Fluorine in PDB 8vri: E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines

Enzymatic activity of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines

All present enzymatic activity of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines:
5.2.1.8;

Protein crystallography data

The structure of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines, PDB code: 8vri was solved by R.L.Frkic, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.12 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.655, 83.442, 122.141, 90, 90, 90
R / Rfree (%) 18.3 / 22.4

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Fluorine atom in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines (pdb code 8vri). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 54 binding sites of Fluorine where determined in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines, PDB code: 8vri:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 54 in 8vri

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Fluorine binding site 1 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F28

b:20.2
occ:0.40
 F1 A:FFL28 0.0 20.2 0.4
CD1 A:FFL28 1.3 17.0 0.6
CD1 A:FFL28 1.4 17.1 0.4
F1 A:FFL28 2.1 20.7 0.6
CG A:FFL28 2.3 14.8 0.6
CG A:FFL28 2.3 14.8 0.4
O A:HOH478 2.4 25.6 1.0
CB A:FFL28 2.8 12.9 0.4
CB A:FFL28 2.9 12.5 0.6
O A:HOH437 3.1 30.3 1.0
O A:VAL24 3.1 9.3 1.0
CG1 A:VAL24 3.2 13.8 1.0
C A:VAL24 3.7 12.2 1.0
CD2 A:FFL28 3.7 17.4 0.6
CD2 A:FFL28 3.7 17.4 0.4
F2 A:FFL28 4.0 22.2 0.6
F2 A:FFL28 4.0 21.2 0.4
CA A:LYS25 4.0 14.0 0.6
CA A:LYS25 4.0 14.0 0.5
N A:LYS25 4.1 12.7 0.6
N A:LYS25 4.1 12.7 0.5
CA A:FFL28 4.2 13.0 0.4
CA A:FFL28 4.2 12.2 0.6
N A:FFL28 4.4 12.0 0.6
N A:FFL28 4.4 11.4 0.4
O A:HOH409 4.4 29.3 1.0
CB A:VAL24 4.4 15.2 1.0
CA A:VAL24 4.6 11.5 1.0
NH2 A:ARG32 4.6 21.7 1.0
O A:LYS25 4.7 12.3 0.5
O A:LYS25 4.8 12.2 0.6
NH1 A:ARG32 4.8 19.2 1.0
C A:LYS25 4.8 13.7 0.6
C A:LYS25 4.8 13.8 0.5
OD2 A:ASP17 4.8 22.8 1.0
O A:HOH384 4.9 32.0 1.0

Fluorine binding site 2 out of 54 in 8vri

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Fluorine binding site 2 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F28

b:20.7
occ:0.60
 F1 A:FFL28 0.0 20.7 0.6
CD1 A:FFL28 1.4 17.0 0.6
CD1 A:FFL28 1.5 17.1 0.4
F1 A:FFL28 2.1 20.2 0.4
CG A:FFL28 2.4 14.8 0.6
CG A:FFL28 2.4 14.8 0.4
F2 A:FFL28 2.5 21.2 0.4
CB A:FFL28 2.8 12.9 0.4
CB A:FFL28 2.8 12.5 0.6
CD2 A:FFL28 3.0 17.4 0.4
CD2 A:FFL28 3.1 17.4 0.6
O A:HOH437 3.2 30.3 1.0
NH1 A:ARG32 3.3 19.2 1.0
F2 A:FFL28 3.4 22.2 0.6
O A:HOH465 3.6 30.7 1.0
O A:HOH409 3.7 29.3 1.0
O A:HOH478 4.0 25.6 1.0
NH2 A:ARG32 4.1 21.7 1.0
CZ A:ARG32 4.2 22.7 1.0
CA A:FFL28 4.2 13.0 0.4
CA A:FFL28 4.2 12.2 0.6
OE1 A:GLU164 4.5 38.6 1.0
O A:VAL24 4.8 9.3 1.0
CG1 A:VAL162 4.9 16.7 1.0
CG1 A:VAL24 4.9 13.8 1.0

Fluorine binding site 3 out of 54 in 8vri

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Fluorine binding site 3 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F28

b:21.2
occ:0.40
 F2 A:FFL28 0.0 21.2 0.4
CD2 A:FFL28 1.4 17.4 0.4
CD2 A:FFL28 1.5 17.4 0.6
F2 A:FFL28 2.0 22.2 0.6
CG A:FFL28 2.3 14.8 0.4
CG A:FFL28 2.3 14.8 0.6
F1 A:FFL28 2.5 20.7 0.6
CD1 A:FFL28 2.7 17.0 0.6
CD1 A:FFL28 2.7 17.1 0.4
CB A:FFL28 3.0 12.9 0.4
CB A:FFL28 3.0 12.5 0.6
CG2 A:VAL2 3.5 18.8 1.0
CG1 A:VAL162 3.5 16.7 1.0
O A:HOH465 3.5 30.7 1.0
CA A:FFL28 3.7 13.0 0.4
CA A:FFL28 3.7 12.2 0.6
O A:HOH409 3.7 29.3 1.0
CG2 A:VAL162 3.9 18.9 1.0
F1 A:FFL28 4.0 20.2 0.4
NH1 A:ARG32 4.2 19.2 1.0
CB A:VAL162 4.3 14.3 1.0
C A:FFL28 4.7 13.7 0.4
C A:FFL28 4.7 13.5 0.6
N A:FFL28 4.7 11.4 0.4
N A:FFL28 4.7 12.0 0.6
O A:FFL28 4.7 13.1 0.4
O A:FFL28 4.8 13.4 0.6
O A:FME1 4.9 16.4 1.0
CB A:VAL2 5.0 21.7 1.0
CZ A:ARG32 5.0 22.7 1.0

Fluorine binding site 4 out of 54 in 8vri

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Fluorine binding site 4 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F28

b:22.2
occ:0.60
 F2 A:FFL28 0.0 22.2 0.6
CD2 A:FFL28 1.3 17.4 0.4
CD2 A:FFL28 1.4 17.4 0.6
F2 A:FFL28 2.0 21.2 0.4
CG A:FFL28 2.3 14.8 0.4
CG A:FFL28 2.3 14.8 0.6
CD1 A:FFL28 2.7 17.1 0.4
CD1 A:FFL28 2.8 17.0 0.6
CG2 A:VAL2 3.1 18.8 1.0
O A:HOH409 3.1 29.3 1.0
CG2 A:THR15 3.4 16.8 1.0
F1 A:FFL28 3.4 20.7 0.6
CB A:FFL28 3.6 12.9 0.4
CB A:FFL28 3.6 12.5 0.6
CD2 A:PHE27 3.9 11.8 1.0
CE2 A:PHE27 3.9 17.6 1.0
F1 A:FFL28 4.0 20.2 0.4
O A:HOH465 4.1 30.7 1.0
CA A:FFL28 4.1 13.0 0.4
CA A:FFL28 4.2 12.2 0.6
OG1 A:THR15 4.3 12.0 1.0
CB A:VAL2 4.4 21.7 1.0
CB A:THR15 4.4 10.0 1.0
N A:FFL28 4.6 11.4 0.4
N A:FFL28 4.6 12.0 0.6
CG1 A:VAL24 4.7 13.8 1.0
O A:VAL24 4.8 9.3 1.0
O A:FME1 4.9 16.4 1.0

Fluorine binding site 5 out of 54 in 8vri

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Fluorine binding site 5 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F76

b:26.8
occ:1.00
 F1 A:FFL76 0.0 26.8 1.0
CD1 A:FFL76 1.4 20.5 1.0
CG A:FFL76 2.3 20.1 1.0
CD2 A:FFL76 2.8 27.2 1.0
CB A:LYS19 3.0 13.8 1.0
CG A:LYS19 3.1 15.5 1.0
F2 A:FFL76 3.2 27.3 1.0
CD2 A:PHE16 3.4 13.2 1.0
CG1 C:VAL127 3.4 16.8 1.0
CB A:FFL76 3.6 13.8 1.0
CB A:PHE16 3.8 11.1 1.0
CG A:PHE16 3.8 10.7 1.0
CE A:LYS19 3.9 27.7 1.0
CE2 A:PHE16 4.1 15.0 1.0
CB C:VAL127 4.1 13.8 1.0
CD A:LYS19 4.1 23.6 1.0
ND2 A:ASN74 4.4 12.9 1.0
CA A:LYS19 4.5 14.2 1.0
O A:VAL122 4.7 10.2 1.0
CG A:ASN74 4.7 17.1 1.0
CA C:VAL127 4.8 11.9 1.0
CA A:FFL76 4.8 14.0 1.0
CD1 A:PHE16 4.9 12.7 1.0
C A:LYS19 5.0 14.2 1.0

Fluorine binding site 6 out of 54 in 8vri

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Fluorine binding site 6 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F76

b:27.3
occ:1.00
 F2 A:FFL76 0.0 27.3 1.0
CD2 A:FFL76 1.4 27.2 1.0
CG A:FFL76 2.4 20.1 1.0
CB A:FFL76 2.9 13.8 1.0
CD1 A:FFL76 3.0 20.5 1.0
F1 A:FFL76 3.2 26.8 1.0
CA A:FFL76 3.4 14.0 1.0
CD C:LYS14 3.4 20.6 1.0
O A:HOH429 3.4 20.3 1.0
O A:HOH393 3.7 28.9 1.0
CE C:LYS14 4.1 29.0 1.0
CG1 C:VAL127 4.2 16.8 1.0
N A:FFL76 4.2 14.8 1.0
OE1 C:GLU125 4.2 28.4 1.0
CG C:LYS14 4.4 16.1 1.0
C A:FFL76 4.5 13.3 1.0
CB C:LYS14 4.6 15.2 1.0
N A:LYS77 4.6 13.1 1.0
CE1 C:PHE16 4.6 23.4 1.0
O A:GLY75 4.8 21.8 1.0
C A:GLY75 4.8 20.9 1.0
O C:HOH319 4.9 36.1 1.0
CE2 A:PHE16 4.9 15.0 1.0
CD C:GLU125 4.9 23.7 1.0

Fluorine binding site 7 out of 54 in 8vri

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Fluorine binding site 7 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F83

b:17.1
occ:1.00
 F1 A:FFL83 0.0 17.1 1.0
CD1 A:FFL83 1.4 10.7 1.0
CG A:FFL83 2.4 10.5 1.0
CB A:FFL83 2.9 7.8 1.0
CD2 A:FFL83 3.0 14.2 1.0
N A:GLU125 3.2 10.4 1.0
CA A:GLU125 3.2 9.4 1.0
C A:ALA124 3.2 10.7 1.0
C A:GLU125 3.3 10.4 1.0
N A:FFL83 3.3 8.9 1.0
N A:VAL126 3.4 9.1 1.0
O A:ALA124 3.4 10.3 1.0
F2 A:FFL83 3.5 20.4 1.0
CG2 A:ILE13 3.5 12.8 1.0
CB A:ALA124 3.6 9.8 1.0
CA A:FFL83 3.6 9.4 1.0
CB A:ILE13 3.8 13.4 1.0
O A:GLU125 3.9 9.8 1.0
O A:GLY81 3.9 11.4 1.0
CA A:ALA124 4.0 9.7 1.0
C A:THR82 4.1 12.6 1.0
CG2 A:VAL126 4.2 9.3 1.0
CD1 A:ILE13 4.3 16.9 1.0
CA A:VAL126 4.4 8.7 1.0
CA A:THR82 4.6 8.4 1.0
CG1 A:ILE13 4.6 17.5 1.0
CB A:GLU125 4.7 12.9 1.0
O A:THR82 4.7 9.0 1.0
N A:ALA124 4.8 10.0 1.0
C A:FFL83 4.9 10.1 1.0
CA A:ILE13 4.9 8.7 1.0
CB A:VAL126 5.0 11.3 1.0
C A:GLY81 5.0 11.5 1.0

Fluorine binding site 8 out of 54 in 8vri

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Fluorine binding site 8 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F83

b:20.4
occ:1.00
 F2 A:FFL83 0.0 20.4 1.0
CD2 A:FFL83 1.4 14.2 1.0
CG A:FFL83 2.3 10.5 1.0
CD1 A:FFL83 2.7 10.7 1.0
CE2 A:PHE4 3.1 20.6 1.0
F1 A:FFL83 3.5 17.1 1.0
CZ A:PHE4 3.5 18.6 1.0
CG2 A:ILE13 3.6 12.8 1.0
CB A:FFL83 3.7 7.8 1.0
CE2 A:PHE98 3.7 16.8 1.0
CD1 A:ILE13 3.8 16.9 1.0
CD2 A:PHE98 3.9 12.8 1.0
CG1 A:ILE100 4.1 9.3 1.0
CD2 A:PHE4 4.2 24.7 1.0
CD1 A:ILE100 4.2 11.8 1.0
CB A:ILE13 4.5 13.4 1.0
CG1 A:ILE13 4.6 17.5 1.0
CZ A:PHE98 4.6 18.9 1.0
CG A:PHE98 4.8 10.7 1.0
CE1 A:PHE4 4.8 21.3 1.0
CA A:FFL83 4.9 9.4 1.0

Fluorine binding site 9 out of 54 in 8vri

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Fluorine binding site 9 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F108

b:19.9
occ:1.00
 F1 A:FFL108 0.0 19.9 1.0
CD1 A:FFL108 1.4 15.0 1.0
CG A:FFL108 2.3 13.1 1.0
CD2 A:FFL108 2.7 14.1 1.0
CE1 A:PHE48 3.1 13.1 1.0
OD1 A:ASN101 3.3 11.3 1.0
CB A:ASN105 3.4 11.1 1.0
ND2 A:ASN105 3.5 11.1 1.0
CG A:ASN105 3.6 13.8 1.0
CE2 A:PHE99 3.6 11.2 1.0
CB A:FFL108 3.6 10.5 1.0
F2 A:FFL108 3.9 23.5 1.0
CZ A:PHE48 3.9 13.5 1.0
CD1 A:PHE48 4.0 12.9 1.0
CZ A:PHE99 4.1 11.0 1.0
CE2 A:PHE107 4.2 15.1 1.0
C5 A:PGE202 4.2 23.6 1.0
CZ A:PHE107 4.3 15.4 1.0
OD1 A:ASN105 4.5 13.3 1.0
CG A:ASN101 4.5 11.6 1.0
CD2 A:PHE99 4.5 9.6 1.0
O A:ASN105 4.7 13.4 1.0
CG A:MET49 4.8 10.7 1.0
CA A:ASN105 4.8 13.2 1.0
CA A:FFL108 4.9 12.1 1.0
OD1 A:ASN78 5.0 10.9 1.0
CD2 A:PHE107 5.0 17.4 1.0

Fluorine binding site 10 out of 54 in 8vri

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Fluorine binding site 10 out of 54 in the E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of E. Coli Peptidyl-Prolyl Cis-Trans Isomerase Containing Difluoro- Leucines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F108

b:23.5
occ:1.00
 F2 A:FFL108 0.0 23.5 1.0
CD2 A:FFL108 1.4 14.1 1.0
CG A:FFL108 2.3 13.1 1.0
CA A:FFL108 3.0 12.1 1.0
CB A:FFL108 3.0 10.5 1.0
CD2 A:PHE107 3.3 17.4 1.0
N A:FFL108 3.5 13.3 1.0
CE2 A:PHE107 3.5 15.1 1.0
CD1 A:FFL108 3.6 15.0 1.0
CE1 A:TYR120 3.7 11.8 1.0
O A:PHE107 3.7 15.7 1.0
C3 A:PGE202 3.8 35.9 1.0
C A:PHE107 3.8 18.5 1.0
CD1 A:TYR120 3.8 12.0 1.0
F1 A:FFL108 3.9 19.9 1.0
C4 A:PGE202 4.2 27.5 1.0
O A:HOH445 4.2 23.4 1.0
C A:FFL108 4.3 13.3 1.0
CG A:PHE107 4.4 17.6 1.0
CZ A:TYR120 4.6 14.3 1.0
O A:HOH432 4.6 31.9 1.0
CZ A:PHE107 4.7 15.4 1.0
O A:FFL108 4.7 13.0 1.0
CG A:TYR120 4.7 9.8 1.0
CB A:PHE107 5.0 16.4 1.0
CA A:PHE107 5.0 14.7 1.0
C5 A:PGE202 5.0 23.6 1.0

Reference:

R.L.Frkic, Y.J.Tan, E.H.Abdelkader, A.Maleckis, E.Tarcoveanu, C.Nitsche, G.Otting, C.J.Jackson. Conformational Preferences of the Non-Canonical Amino Acids (2S,4S)-5-Fluoroleucine, (2S,4R)-5-Fluoroleucine, and 5,5'-Difluoroleucine in A Protein Biochemistry 2024.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.4C00081
Page generated: Sat Aug 3 01:32:50 2024

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