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Fluorine in PDB 9dyy: Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet

Protein crystallography data

The structure of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet, PDB code: 9dyy was solved by M.R.Sawaya, J.A.Raskatov, A.Hazari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.52 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.12, 44.27, 9.34, 90, 90, 90
R / Rfree (%) 18.1 / 18.8

Fluorine Binding Sites:

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 Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet (pdb code 9dyy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet, PDB code: 9dyy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 9dyy

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Fluorine binding site 1 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:35.1
occ:1.00
 F7 C:CFH101 0.0 35.1 1.0
C1 C:CFH101 1.3 24.0 1.0
F5 C:CFH101 2.2 25.6 1.0
F6 C:CFH101 2.2 24.5 1.0
C2 C:CFH101 2.3 21.4 1.0
HA3 C:GLY3 2.5 9.9 1.0
H2 C:CFH101 2.5 21.4 1.0
O4 C:CFH101 2.8 15.9 1.0
HG22 B:DVA6 2.9 14.9 1.0
HB B:DVA6 2.9 12.5 1.0
HG21 B:DVA6 3.1 15.0 1.0
CA C:GLY3 3.2 10.0 1.0
CG2 B:DVA6 3.3 15.5 1.0
N C:GLY3 3.4 9.9 1.0
H3 A:VAL1 3.4 12.7 1.0
C C:GLY3 3.6 9.0 1.0
C3 C:CFH101 3.7 23.4 1.0
H C:GLY3 3.7 9.9 1.0
CB B:DVA6 3.7 12.6 1.0
C C:VAL2 3.8 9.4 1.0
HN1 B:NH27 3.8 11.2 1.0
O C:VAL2 3.9 9.6 1.0
O C:GLY3 4.0 9.2 1.0
HA B:DVA6 4.0 10.6 1.0
HA2 C:GLY3 4.0 9.8 1.0
F10 C:CFH101 4.1 25.0 1.0
F8 C:CFH101 4.1 24.2 1.0
N C:GLY4 4.1 8.6 1.0
N A:VAL1 4.2 13.1 1.0
H C:GLY4 4.2 8.8 1.0
H1 A:VAL1 4.2 12.6 1.0
HG23 B:DVA6 4.3 15.1 1.0
CA B:DVA6 4.5 10.2 1.0
H2 A:VAL1 4.5 12.6 1.0
N B:NH27 4.6 11.5 1.0
F9 C:CFH101 4.7 35.0 1.0
HG11 B:DVA6 4.7 13.1 1.0
HA C:VAL2 4.7 9.4 1.0
CG1 B:DVA6 4.7 13.1 1.0
CA C:VAL2 4.7 9.1 1.0
HA2 C:GLY4 4.8 9.1 1.0
H C:VAL2 4.8 8.8 1.0
HB C:VAL1 4.9 11.8 1.0
N C:VAL2 4.9 9.0 1.0
HG13 B:DVA6 5.0 13.1 1.0
C B:DVA6 5.0 11.2 1.0

Fluorine binding site 2 out of 24 in 9dyy

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Fluorine binding site 2 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:25.6
occ:1.00
 F5 C:CFH101 0.0 25.6 1.0
C1 C:CFH101 1.3 24.0 1.0
F7 C:CFH101 2.2 35.1 1.0
F6 C:CFH101 2.2 24.5 1.0
C2 C:CFH101 2.3 21.4 1.0
F8 C:CFH101 2.6 24.2 1.0
O4 C:CFH101 2.6 15.9 1.0
C3 C:CFH101 2.9 23.4 1.0
HB B:DVA6 3.0 12.5 1.0
HN1 B:NH27 3.1 11.2 1.0
H2 C:CFH101 3.1 21.4 1.0
HG22 C:VAL1 3.5 12.9 1.0
F10 C:CFH101 3.5 25.0 1.0
HB C:VAL1 3.6 11.8 1.0
N B:NH27 3.7 11.5 1.0
HN2 B:NH27 4.1 11.4 1.0
F9 C:CFH101 4.1 35.0 1.0
CB B:DVA6 4.1 12.6 1.0
CG2 C:VAL1 4.2 13.0 1.0
HA3 C:GLY3 4.2 9.9 1.0
HG23 C:VAL1 4.2 12.8 1.0
HG22 B:DVA6 4.2 14.9 1.0
CB C:VAL1 4.3 12.0 1.0
HA B:DVA6 4.3 10.6 1.0
HG21 B:DVA6 4.4 15.0 1.0
H3 A:VAL1 4.4 12.7 1.0
C B:DVA6 4.5 11.2 1.0
CG2 B:DVA6 4.5 15.5 1.0
H C:VAL2 4.6 8.8 1.0
O C:VAL2 4.6 9.6 1.0
CA B:DVA6 4.6 10.2 1.0
C C:VAL2 4.7 9.4 1.0
HG13 B:DVA6 4.7 13.1 1.0
H1 A:VAL1 4.7 12.6 1.0
HG12 C:VAL1 4.8 14.6 1.0
N C:GLY3 4.8 9.9 1.0
N C:VAL2 4.8 9.0 1.0
CG1 B:DVA6 4.9 13.1 1.0
CA C:GLY3 4.9 10.0 1.0

Fluorine binding site 3 out of 24 in 9dyy

Go back to Fluorine Binding Sites List in 9dyy
Fluorine binding site 3 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:24.5
occ:1.00
 F6 C:CFH101 0.0 24.5 1.0
C1 C:CFH101 1.3 24.0 1.0
F5 C:CFH101 2.2 25.6 1.0
F7 C:CFH101 2.2 35.1 1.0
C2 C:CFH101 2.3 21.4 1.0
F10 C:CFH101 2.6 25.0 1.0
H2 C:CFH101 2.6 21.4 1.0
C3 C:CFH101 2.8 23.4 1.0
HG23 C:VAL1 3.1 12.8 1.0
F8 C:CFH101 3.2 24.2 1.0
HG22 C:VAL1 3.2 12.9 1.0
HB C:VAL1 3.3 11.8 1.0
C C:VAL2 3.3 9.4 1.0
N C:GLY3 3.4 9.9 1.0
N C:VAL2 3.4 9.0 1.0
HA C:VAL2 3.4 9.4 1.0
O4 C:CFH101 3.5 15.9 1.0
H C:GLY3 3.5 9.9 1.0
CG2 C:VAL1 3.5 13.0 1.0
H C:VAL2 3.6 8.8 1.0
CA C:VAL2 3.6 9.1 1.0
HA3 C:GLY3 3.7 9.9 1.0
C C:VAL1 3.8 8.8 1.0
O C:VAL2 3.8 9.6 1.0
CB C:VAL1 3.9 12.0 1.0
F9 C:CFH101 4.1 35.0 1.0
CA C:GLY3 4.1 10.0 1.0
O C:VAL1 4.1 9.4 1.0
HG21 C:VAL1 4.4 12.9 1.0
CA C:VAL1 4.5 9.9 1.0
H3 A:VAL1 4.6 12.7 1.0
HB B:DVA6 4.7 12.5 1.0
C C:GLY3 4.8 9.0 1.0
O C:GLY3 4.8 9.2 1.0
HN1 B:NH27 4.8 11.2 1.0
HA2 C:GLY3 4.9 9.8 1.0
H1 A:VAL1 4.9 12.6 1.0

Fluorine binding site 4 out of 24 in 9dyy

Go back to Fluorine Binding Sites List in 9dyy
Fluorine binding site 4 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:25.0
occ:1.00
 F10 C:CFH101 0.0 25.0 1.0
C3 C:CFH101 1.3 23.4 1.0
F8 C:CFH101 2.2 24.2 1.0
F9 C:CFH101 2.2 35.0 1.0
C2 C:CFH101 2.3 21.4 1.0
H2 C:CFH101 2.6 21.4 1.0
F6 C:CFH101 2.6 24.5 1.0
HG23 C:VAL1 2.8 12.8 1.0
HG22 C:VAL1 2.9 12.9 1.0
C1 C:CFH101 2.9 24.0 1.0
CG2 C:VAL1 3.3 13.0 1.0
F5 C:CFH101 3.5 25.6 1.0
O4 C:CFH101 3.5 15.9 1.0
HG21 C:VAL1 3.8 12.9 1.0
F7 C:CFH101 4.1 35.1 1.0
H1 A:VAL1 4.3 12.6 1.0
HB C:VAL1 4.4 11.8 1.0
CB C:VAL1 4.5 12.0 1.0
O C:VAL1 4.7 9.4 1.0
H3 A:VAL1 4.8 12.7 1.0
C C:VAL1 4.9 8.8 1.0
N A:VAL1 4.9 13.1 1.0

Fluorine binding site 5 out of 24 in 9dyy

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Fluorine binding site 5 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:24.2
occ:1.00
 F8 C:CFH101 0.0 24.2 1.0
C3 C:CFH101 1.3 23.4 1.0
F10 C:CFH101 2.2 25.0 1.0
F9 C:CFH101 2.2 35.0 1.0
C2 C:CFH101 2.3 21.4 1.0
F5 C:CFH101 2.6 25.6 1.0
HG22 C:VAL1 2.7 12.9 1.0
O4 C:CFH101 2.8 15.9 1.0
C1 C:CFH101 2.8 24.0 1.0
H2 C:CFH101 3.2 21.4 1.0
F6 C:CFH101 3.2 24.5 1.0
CG2 C:VAL1 3.6 13.0 1.0
HN1 B:NH27 3.6 11.2 1.0
HG23 C:VAL1 3.7 12.8 1.0
HG21 C:VAL1 4.1 12.9 1.0
F7 C:CFH101 4.1 35.1 1.0
HG23 A:VAL1 4.2 14.2 1.0
H1 A:VAL1 4.2 12.6 1.0
HN2 B:NH27 4.3 11.4 1.0
N B:NH27 4.3 11.5 1.0
HB C:VAL1 4.3 11.8 1.0
CB C:VAL1 4.6 12.0 1.0
H3 A:VAL1 4.7 12.7 1.0
HG12 C:VAL1 4.8 14.6 1.0
N A:VAL1 4.9 13.1 1.0
HG21 A:VAL1 5.0 14.6 1.0

Fluorine binding site 6 out of 24 in 9dyy

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Fluorine binding site 6 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:35.0
occ:1.00
 F9 C:CFH101 0.0 35.0 1.0
C3 C:CFH101 1.3 23.4 1.0
F10 C:CFH101 2.2 25.0 1.0
F8 C:CFH101 2.2 24.2 1.0
C2 C:CFH101 2.3 21.4 1.0
H2 C:CFH101 2.6 21.4 1.0
O4 C:CFH101 2.7 15.9 1.0
H1 A:VAL1 2.9 12.6 1.0
HG23 A:VAL1 3.0 14.2 1.0
C1 C:CFH101 3.7 24.0 1.0
N A:VAL1 3.7 13.1 1.0
H3 A:VAL1 3.9 12.7 1.0
CG2 A:VAL1 4.0 14.7 1.0
H2 A:VAL1 4.0 12.6 1.0
F6 C:CFH101 4.1 24.5 1.0
F5 C:CFH101 4.1 25.6 1.0
HN1 B:NH27 4.2 11.2 1.0
HG21 A:VAL1 4.3 14.6 1.0
HG22 C:VAL1 4.4 12.9 1.0
HB A:VAL1 4.4 12.7 1.0
HG22 A:VAL1 4.5 14.3 1.0
CB A:VAL1 4.6 12.8 1.0
F7 C:CFH101 4.7 35.1 1.0
CA A:VAL1 4.8 10.6 1.0
HG23 C:VAL1 4.8 12.8 1.0

Fluorine binding site 7 out of 24 in 9dyy

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Fluorine binding site 7 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F102

b:28.4
occ:1.00
 F7 C:CFH102 0.0 28.4 1.0
C1 C:CFH102 1.3 28.2 1.0
F5 C:CFH102 2.2 36.6 1.0
F6 C:CFH102 2.2 36.2 1.0
C2 C:CFH102 2.3 23.5 1.0
H2 C:CFH102 2.6 23.2 1.0
O4 C:CFH102 2.7 14.6 1.0
H2 C:VAL1 2.7 10.8 1.0
HG23 C:VAL2 2.8 14.1 1.0
HA C:VAL1 3.1 10.0 1.0
N C:VAL1 3.4 10.8 1.0
H3 C:VAL1 3.5 10.8 1.0
CA C:VAL1 3.6 9.9 1.0
C3 C:CFH102 3.7 33.3 1.0
CG2 C:VAL2 3.7 14.6 1.0
C C:VAL1 3.9 8.8 1.0
HG22 C:VAL2 3.9 14.0 1.0
F10 C:CFH102 4.0 37.5 1.0
H1 C:VAL1 4.2 10.8 1.0
O C:VAL1 4.2 9.4 1.0
HG21 C:VAL2 4.2 14.1 1.0
F8 C:CFH102 4.3 30.7 1.0
N C:VAL2 4.3 9.0 1.0
HB C:VAL2 4.5 11.5 1.0
H C:VAL2 4.5 8.8 1.0
F9 C:CFH102 4.6 46.3 1.0
CB C:VAL2 4.7 11.5 1.0

Fluorine binding site 8 out of 24 in 9dyy

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Fluorine binding site 8 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F102

b:36.6
occ:1.00
 F5 C:CFH102 0.0 36.6 1.0
C1 C:CFH102 1.3 28.2 1.0
F7 C:CFH102 2.2 28.4 1.0
F6 C:CFH102 2.2 36.2 1.0
C2 C:CFH102 2.3 23.5 1.0
O4 C:CFH102 2.8 14.6 1.0
C3 C:CFH102 2.8 33.3 1.0
F8 C:CFH102 2.9 30.7 1.0
F10 C:CFH102 2.9 37.5 1.0
H2 C:CFH102 3.2 23.2 1.0
F9 C:CFH102 4.1 46.3 1.0
H2 C:VAL1 4.3 10.8 1.0
HA C:VAL1 4.5 10.0 1.0
H3 C:VAL1 4.5 10.8 1.0
N C:VAL1 4.8 10.8 1.0
HG23 C:VAL2 4.9 14.1 1.0

Fluorine binding site 9 out of 24 in 9dyy

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Fluorine binding site 9 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F102

b:36.2
occ:1.00
 F6 C:CFH102 0.0 36.2 1.0
C1 C:CFH102 1.3 28.2 1.0
F7 C:CFH102 2.2 28.4 1.0
F5 C:CFH102 2.2 36.6 1.0
C2 C:CFH102 2.3 23.5 1.0
F10 C:CFH102 2.5 37.5 1.0
H2 C:CFH102 2.5 23.2 1.0
C3 C:CFH102 2.9 33.3 1.0
O4 C:CFH102 3.5 14.6 1.0
F8 C:CFH102 3.8 30.7 1.0
F9 C:CFH102 3.9 46.3 1.0
H2 C:VAL1 4.0 10.8 1.0
HG23 C:VAL2 4.4 14.1 1.0
H3 C:VAL1 4.7 10.8 1.0
N C:VAL1 4.7 10.8 1.0

Fluorine binding site 10 out of 24 in 9dyy

Go back to Fluorine Binding Sites List in 9dyy
Fluorine binding site 10 out of 24 in the Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Peptide of Mixed Chirality, Vvgg(Dva)(Dva), Assembles Into A Rippled Beta Sheet within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F102

b:37.5
occ:1.00
 F10 C:CFH102 0.0 37.5 1.0
C3 C:CFH102 1.3 33.3 1.0
F8 C:CFH102 2.1 30.7 1.0
F9 C:CFH102 2.2 46.3 1.0
C2 C:CFH102 2.3 23.5 1.0
F6 C:CFH102 2.5 36.2 1.0
C1 C:CFH102 2.7 28.2 1.0
H2 C:CFH102 2.7 23.2 1.0
F5 C:CFH102 2.9 36.6 1.0
O4 C:CFH102 3.5 14.6 1.0
F7 C:CFH102 4.0 28.4 1.0
H2 C:VAL1 4.9 10.8 1.0
H3 C:VAL1 5.0 10.8 1.0

Reference:

A.Hazari, M.R.Sawaya, H.Lee, M.Sajimon, H.Kim, W.A.Goddard Iii, D.Eisenberg, J.A.Raskatov. Formation of Rippled Beta-Sheets From Mixed Chirality Linear and Cyclic Peptides-New Structural Motifs Based on the Pauling-Corey Rippled Beta-Sheet. Chem Sci 2025.
ISSN: ISSN 2041-6520
PubMed: 40060095
DOI: 10.1039/D4SC08079C
Page generated: Wed Jul 16 10:52:21 2025

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