Fluorine in PDB 6ucx: S2 Symmetric Peptide Design Number 1, Wednesday

The structure of S2 Symmetric Peptide Design Number 1, Wednesday, PDB code: 6ucx was solved by V.K.Mulligan, C.S.Kang, I.Antselovich, M.R.Sawaya, T.O.Yeates, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.90 / 0.85
Space group	P 1 21/c 1
Cell size a, b, c (Å), α, β, γ (°)	12.580, 29.810, 15.260, 90.00, 94.21, 90.00
R / Rfree (%)	7.6 / 8.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the S2 Symmetric Peptide Design Number 1, Wednesday (pdb code 6ucx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the S2 Symmetric Peptide Design Number 1, Wednesday, PDB code: 6ucx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:6.4 occ:0.45 F1 A:TFA101 0.0 6.4 0.5 F2 A:TFA101 0.7 9.4 0.5 C2 A:TFA101 1.1 5.9 0.5 C2 A:TFA101 1.3 3.3 0.5 F3 A:TFA101 1.5 11.7 0.5 F2 A:TFA101 2.1 4.0 0.5 F3 A:TFA101 2.1 5.6 0.5 F1 A:TFA101 2.2 15.3 0.5 C1 A:TFA101 2.2 5.6 0.5 C1 A:TFA101 2.4 2.9 0.5 OXT A:TFA101 2.6 4.3 0.5 O A:TFA101 2.8 4.5 0.5 HG2 A:DPR5 2.8 5.2 0.5 HG3 A:DPR5 2.9 9.4 0.5 HG2 A:DPR5 3.1 9.4 0.5 O A:TFA101 3.2 6.5 0.5 OXT A:TFA101 3.3 3.9 0.5 CG A:DPR5 3.4 7.9 0.5 HB3 A:DPR5 3.4 8.0 0.5 HB3 A:DPR5 3.5 8.6 0.5 CG A:DPR5 3.6 4.3 0.5 HB2 A:DPR5 3.6 8.0 0.5 HB2 A:DPR5 3.6 8.6 0.5 CB A:DPR5 3.7 7.2 0.5 CB A:DPR5 3.7 6.7 0.5 HG3 A:DPR5 3.9 5.2 0.5 OXT A:TFA102 4.4 5.1 0.4 OXT A:TFA102 4.4 5.0 0.5 C1 A:TFA102 4.7 4.8 0.4 HD3 A:DPR5 4.7 4.5 0.5 CD A:DPR5 4.8 5.5 0.5 CD A:DPR5 4.8 3.7 0.5 O A:TFA102 4.8 5.1 0.4 O A:TFA102 5.0 6.0 0.5 C1 A:TFA102 5.0 4.4 0.5

Fluorine binding site 2 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:15.3 occ:0.45 F1 A:TFA101 0.0 15.3 0.5 F2 A:TFA101 0.3 4.0 0.5 C2 A:TFA101 1.2 3.3 0.5 C2 A:TFA101 1.3 5.9 0.5 F3 A:TFA101 1.9 5.6 0.5 F3 A:TFA101 2.1 11.7 0.5 F2 A:TFA101 2.1 9.4 0.5 F1 A:TFA101 2.2 6.4 0.5 C1 A:TFA101 2.3 5.6 0.5 C1 A:TFA101 2.3 2.9 0.5 HB2 A:DPR5 2.5 8.6 0.5 HB2 A:DPR5 2.5 8.0 0.5 OXT A:TFA101 2.6 3.9 0.5 O A:TFA101 2.8 6.5 0.5 HG3 A:DPR5 3.0 9.4 0.5 HG2 A:DPR5 3.0 5.2 0.5 HB3 A:DPR5 3.1 8.6 0.5 CB A:DPR5 3.1 7.2 0.5 CB A:DPR5 3.2 6.7 0.5 HG3 A:DPR5 3.2 5.2 0.5 OXT A:TFA101 3.3 4.3 0.5 CG A:DPR5 3.3 4.3 0.5 HB3 A:DPR5 3.3 8.0 0.5 O A:TFA101 3.4 4.5 0.5 CG A:DPR5 3.5 7.9 0.5 HG2 A:DPR5 3.8 9.4 0.5 CA A:DPR5 4.6 4.8 0.5 CA A:DPR5 4.6 4.4 0.5 CD A:DPR5 4.8 3.7 0.5 CD A:DPR5 4.9 5.5 0.5 C A:DPR5 4.9 4.2 1.0

Fluorine binding site 3 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:4.0 occ:0.45 F2 A:TFA101 0.0 4.0 0.5 F1 A:TFA101 0.3 15.3 0.5 C2 A:TFA101 1.3 5.9 0.5 C2 A:TFA101 1.3 3.3 0.5 F3 A:TFA101 1.8 11.7 0.5 F1 A:TFA101 2.1 6.4 0.5 F3 A:TFA101 2.1 5.6 0.5 F2 A:TFA101 2.2 9.4 0.5 C1 A:TFA101 2.4 5.6 0.5 C1 A:TFA101 2.4 2.9 0.5 HB2 A:DPR5 2.6 8.6 0.5 OXT A:TFA101 2.6 3.9 0.5 HB2 A:DPR5 2.7 8.0 0.5 O A:TFA101 2.8 6.5 0.5 HG3 A:DPR5 2.9 9.4 0.5 HG2 A:DPR5 2.9 5.2 0.5 HG3 A:DPR5 3.1 5.2 0.5 CB A:DPR5 3.2 7.2 0.5 CB A:DPR5 3.2 6.7 0.5 CG A:DPR5 3.2 4.3 0.5 HB3 A:DPR5 3.3 8.6 0.5 OXT A:TFA101 3.4 4.3 0.5 HB3 A:DPR5 3.4 8.0 0.5 CG A:DPR5 3.5 7.9 0.5 O A:TFA101 3.5 4.5 0.5 HG2 A:DPR5 3.8 9.4 0.5 CA A:DPR5 4.6 4.8 0.5 CA A:DPR5 4.7 4.4 0.5 CD A:DPR5 4.7 3.7 0.5 CD A:DPR5 4.8 5.5 0.5 HD2 A:DPR5 4.9 6.6 0.5 C A:DPR5 5.0 4.2 1.0

Fluorine binding site 4 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:9.4 occ:0.45 F2 A:TFA101 0.0 9.4 0.5 F1 A:TFA101 0.7 6.4 0.5 C2 A:TFA101 1.2 3.3 0.5 C2 A:TFA101 1.3 5.9 0.5 F3 A:TFA101 1.6 5.6 0.5 F3 A:TFA101 2.1 11.7 0.5 F1 A:TFA101 2.1 15.3 0.5 F2 A:TFA101 2.2 4.0 0.5 C1 A:TFA101 2.4 5.6 0.5 C1 A:TFA101 2.5 2.9 0.5 OXT A:TFA101 2.6 4.3 0.5 O A:TFA101 2.8 4.5 0.5 HG2 A:DPR5 2.9 5.2 0.5 HG2 A:DPR5 2.9 9.4 0.5 HG3 A:DPR5 2.9 9.4 0.5 HB3 A:DPR5 2.9 8.0 0.5 HB3 A:DPR5 3.0 8.6 0.5 CG A:DPR5 3.2 7.9 0.5 HB2 A:DPR5 3.2 8.0 0.5 HB2 A:DPR5 3.3 8.6 0.5 CB A:DPR5 3.4 7.2 0.5 CB A:DPR5 3.4 6.7 0.5 OXT A:TFA101 3.4 3.9 0.5 O A:TFA101 3.5 6.5 0.5 CG A:DPR5 3.5 4.3 0.5 HG3 A:DPR5 4.0 5.2 0.5 OXT A:TFA102 4.0 5.1 0.4 OXT A:TFA102 4.0 5.0 0.5 C1 A:TFA102 4.2 4.8 0.4 O A:TFA102 4.3 5.1 0.4 O A:TFA102 4.4 6.0 0.5 C1 A:TFA102 4.5 4.4 0.5 CD A:DPR5 4.7 5.5 0.5 HD3 A:DPR5 4.7 4.5 0.5 CD A:DPR5 4.7 3.7 0.5 CA A:DPR5 4.9 4.8 0.5 CA A:DPR5 4.9 4.4 0.5 HD3 A:DPR5 5.0 6.6 0.5

Fluorine binding site 5 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:5.6 occ:0.45 F3 A:TFA101 0.0 5.6 0.5 C2 A:TFA101 1.3 3.3 0.5 F2 A:TFA101 1.6 9.4 0.5 C2 A:TFA101 1.8 5.9 0.5 F1 A:TFA101 1.9 15.3 0.5 F2 A:TFA101 2.1 4.0 0.5 F1 A:TFA101 2.1 6.4 0.5 C1 A:TFA101 2.4 2.9 0.5 C1 A:TFA101 2.4 5.6 0.5 OXT A:TFA101 2.6 4.3 0.5 HB3 A:DPR5 2.7 8.6 0.5 O A:TFA101 2.8 4.5 0.5 HB2 A:DPR5 2.9 8.0 0.5 HB3 A:DPR5 3.0 8.0 0.5 HB2 A:DPR5 3.1 8.6 0.5 F3 A:TFA101 3.1 11.7 0.5 OXT A:TFA101 3.2 3.9 0.5 CB A:DPR5 3.3 7.2 0.5 CB A:DPR5 3.3 6.7 0.5 O A:TFA101 3.3 6.5 0.5 HG2 A:DPR5 3.6 9.4 0.5 HG2 A:DPR5 3.7 5.2 0.5 HG3 A:DPR5 3.7 9.4 0.5 CG A:DPR5 3.8 7.9 0.5 CG A:DPR5 4.0 4.3 0.5 HG3 A:DPR5 4.3 5.2 0.5 O A:TFA102 4.4 5.1 0.4 C1 A:TFA102 4.5 4.8 0.4 O A:TFA102 4.5 6.0 0.5 OXT A:TFA102 4.7 5.1 0.4 OXT A:TFA102 4.7 5.0 0.5 CA A:DPR5 4.7 4.8 0.5 CA A:DPR5 4.7 4.4 0.5 C1 A:TFA102 4.8 4.4 0.5 F1 A:TFA102 4.8 10.0 0.4 HA A:DPR5 4.8 5.3 0.5 HA A:DPR5 4.9 5.8 0.5

Fluorine binding site 6 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:11.7 occ:0.45 F3 A:TFA101 0.0 11.7 0.5 C2 A:TFA101 1.3 5.9 0.5 F1 A:TFA101 1.5 6.4 0.5 F2 A:TFA101 1.8 4.0 0.5 C2 A:TFA101 1.9 3.3 0.5 F1 A:TFA101 2.1 15.3 0.5 F2 A:TFA101 2.1 9.4 0.5 C1 A:TFA101 2.3 5.6 0.5 C1 A:TFA101 2.5 2.9 0.5 O A:TFA101 2.8 6.5 0.5 OXT A:TFA101 2.9 3.9 0.5 HG2 A:DPR5 2.9 5.2 0.5 HG3 A:DPR5 3.0 9.4 0.5 F3 A:TFA101 3.1 5.6 0.5 OXT A:TFA101 3.3 4.3 0.5 O A:TFA101 3.4 4.5 0.5 HG3 A:DPR5 3.6 5.2 0.5 CG A:DPR5 3.7 4.3 0.5 CG A:DPR5 3.8 7.9 0.5 HB2 A:DPR5 3.8 8.6 0.5 HG2 A:DPR5 3.9 9.4 0.5 HB2 A:DPR5 3.9 8.0 0.5 CB A:DPR5 4.2 6.7 0.5 HB3 A:DPR5 4.2 8.0 0.5 CB A:DPR5 4.2 7.2 0.5 HB3 A:DPR5 4.3 8.6 0.5 CD A:DPR5 4.9 3.7 0.5 HD2 A:DPR5 5.0 6.6 0.5 CD A:DPR5 5.0 5.5 0.5

Fluorine binding site 7 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F102 b:10.0 occ:0.40 F1 A:TFA102 0.0 10.0 0.4 C2 A:TFA102 1.3 5.1 0.4 F2 A:TFA102 1.7 9.6 0.5 C2 A:TFA102 2.0 5.6 0.5 F3 A:TFA102 2.1 10.5 0.4 F2 A:TFA102 2.1 7.0 0.4 F1 A:TFA102 2.2 6.1 0.5 C1 A:TFA102 2.4 4.8 0.4 C1 A:TFA102 2.4 4.4 0.5 O A:TFA102 2.4 6.0 0.5 O A:TFA102 2.7 5.1 0.4 F3 A:TFA102 3.3 6.0 0.5 HB3 A:DPR5 3.4 8.6 0.5 OXT A:TFA102 3.4 5.1 0.4 OXT A:TFA102 3.4 5.0 0.5 HA A:DPR5 3.4 5.3 0.5 HA A:DPR5 3.4 5.8 0.5 HB3 A:DPR5 3.5 8.0 0.5 CB A:DPR5 4.1 7.2 0.5 HG11 A:VAL3 4.2 10.1 0.5 CA A:DPR5 4.2 4.8 0.5 CA A:DPR5 4.2 4.4 0.5 CB A:DPR5 4.2 6.7 0.5 HG13 A:VAL3 4.3 10.1 0.5 HG2 A:DPR5 4.3 9.4 0.5 HG12 A:VAL3 4.4 10.1 0.5 H A:GLU6 4.5 5.0 1.0 CG1 A:VAL3 4.5 6.7 0.5 HB2 A:DPR5 4.6 8.0 0.5 HE3 A:LYS8 4.6 8.2 1.0 CG A:DPR5 4.8 7.9 0.5 F3 A:TFA101 4.8 5.6 0.5 HB2 A:DPR5 4.9 8.6 0.5 HB A:VAL3 5.0 5.5 0.5

Fluorine binding site 8 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F102 b:6.1 occ:0.50 F1 A:TFA102 0.0 6.1 0.5 F3 A:TFA102 0.4 10.5 0.4 C2 A:TFA102 1.3 5.1 0.4 C2 A:TFA102 1.3 5.6 0.5 F2 A:TFA102 1.9 7.0 0.4 F2 A:TFA102 2.1 9.6 0.5 F1 A:TFA102 2.2 10.0 0.4 F3 A:TFA102 2.2 6.0 0.5 HG11 A:VAL3 2.2 10.1 0.5 C1 A:TFA102 2.4 4.4 0.5 C1 A:TFA102 2.5 4.8 0.4 HG12 A:VAL3 2.6 10.1 0.5 CG1 A:VAL3 2.7 6.7 0.5 HA A:DPR5 2.7 5.3 0.5 OXT A:TFA102 2.7 5.1 0.4 OXT A:TFA102 2.7 5.0 0.5 HA A:DPR5 2.7 5.8 0.5 HG13 A:VAL3 2.8 10.1 0.5 HB A:VAL3 3.1 5.5 0.5 HB3 A:DPR5 3.2 8.0 0.5 O A:TFA102 3.3 6.0 0.5 HB3 A:DPR5 3.5 8.6 0.5 CA A:DPR5 3.5 4.8 0.5 CA A:DPR5 3.5 4.4 0.5 HG21 A:VAL3 3.5 7.9 0.5 O A:TFA102 3.5 5.1 0.4 HG2 A:DPR5 3.5 9.4 0.5 N A:DPR5 3.6 4.1 1.0 HG22 A:VAL3 3.7 7.9 0.5 O A:VAL3 3.8 4.8 1.0 CB A:DPR5 3.8 7.2 0.5 HD3 A:DPR5 3.8 6.6 0.5 CB A:DPR5 3.8 6.7 0.5 CB A:VAL3 3.9 4.5 0.5 CG2 A:VAL3 3.9 5.3 0.5 HD3 A:DPR5 3.9 4.5 0.5 CG A:DPR5 4.0 7.9 0.5 CD A:DPR5 4.0 5.5 0.5 C A:DLY4 4.1 3.8 1.0 CB A:VAL3 4.1 4.8 0.5 C A:VAL3 4.2 4.1 1.0 CD A:DPR5 4.3 3.7 0.5 O A:DLY4 4.3 3.9 1.0 HD3 A:LYS8 4.4 8.3 1.0 HB A:VAL3 4.5 5.8 0.5 HB2 A:DPR5 4.5 8.0 0.5 H A:GLU6 4.5 5.0 1.0 CA A:VAL3 4.6 4.3 0.5 CG A:DPR5 4.6 4.3 0.5 CA A:VAL3 4.7 4.2 0.5 HD2 A:LYS8 4.7 8.3 1.0 N A:DLY4 4.7 3.9 1.0 HB2 A:DPR5 4.7 8.6 0.5 C A:DPR5 4.8 4.2 1.0 HE3 A:LYS8 4.8 8.2 1.0 HA A:VAL3 4.8 5.2 0.5 HG13 A:VAL3 4.8 8.1 0.5 HG23 A:VAL3 4.8 7.9 0.5 CA A:DLY4 4.9 4.0 1.0 HG3 A:DPR5 4.9 9.4 0.5 HG2 A:DPR5 4.9 5.2 0.5 HA A:DLY4 4.9 4.8 1.0 CG1 A:VAL3 5.0 5.4 0.5 CD A:LYS8 5.0 6.9 1.0

Fluorine binding site 9 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F102 b:7.0 occ:0.40 F2 A:TFA102 0.0 7.0 0.4 F2 A:TFA102 0.7 9.6 0.5 C2 A:TFA102 0.8 5.6 0.5 C2 A:TFA102 1.3 5.1 0.4 F3 A:TFA102 1.4 6.0 0.5 F1 A:TFA102 1.9 6.1 0.5 C1 A:TFA102 2.1 4.4 0.5 F1 A:TFA102 2.1 10.0 0.4 F3 A:TFA102 2.2 10.5 0.4 C1 A:TFA102 2.3 4.8 0.4 O A:TFA102 2.6 6.0 0.5 HG12 A:VAL3 2.8 10.1 0.5 O A:TFA102 2.9 5.1 0.4 HG13 A:VAL3 3.1 10.1 0.5 OXT A:TFA102 3.1 5.0 0.5 OXT A:TFA102 3.1 5.1 0.4 CG1 A:VAL3 3.3 6.7 0.5 HG11 A:VAL3 3.3 10.1 0.5 HB A:VAL3 3.5 5.5 0.5 HG22 A:VAL3 4.2 7.9 0.5 CB A:VAL3 4.4 4.5 0.5 HA A:DPR5 4.5 5.3 0.5 HA A:DPR5 4.5 5.8 0.5 HG13 A:VAL3 4.6 8.1 0.5 HB3 A:DPR5 4.6 8.0 0.5 HG21 A:VAL3 4.7 7.9 0.5 CG2 A:VAL3 4.7 5.3 0.5 CB A:VAL3 4.7 4.8 0.5 HB3 A:DPR5 4.8 8.6 0.5 HG2 A:DPR5 4.9 9.4 0.5 CG1 A:VAL3 5.0 5.4 0.5

Fluorine binding site 10 out of 12 in the S2 Symmetric Peptide Design Number 1, Wednesday


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of S2 Symmetric Peptide Design Number 1, Wednesday within 5.0Å range: probe atom residue distance (Å) B Occ A:F102 b:9.6 occ:0.50 F2 A:TFA102 0.0 9.6 0.5 F2 A:TFA102 0.7 7.0 0.4 C2 A:TFA102 1.3 5.6 0.5 C2 A:TFA102 1.4 5.1 0.4 F1 A:TFA102 1.7 10.0 0.4 F3 A:TFA102 2.1 6.0 0.5 F1 A:TFA102 2.1 6.1 0.5 C1 A:TFA102 2.4 4.4 0.5 F3 A:TFA102 2.4 10.5 0.4 C1 A:TFA102 2.5 4.8 0.4 O A:TFA102 2.6 6.0 0.5 O A:TFA102 2.9 5.1 0.4 HG13 A:VAL3 3.4 10.1 0.5 HG12 A:VAL3 3.4 10.1 0.5 OXT A:TFA102 3.5 5.0 0.5 OXT A:TFA102 3.5 5.1 0.4 CG1 A:VAL3 3.7 6.7 0.5 HG11 A:VAL3 3.7 10.1 0.5 HB A:VAL3 4.1 5.5 0.5 HA A:DPR5 4.4 5.3 0.5 HA A:DPR5 4.5 5.8 0.5 HG22 A:VAL3 4.5 7.9 0.5 HB3 A:DPR5 4.7 8.0 0.5 HB3 A:DPR5 4.7 8.6 0.5 CB A:VAL3 4.9 4.5 0.5 HG21 A:VAL3 5.0 7.9 0.5 HG13 A:VAL3 5.0 8.1 0.5 CG2 A:VAL3 5.0 5.3 0.5

V.K.Mulligan, C.S.Kang, M.R.Sawaya, S.Rettie, X.Li, I.Antselovich, T.W.Craven, A.M.Watkins, J.W.Labonte, F.Dimaio, T.O.Yeates, D.Baker. Computational Design of Mixed Chirality Peptide Macrocycles with Internal Symmetry. Protein Sci. V. 29 2433 2020.
ISSN: ESSN 1469-896X
PubMed: 33058266
DOI: 10.1002/PRO.3974