 37.8 1.0
OE2 A:GLU233 4.9 20.6 1.0

Fluorine binding site 2 out of 9 in 6bmf

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Fluorine binding site 2 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:37.8
occ:1.00
 F2 A:BEF502 0.0 37.8 1.0
BE A:BEF502 1.5 37.8 1.0
O1B A:ADP501 2.2 37.8 1.0
O3B A:ADP501 2.4 37.8 1.0
NZ A:LYS179 2.4 12.8 1.0
F3 A:BEF502 2.6 37.8 1.0
F1 A:BEF502 2.6 37.8 1.0
N A:GLY176 2.8 11.2 1.0
PB A:ADP501 2.9 37.8 1.0
CE A:LYS179 3.1 12.8 1.0
O A:PRO174 3.5 12.3 1.0
OD1 A:ASN277 3.6 13.2 1.0
O2B A:ADP501 3.6 37.8 1.0
CA A:PRO175 3.6 9.6 1.0
C A:PRO175 3.7 9.6 1.0
CA A:GLY176 3.7 11.2 1.0
N A:THR177 3.8 10.8 1.0
O3A A:ADP501 4.2 37.8 1.0
C A:GLY176 4.2 11.2 1.0
CD A:LYS179 4.3 12.8 1.0
MG A:MG503 4.3 37.8 1.0
CG A:LYS179 4.4 12.8 1.0
C A:PRO174 4.4 12.3 1.0
CG A:ASN277 4.5 13.2 1.0
N A:PRO175 4.5 9.6 1.0
CB A:LYS179 4.6 12.8 1.0
OG1 A:THR177 4.6 10.8 1.0
ND2 A:ASN277 4.7 13.2 1.0
CB A:PRO175 4.7 9.6 1.0
N A:GLY178 4.8 15.5 1.0
N A:LYS179 4.8 12.8 1.0
O A:PRO175 4.8 9.6 1.0
CA A:THR177 5.0 10.8 1.0

Fluorine binding site 3 out of 9 in 6bmf

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Fluorine binding site 3 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:37.8
occ:1.00
 F3 A:BEF502 0.0 37.8 1.0
BE A:BEF502 1.5 37.8 1.0
O3B A:ADP501 2.4 37.8 1.0
F2 A:BEF502 2.6 37.8 1.0
F1 A:BEF502 2.6 37.8 1.0
N A:GLY176 3.0 11.2 1.0
NE B:ARG288 3.3 27.4 1.0
CA A:PRO175 3.5 9.6 1.0
C A:PRO175 3.7 9.6 1.0
CA A:GLY176 3.8 11.2 1.0
PB A:ADP501 3.8 37.8 1.0
CB A:PRO175 3.8 9.6 1.0
CD B:ARG288 3.9 27.4 1.0
CZ B:ARG288 3.9 27.4 1.0
ND2 A:ASN277 4.0 13.2 1.0
NH2 B:ARG288 4.0 27.4 1.0
NH1 B:ARG289 4.0 27.4 1.0
O1B A:ADP501 4.1 37.8 1.0
OD1 A:ASN277 4.1 13.2 1.0
MG A:MG503 4.2 37.8 1.0
O2B A:ADP501 4.2 37.8 1.0
CG A:ASN277 4.4 13.2 1.0
O A:PRO175 4.7 9.6 1.0
NZ A:LYS179 4.8 12.8 1.0
O3A A:ADP501 4.8 37.8 1.0
NH1 B:ARG288 4.9 27.4 1.0
N A:PRO175 4.9 9.6 1.0
CG A:PRO175 4.9 9.6 1.0
CZ B:ARG289 4.9 27.4 1.0
NH2 B:ARG289 5.0 27.4 1.0

Fluorine binding site 4 out of 9 in 6bmf

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Fluorine binding site 4 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:19.7
occ:1.00
 F1 B:BEF502 0.0 19.7 1.0
BE B:BEF502 1.5 19.7 1.0
MG B:MG503 2.0 19.7 1.0
O2B B:ADP501 2.1 19.7 1.0
O1B B:ADP501 2.5 19.7 1.0
F2 B:BEF502 2.6 19.7 1.0
PB B:ADP501 2.6 19.7 1.0
F3 B:BEF502 2.6 19.7 1.0
O3B B:ADP501 2.8 19.7 1.0
OG B:SER180 3.4 20.8 1.0
CE B:LYS179 3.9 19.7 1.0
O3A B:ADP501 4.1 19.7 1.0
NZ B:LYS179 4.2 19.7 1.0
CB B:SER180 4.4 20.8 1.0
N B:SER180 4.5 20.8 1.0
CB B:LYS179 4.5 19.7 1.0
OD1 B:ASN277 4.8 24.5 1.0
O1A B:ADP501 4.8 19.7 1.0
PA B:ADP501 4.9 19.7 1.0

Fluorine binding site 5 out of 9 in 6bmf

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Fluorine binding site 5 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:19.7
occ:1.00
 F2 B:BEF502 0.0 19.7 1.0
BE B:BEF502 1.5 19.7 1.0
O3B B:ADP501 2.2 19.7 1.0
O1B B:ADP501 2.3 19.7 1.0
F1 B:BEF502 2.6 19.7 1.0
NZ B:LYS179 2.6 19.7 1.0
F3 B:BEF502 2.6 19.7 1.0
N B:GLY176 2.8 23.1 1.0
PB B:ADP501 2.9 19.7 1.0
CE B:LYS179 3.2 19.7 1.0
CA B:PRO175 3.5 18.3 1.0
O B:PRO174 3.6 21.5 1.0
C B:PRO175 3.6 18.3 1.0
O2B B:ADP501 3.7 19.7 1.0
CA B:GLY176 3.7 23.1 1.0
OD1 B:ASN277 3.9 24.5 1.0
N B:THR177 4.1 23.8 1.0
O3A B:ADP501 4.1 19.7 1.0
C B:GLY176 4.4 23.1 1.0
C B:PRO174 4.4 21.5 1.0
N B:PRO175 4.5 18.3 1.0
CD B:LYS179 4.5 19.7 1.0
MG B:MG503 4.5 19.7 1.0
CB B:PRO175 4.6 18.3 1.0
CG B:LYS179 4.6 19.7 1.0
CG B:ASN277 4.8 24.5 1.0
CB B:LYS179 4.8 19.7 1.0
O B:PRO175 4.8 18.3 1.0
OG1 B:THR177 4.9 23.8 1.0
ND2 B:ASN277 4.9 24.5 1.0

Fluorine binding site 6 out of 9 in 6bmf

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Fluorine binding site 6 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:19.7
occ:1.00
 F3 B:BEF502 0.0 19.7 1.0
BE B:BEF502 1.5 19.7 1.0
O1B B:ADP501 2.4 19.7 1.0
F1 B:BEF502 2.6 19.7 1.0
F2 B:BEF502 2.6 19.7 1.0
NE C:ARG288 3.6 18.5 1.0
NH1 C:ARG289 3.7 19.1 1.0
PB B:ADP501 3.7 19.7 1.0
MG B:MG503 3.8 19.7 1.0
N B:GLY176 3.8 23.1 1.0
O2B B:ADP501 4.0 19.7 1.0
O3B B:ADP501 4.0 19.7 1.0
NH2 C:ARG288 4.1 18.5 1.0
CA B:PRO175 4.1 18.3 1.0
ND2 B:ASN277 4.2 24.5 1.0
CZ C:ARG288 4.2 18.5 1.0
NH2 C:ARG289 4.3 19.1 1.0
CB B:PRO175 4.3 18.3 1.0
CZ C:ARG289 4.4 19.1 1.0
CD C:ARG288 4.4 18.5 1.0
C B:PRO175 4.4 18.3 1.0
OD1 B:ASN277 4.5 24.5 1.0
CA B:GLY176 4.6 23.1 1.0
CG B:ASN277 4.8 24.5 1.0
O3A B:ADP501 4.8 19.7 1.0
CB C:ALA285 4.9 20.8 1.0
NZ B:LYS179 5.0 19.7 1.0

Fluorine binding site 7 out of 9 in 6bmf

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Fluorine binding site 7 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:17.2
occ:1.00
 F1 C:BEF502 0.0 17.2 1.0
BE C:BEF502 1.5 17.2 1.0
MG C:MG503 2.0 17.2 1.0
O2B C:ADP501 2.4 17.2 1.0
F3 C:BEF502 2.5 17.2 1.0
O1B C:ADP501 2.6 17.2 1.0
F2 C:BEF502 2.6 17.2 1.0
PB C:ADP501 2.8 17.2 1.0
O3B C:ADP501 2.8 17.2 1.0
OG C:SER180 3.5 20.1 1.0
CE C:LYS179 4.0 18.0 1.0
NZ C:LYS179 4.2 18.0 1.0
O3A C:ADP501 4.3 17.2 1.0
CB C:SER180 4.6 20.1 1.0
N C:SER180 4.6 20.1 1.0
O1A C:ADP501 4.6 17.2 1.0
CB C:LYS179 4.6 18.0 1.0
OE2 C:GLU233 4.8 25.5 1.0
OD1 C:ASN277 4.9 20.6 1.0
NH2 D:ARG289 4.9 18.8 1.0

Fluorine binding site 8 out of 9 in 6bmf

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Fluorine binding site 8 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:17.2
occ:1.00
 F2 C:BEF502 0.0 17.2 1.0
BE C:BEF502 1.5 17.2 1.0
O3B C:ADP501 2.1 17.2 1.0
O1B C:ADP501 2.3 17.2 1.0
NZ C:LYS179 2.5 18.0 1.0
F1 C:BEF502 2.6 17.2 1.0
F3 C:BEF502 2.6 17.2 1.0
N C:GLY176 2.9 21.3 1.0
PB C:ADP501 2.9 17.2 1.0
CE C:LYS179 3.2 18.0 1.0
CA C:GLY176 3.7 21.3 1.0
O C:PRO174 3.7 20.6 1.0
O2B C:ADP501 3.7 17.2 1.0
CA C:PRO175 3.8 20.2 1.0
C C:PRO175 3.8 20.2 1.0
N C:THR177 3.9 18.8 1.0
O3A C:ADP501 4.0 17.2 1.0
C C:GLY176 4.3 21.3 1.0
OD1 C:ASN277 4.3 20.6 1.0
CD C:LYS179 4.4 18.0 1.0
CG C:LYS179 4.4 18.0 1.0
MG C:MG503 4.4 17.2 1.0
CB C:LYS179 4.5 18.0 1.0
C C:PRO174 4.6 20.6 1.0
N C:PRO175 4.7 20.2 1.0
OG1 C:THR177 4.7 18.8 1.0
N C:LYS179 4.7 18.0 1.0
N C:GLY178 4.8 20.6 1.0
CB C:PRO175 4.8 20.2 1.0
O C:PRO175 4.9 20.2 1.0

Fluorine binding site 9 out of 9 in 6bmf

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Fluorine binding site 9 out of 9 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:17.2
occ:1.00
 F3 C:BEF502 0.0 17.2 1.0
BE C:BEF502 1.5 17.2 1.0
O1B C:ADP501 2.4 17.2 1.0
F1 C:BEF502 2.5 17.2 1.0
F2 C:BEF502 2.6 17.2 1.0
NE D:ARG288 3.5 15.5 1.0
N C:GLY176 3.5 21.3 1.0
NH1 D:ARG289 3.6 18.8 1.0
PB C:ADP501 3.8 17.2 1.0
NH2 D:ARG288 3.8 15.5 1.0
CA C:PRO175 3.9 20.2 1.0
CZ D:ARG288 3.9 15.5 1.0
MG C:MG503 4.0 17.2 1.0
O3B C:ADP501 4.0 17.2 1.0
O2B C:ADP501 4.0 17.2 1.0
C C:PRO175 4.1 20.2 1.0
CB C:PRO175 4.1 20.2 1.0
CA C:GLY176 4.3 21.3 1.0
NH2 D:ARG289 4.3 18.8 1.0
CD D:ARG288 4.3 15.5 1.0
CZ D:ARG289 4.3 18.8 1.0
ND2 C:ASN277 4.6 20.6 1.0
OD1 C:ASN277 4.7 20.6 1.0
NZ C:LYS179 4.8 18.0 1.0
O1A C:ADP501 4.8 17.2 1.0
O3A C:ADP501 4.9 17.2 1.0

Reference:

H.Han, N.Monroe, W.I.Sundquist, P.S.Shen, C.P.Hill. The Aaa Atpase VPS4 Binds Escrt-III Substrates Through A Repeating Array of Dipeptide-Binding Pockets. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 29165244
DOI: 10.7554/ELIFE.31324
Page generated: Tue Jul 15 10:08:00 2025

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