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Fluorine in PDB 3cf1: Structure of P97/Vcp in Complex with Adp/Adp.Alfx

Protein crystallography data

The structure of Structure of P97/Vcp in Complex with Adp/Adp.Alfx, PDB code: 3cf1 was solved by J.M.Davies, B.Delabarre, A.T.Brunger, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 4.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 162.660, 178.020, 321.140, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.6

Other elements in 3cf1:

The structure of Structure of P97/Vcp in Complex with Adp/Adp.Alfx also contains other interesting chemical elements:

Aluminium (Al) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx (pdb code 3cf1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx, PDB code: 3cf1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 1 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F915

b:0.3
occ:0.94
 F1 A:AF3915 0.0 0.3 0.9
AL A:AF3915 1.9 0.3 0.9
O3B A:ADP900 2.2 0.3 1.0
O2B A:ADP900 2.5 0.3 1.0
PB A:ADP900 2.7 0.3 1.0
N A:GLY521 2.9 0.3 1.0
CA A:PRO520 3.2 0.1 1.0
F3 A:AF3915 3.2 0.3 0.9
F2 A:AF3915 3.2 0.3 0.9
O3A A:ADP900 3.3 0.3 1.0
C A:PRO520 3.4 0.1 1.0
CB A:PRO520 3.8 0.5 1.0
CA A:GLY521 3.9 0.3 1.0
N A:CYS522 4.1 0.4 1.0
O1B A:ADP900 4.1 0.3 1.0
N A:PRO520 4.4 0.1 1.0
C A:GLY521 4.6 0.3 1.0
O A:PRO520 4.6 0.1 1.0
CG A:PRO520 4.7 0.5 1.0
O A:PRO519 4.7 0.5 1.0
PA A:ADP900 4.7 0.3 1.0
O2A A:ADP900 4.9 0.3 1.0
N A:GLY523 5.0 0.5 1.0

Fluorine binding site 2 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 2 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F915

b:0.3
occ:0.94
 F2 A:AF3915 0.0 0.3 0.9
AL A:AF3915 1.9 0.3 0.9
O3B A:ADP900 2.5 0.3 1.0
CB A:LYS524 2.9 0.5 1.0
O2B A:ADP900 3.0 0.3 1.0
PB A:ADP900 3.0 0.3 1.0
O1B A:ADP900 3.2 0.3 1.0
F3 A:AF3915 3.2 0.3 0.9
F1 A:AF3915 3.2 0.3 0.9
N A:THR525 3.6 0.8 1.0
CG A:LYS524 3.6 0.5 1.0
OG1 A:THR525 3.7 0.7 1.0
CD A:LYS524 3.7 0.5 1.0
N A:LYS524 3.7 0.1 1.0
CA A:LYS524 3.8 0.1 1.0
CB A:ALA622 3.9 1.0 1.0
C A:LYS524 4.1 0.1 1.0
OD1 A:ASP577 4.4 0.7 1.0
O3A A:ADP900 4.5 0.3 1.0
CA A:THR525 4.6 0.8 1.0
CB A:THR525 4.6 0.7 1.0
C A:GLY523 4.8 0.5 1.0

Fluorine binding site 3 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 3 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F915

b:0.3
occ:0.94
 F3 A:AF3915 0.0 0.3 0.9
AL A:AF3915 1.9 0.3 0.9
O2B A:ADP900 2.3 0.3 1.0
CG A:LYS524 2.9 0.5 1.0
NZ A:LYS524 3.0 0.5 1.0
CD A:LYS524 3.1 0.5 1.0
F2 A:AF3915 3.2 0.3 0.9
F1 A:AF3915 3.2 0.3 0.9
O A:PRO519 3.4 0.5 1.0
CB A:LYS524 3.4 0.5 1.0
CB A:CYS522 3.5 0.5 1.0
N A:CYS522 3.6 0.4 1.0
CE A:LYS524 3.6 0.5 1.0
N A:LYS524 3.6 0.1 1.0
PB A:ADP900 3.8 0.3 1.0
C A:CYS522 3.8 0.4 1.0
CA A:CYS522 3.8 0.4 1.0
O A:CYS522 4.0 0.4 1.0
O3B A:ADP900 4.1 0.3 1.0
CA A:LYS524 4.1 0.1 1.0
CA A:PRO520 4.2 0.1 1.0
C A:PRO520 4.3 0.1 1.0
C A:PRO519 4.3 0.5 1.0
N A:GLY523 4.3 0.5 1.0
N A:GLY521 4.3 0.3 1.0
O1B A:ADP900 4.5 0.3 1.0
SG A:CYS522 4.5 0.5 1.0
N A:PRO520 4.6 0.1 1.0
C A:GLY521 4.7 0.3 1.0
C A:GLY523 4.7 0.5 1.0
O A:PRO520 4.8 0.1 1.0
O3A A:ADP900 4.8 0.3 1.0
O A:GLY518 4.9 0.3 1.0
CA A:GLY523 5.0 0.5 1.0

Fluorine binding site 4 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 4 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F915

b:0.3
occ:0.94
 F1 B:AF3915 0.0 0.3 0.9
AL B:AF3915 1.9 0.3 0.9
O3B B:ADP900 2.2 0.3 1.0
O2B B:ADP900 2.2 0.3 1.0
N B:GLY521 2.3 0.0 1.0
PB B:ADP900 2.7 0.3 1.0
CA B:GLY521 3.2 0.0 1.0
F2 B:AF3915 3.2 0.3 0.9
F3 B:AF3915 3.2 0.3 0.9
C B:PRO520 3.3 0.2 1.0
CA B:PRO520 3.4 0.2 1.0
O1B B:ADP900 3.6 0.3 1.0
O3A B:ADP900 3.9 0.3 1.0
CB B:PRO520 4.0 0.3 1.0
N B:CYS522 4.0 0.2 1.0
C B:GLY521 4.1 0.0 1.0
O B:PRO520 4.4 0.2 1.0
N B:PRO520 4.7 0.2 1.0
NH2 A:ARG635 4.8 0.5 1.0
O B:PRO519 4.8 0.1 1.0
C5' B:ADP900 4.9 0.3 1.0
NZ B:LYS524 4.9 0.0 1.0

Fluorine binding site 5 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 5 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F915

b:0.3
occ:0.94
 F2 B:AF3915 0.0 0.3 0.9
AL B:AF3915 1.9 0.3 0.9
O B:PRO519 2.6 0.1 1.0
CA B:PRO520 2.7 0.2 1.0
C B:PRO519 2.9 0.1 1.0
N B:PRO520 2.9 0.2 1.0
CE B:LYS524 3.0 0.0 1.0
F1 B:AF3915 3.2 0.3 0.9
F3 B:AF3915 3.2 0.3 0.9
C B:PRO520 3.4 0.2 1.0
N B:GLY521 3.7 0.0 1.0
NZ B:LYS524 3.8 0.0 1.0
CD B:LYS524 3.8 0.0 1.0
O B:GLY518 3.9 0.7 1.0
CB B:PRO520 3.9 0.3 1.0
CD B:PRO520 4.0 0.3 1.0
CG B:PRO520 4.1 0.3 1.0
CB B:ASN624 4.1 0.5 1.0
CA B:PRO519 4.1 0.1 1.0
O2B B:ADP900 4.2 0.3 1.0
CG B:LYS524 4.2 0.0 1.0
C B:GLY518 4.2 0.7 1.0
O B:PRO520 4.3 0.2 1.0
N B:PRO519 4.3 0.1 1.0
N B:CYS522 4.4 0.2 1.0
CA B:ASN624 4.6 0.4 1.0
O3B B:ADP900 4.7 0.3 1.0
PB B:ADP900 4.8 0.3 1.0
CB B:LYS524 4.8 0.0 1.0
CB B:CYS522 4.8 0.6 1.0
CA B:GLY521 4.9 0.0 1.0
O1B B:ADP900 4.9 0.3 1.0

Fluorine binding site 6 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 6 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F915

b:0.3
occ:0.94
 F3 B:AF3915 0.0 0.3 0.9
AL B:AF3915 1.9 0.3 0.9
O1B B:ADP900 2.2 0.3 1.0
O2B B:ADP900 2.3 0.3 1.0
N B:LYS524 2.6 0.2 1.0
PB B:ADP900 2.6 0.3 1.0
CB B:LYS524 2.7 0.0 1.0
CG B:LYS524 3.0 0.0 1.0
F2 B:AF3915 3.2 0.3 0.9
CA B:LYS524 3.2 0.2 1.0
F1 B:AF3915 3.2 0.3 0.9
NZ B:LYS524 3.2 0.0 1.0
CE B:LYS524 3.3 0.0 1.0
O3B B:ADP900 3.4 0.3 1.0
N B:GLY523 3.6 0.3 1.0
N B:CYS522 3.7 0.2 1.0
CD B:LYS524 3.7 0.0 1.0
C B:GLY523 3.7 0.3 1.0
N B:THR525 3.8 0.4 1.0
C B:CYS522 4.0 0.2 1.0
O3A B:ADP900 4.0 0.3 1.0
C B:LYS524 4.1 0.2 1.0
O1A B:ADP900 4.1 0.3 1.0
CA B:GLY523 4.1 0.3 1.0
CA B:CYS522 4.3 0.2 1.0
N B:GLY521 4.3 0.0 1.0
O B:PRO519 4.5 0.1 1.0
CB B:CYS522 4.6 0.6 1.0
O B:CYS522 4.6 0.2 1.0
C B:GLY521 4.7 0.0 1.0
PA B:ADP900 4.7 0.3 1.0
CA B:GLY521 4.7 0.0 1.0
O B:GLY523 4.8 0.3 1.0
OG1 B:THR525 4.8 0.1 1.0
C B:PRO520 4.9 0.2 1.0

Fluorine binding site 7 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 7 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F915

b:0.3
occ:0.94
 F1 C:AF3915 0.0 0.3 0.9
AL C:AF3915 1.9 0.3 0.9
O3B C:ADP900 2.1 0.3 1.0
O2B C:ADP900 2.7 0.3 1.0
PB C:ADP900 2.9 0.3 1.0
F3 C:AF3915 3.2 0.3 0.9
F2 C:AF3915 3.2 0.3 0.9
N C:GLY521 3.6 0.3 1.0
CA C:PRO520 3.7 0.2 1.0
O3A C:ADP900 3.8 0.3 1.0
CB C:PRO520 3.9 0.5 1.0
O1B C:ADP900 4.1 0.3 1.0
C C:PRO520 4.2 0.2 1.0
NH2 B:ARG635 4.3 0.9 1.0
CG C:PRO520 4.5 0.5 1.0
CA C:GLY521 4.7 0.3 1.0
N C:PRO520 4.8 0.2 1.0

Fluorine binding site 8 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 8 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F915

b:0.3
occ:0.94
 F2 C:AF3915 0.0 0.3 0.9
AL C:AF3915 1.8 0.3 0.9
O1B C:ADP900 2.3 0.3 1.0
O3B C:ADP900 2.5 0.3 1.0
PB C:ADP900 2.6 0.3 1.0
CB C:LYS524 2.7 0.2 1.0
O2B C:ADP900 2.8 0.3 1.0
N C:LYS524 3.1 0.7 1.0
CG C:LYS524 3.1 0.2 1.0
CD C:LYS524 3.2 0.2 1.0
F3 C:AF3915 3.2 0.3 0.9
F1 C:AF3915 3.2 0.3 0.9
CA C:LYS524 3.4 0.7 1.0
N C:THR525 3.8 0.2 1.0
C C:GLY523 4.0 0.5 1.0
C C:LYS524 4.1 0.7 1.0
O3A C:ADP900 4.1 0.3 1.0
N C:GLY523 4.3 0.5 1.0
CE C:LYS524 4.3 0.2 1.0
OG1 C:THR525 4.4 0.5 1.0
NZ C:LYS524 4.4 0.2 1.0
CA C:GLY523 4.5 0.5 1.0
CB C:ALA622 4.8 0.6 1.0
O C:GLY523 4.9 0.5 1.0
CA C:THR525 5.0 0.2 1.0

Fluorine binding site 9 out of 9 in 3cf1

Go back to Fluorine Binding Sites List in 3cf1
Fluorine binding site 9 out of 9 in the Structure of P97/Vcp in Complex with Adp/Adp.Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of P97/Vcp in Complex with Adp/Adp.Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F915

b:0.3
occ:0.94
 F3 C:AF3915 0.0 0.3 0.9
AL C:AF3915 1.8 0.3 0.9
O2B C:ADP900 2.2 0.3 1.0
N C:CYS522 2.7 1.0 1.0
CB C:CYS522 2.8 0.3 1.0
N C:GLY523 3.0 0.5 1.0
N C:GLY521 3.1 0.3 1.0
CA C:CYS522 3.1 1.0 1.0
F2 C:AF3915 3.2 0.3 0.9
F1 C:AF3915 3.2 0.3 0.9
O C:PRO519 3.3 0.3 1.0
C C:GLY521 3.5 0.3 1.0
C C:CYS522 3.5 1.0 1.0
PB C:ADP900 3.6 0.3 1.0
CA C:PRO520 3.6 0.2 1.0
C C:PRO520 3.6 0.2 1.0
NZ C:LYS524 3.7 0.2 1.0
SG C:CYS522 3.7 0.3 1.0
N C:LYS524 3.9 0.7 1.0
CA C:GLY521 3.9 0.3 1.0
O3B C:ADP900 4.0 0.3 1.0
CA C:GLY523 4.0 0.5 1.0
C C:PRO519 4.1 0.3 1.0
CG C:LYS524 4.2 0.2 1.0
O1B C:ADP900 4.2 0.3 1.0
N C:PRO520 4.2 0.2 1.0
CD C:LYS524 4.4 0.2 1.0
O C:GLY521 4.5 0.3 1.0
C C:GLY523 4.5 0.5 1.0
CE C:LYS524 4.6 0.2 1.0
O C:PRO520 4.6 0.2 1.0
CB C:LYS524 4.7 0.2 1.0
O C:CYS522 4.7 1.0 1.0
O3A C:ADP900 4.8 0.3 1.0
CB C:PRO520 4.9 0.5 1.0
CA C:LYS524 4.9 0.7 1.0

Reference:

J.M.Davies, A.T.Brunger, W.I.Weis. Improved Structures of Full-Length P97, An Aaa Atpase: Implications For Mechanisms of Nucleotide-Dependent Conformational Change. Structure V. 16 715 2008.
ISSN: ISSN 0969-2126
PubMed: 18462676
DOI: 10.1016/J.STR.2008.02.010
Page generated: Wed Jul 31 17:27:59 2024

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