Fluorine in PDB 9dyx: Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets

The structure of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets, PDB code: 9dyx 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)	12.29 / 1.10
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	12.29, 12.46, 11.78, 76, 89.29, 88.49
R / Rfree (%)	17.9 / 17.8

The binding sites of Fluorine atom in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets (pdb code 9dyx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets, PDB code: 9dyx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:16.3 occ:1.00 F01 A:YWK101 0.0 16.3 1.0 C01 A:YWK101 1.4 16.0 1.0 C02 A:YWK101 2.3 16.6 1.0 F02 A:YWK101 2.3 16.5 1.0 C03 A:YWK101 2.4 14.7 1.0 F03 A:YWK101 2.6 16.5 1.0 O01 A:YWK101 2.6 14.1 1.0 F05 A:YWK101 2.6 17.5 1.0 F04 A:YWK101 3.5 17.2 1.0 O02 A:YWK101 3.5 14.1 1.0 H1 A:VAL1 5.0 12.3 1.0

Fluorine binding site 2 out of 5 in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:16.5 occ:1.00 F02 A:YWK101 0.0 16.5 1.0 C01 A:YWK101 1.4 16.0 1.0 C02 A:YWK101 2.3 16.6 1.0 F01 A:YWK101 2.3 16.3 1.0 C03 A:YWK101 2.4 14.7 1.0 F03 A:YWK101 2.6 16.5 1.0 F04 A:YWK101 2.6 17.2 1.0 O02 A:YWK101 3.0 14.1 1.0 O01 A:YWK101 3.3 14.1 1.0 F05 A:YWK101 3.5 17.5 1.0 HG13 A:VAL1 4.6 15.3 1.0 H1 A:VAL1 4.8 12.3 1.0

Fluorine binding site 3 out of 5 in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:16.5 occ:1.00 F03 A:YWK101 0.0 16.5 1.0 C02 A:YWK101 1.4 16.6 1.0 F04 A:YWK101 2.2 17.2 1.0 C01 A:YWK101 2.3 16.0 1.0 F05 A:YWK101 2.3 17.5 1.0 F01 A:YWK101 2.6 16.3 1.0 F02 A:YWK101 2.6 16.5 1.0 C03 A:YWK101 3.6 14.7 1.0 O02 A:YWK101 4.2 14.1 1.0 O01 A:YWK101 4.5 14.1 1.0 HG13 A:VAL1 4.6 15.3 1.0

Fluorine binding site 4 out of 5 in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:17.2 occ:1.00 F04 A:YWK101 0.0 17.2 1.0 C02 A:YWK101 1.4 16.6 1.0 F03 A:YWK101 2.2 16.5 1.0 F05 A:YWK101 2.3 17.5 1.0 C01 A:YWK101 2.3 16.0 1.0 HG13 A:VAL1 2.5 15.3 1.0 F02 A:YWK101 2.6 16.5 1.0 O02 A:YWK101 2.7 14.1 1.0 C03 A:YWK101 2.9 14.7 1.0 CG1 A:VAL1 3.4 12.7 1.0 F01 A:YWK101 3.5 16.3 1.0 HG12 A:VAL1 3.6 15.3 1.0 HG11 A:VAL1 3.8 15.3 1.0 H1 A:VAL1 3.8 12.3 1.0 HG21 A:VAL1 3.9 15.7 1.0 O01 A:YWK101 4.1 14.1 1.0 HG22 A:VAL1 4.3 15.7 1.0 CG2 A:VAL1 4.4 13.1 1.0 CB A:VAL1 4.5 11.6 1.0 N A:VAL1 4.7 10.2 1.0

Fluorine binding site 5 out of 5 in the Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Racemic Mixture of Peptide Vvggvv Forms Rippled Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:17.5 occ:1.00 F05 A:YWK101 0.0 17.5 1.0 C02 A:YWK101 1.4 16.6 1.0 F04 A:YWK101 2.3 17.2 1.0 C01 A:YWK101 2.3 16.0 1.0 F03 A:YWK101 2.3 16.5 1.0 F01 A:YWK101 2.6 16.3 1.0 C03 A:YWK101 2.7 14.7 1.0 O02 A:YWK101 3.1 14.1 1.0 HG21 A:VAL1 3.2 15.7 1.0 F02 A:YWK101 3.5 16.5 1.0 O01 A:YWK101 3.5 14.1 1.0 HG13 A:VAL1 3.5 15.3 1.0 H1 A:VAL1 3.8 12.3 1.0 HG22 A:VAL1 4.0 15.7 1.0 CG2 A:VAL1 4.0 13.1 1.0 H2 A:VAL1 4.4 12.3 1.0 CG1 A:VAL1 4.4 12.7 1.0 N A:VAL1 4.5 10.2 1.0 HG12 A:VAL1 4.7 15.3 1.0 HG23 A:VAL1 4.8 15.7 1.0 CB A:VAL1 4.8 11.6 1.0

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