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Fluorine in PDB 8gjc: X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm

Protein crystallography data

The structure of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm, PDB code: 8gjc was solved by A.G.Kreutzer, S.M.Ruttenberg, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.01 / 1.43
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 38.164, 38.164, 32.054, 90, 90, 120
R / Rfree (%) 15.5 / 18.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm (pdb code 8gjc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm, PDB code: 8gjc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8gjc

Go back to Fluorine Binding Sites List in 8gjc
Fluorine binding site 1 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F102

b:58.0
occ:1.00
 F1 A:TFA102 0.0 58.0 1.0
C2 A:TFA102 1.4 52.8 1.0
F3 A:TFA102 2.2 40.8 1.0
F2 A:TFA102 2.2 40.9 1.0
C1 A:TFA102 2.3 51.9 1.0
OXT A:TFA102 2.8 39.2 1.0
O A:HOH201 3.1 41.2 1.0
O A:TFA102 3.4 49.9 1.0
HN2 A:IML13 4.6 17.6 1.0
HB A:IML13 5.0 16.2 1.0

Fluorine binding site 2 out of 9 in 8gjc

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Fluorine binding site 2 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F102

b:40.9
occ:1.00
 F2 A:TFA102 0.0 40.9 1.0
C2 A:TFA102 1.4 52.8 1.0
F3 A:TFA102 2.2 40.8 1.0
F1 A:TFA102 2.2 58.0 1.0
C1 A:TFA102 2.3 51.9 1.0
HN2 A:IML13 2.5 17.6 1.0
OXT A:TFA102 2.8 39.2 1.0
O A:IML13 3.0 13.9 1.0
HB A:IML13 3.2 16.2 1.0
O A:TFA102 3.3 49.9 1.0
CN A:IML13 3.5 14.5 1.0
HN1 A:IML13 3.8 17.6 1.0
HN3 A:IML13 3.9 17.6 1.0
C A:IML13 4.0 12.1 1.0
O A:HOH201 4.1 41.2 1.0
CB A:IML13 4.2 13.3 1.0
CA A:IML13 4.4 14.7 1.0
N A:IML13 4.5 15.1 1.0
HG A:LEU15 4.5 16.1 1.0
HG22 A:IML13 4.6 16.4 1.0
HD11 A:IML13 4.9 18.4 1.0
CG2 A:IML13 4.9 13.6 1.0

Fluorine binding site 3 out of 9 in 8gjc

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Fluorine binding site 3 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F102

b:40.8
occ:1.00
 F3 A:TFA102 0.0 40.8 1.0
C2 A:TFA102 1.4 52.8 1.0
F2 A:TFA102 2.2 40.9 1.0
F1 A:TFA102 2.2 58.0 1.0
C1 A:TFA102 2.4 51.9 1.0
O A:TFA102 2.7 49.9 1.0
HG A:LEU15 3.2 16.1 1.0
HD12 A:LEU15 3.3 21.6 1.0
HD11 A:LEU15 3.4 21.6 1.0
OXT A:TFA102 3.6 39.2 1.0
CD1 A:LEU15 3.7 17.8 1.0
CG A:LEU15 3.9 13.3 1.0
O A:IML13 3.9 13.9 1.0
HB A:IML13 4.3 16.2 1.0
HN2 A:IML13 4.4 17.6 1.0
HD21 A:LEU15 4.5 17.8 1.0
H A:LEU15 4.6 13.4 1.0
HD13 A:LEU15 4.6 21.6 1.0
HG22 A:IML13 4.7 16.4 1.0
HB2 A:LEU15 4.7 16.4 1.0
CD2 A:LEU15 4.8 14.7 1.0
O A:HOH201 4.9 41.2 1.0
CB A:LEU15 4.9 13.6 1.0
C A:IML13 4.9 12.1 1.0

Fluorine binding site 4 out of 9 in 8gjc

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Fluorine binding site 4 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:55.8
occ:1.00
 F1 A:TFA103 0.0 55.8 1.0
C2 A:TFA103 1.4 48.0 1.0
F2 A:TFA103 2.2 41.3 1.0
F3 A:TFA103 2.2 37.2 1.0
C1 A:TFA103 2.4 41.3 1.0
O A:TFA103 2.9 44.7 1.0
O A:HOH202 3.3 69.3 1.0
OXT A:TFA103 3.3 53.2 1.0
O A:HOH203 3.4 37.9 1.0
HG3 A:ORN1 3.8 15.4 1.0
O A:HOH215 3.9 38.9 1.0
CG A:ORN1 4.9 12.7 1.0
HB2 A:ORN1 4.9 15.7 1.0

Fluorine binding site 5 out of 9 in 8gjc

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Fluorine binding site 5 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:41.3
occ:1.00
 F2 A:TFA103 0.0 41.3 1.0
C2 A:TFA103 1.4 48.0 1.0
F1 A:TFA103 2.2 55.8 1.0
F3 A:TFA103 2.2 37.2 1.0
C1 A:TFA103 2.4 41.3 1.0
HG3 A:ORN1 2.6 15.4 1.0
O A:HOH203 2.7 37.9 1.0
O A:TFA103 2.9 44.7 1.0
O A:HOH215 3.1 38.9 1.0
OXT A:TFA103 3.3 53.2 1.0
CG A:ORN1 3.6 12.7 1.0
HD3 A:ORN1 3.8 15.6 1.0
HG2 A:ORN1 3.9 15.4 1.0
HE1 A:ORN1 4.1 15.0 1.0
CD A:ORN1 4.2 12.8 1.0
O A:HOH202 4.4 69.3 1.0
NE A:ORN1 4.6 12.3 1.0
HB2 A:ORN1 4.6 15.7 1.0
CB A:ORN1 4.7 12.9 1.0
HB3 A:ORN1 5.0 15.7 1.0

Fluorine binding site 6 out of 9 in 8gjc

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Fluorine binding site 6 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:37.2
occ:1.00
 F3 A:TFA103 0.0 37.2 1.0
C2 A:TFA103 1.4 48.0 1.0
F2 A:TFA103 2.2 41.3 1.0
F1 A:TFA103 2.2 55.8 1.0
C1 A:TFA103 2.4 41.3 1.0
OXT A:TFA103 2.6 53.2 1.0
HG3 A:ORN1 3.2 15.4 1.0
O A:TFA103 3.6 44.7 1.0
HB3 A:LEU15 3.8 16.4 1.0
O A:LEU15 3.8 11.3 1.0
HE1 A:ORN1 3.9 15.0 1.0
HB2 A:LEU15 4.0 16.4 1.0
CG A:ORN1 4.2 12.7 1.0
CB A:LEU15 4.3 13.6 1.0
HB2 A:ORN1 4.4 15.7 1.0
HB3 A:ORN1 4.5 15.7 1.0
C A:LEU15 4.5 11.3 1.0
O A:HOH203 4.5 37.9 1.0
NE A:ORN1 4.6 12.3 1.0
CB A:ORN1 4.7 12.9 1.0
CD A:ORN1 4.8 12.8 1.0
HD3 A:ORN1 4.8 15.6 1.0
HG2 A:ORN1 4.9 15.4 1.0
O A:HOH202 5.0 69.3 1.0
HD13 A:LEU15 5.0 21.6 1.0

Fluorine binding site 7 out of 9 in 8gjc

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Fluorine binding site 7 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:53.0
occ:1.00
 F1 B:TFA102 0.0 53.0 1.0
C2 B:TFA102 1.4 47.8 1.0
F3 B:TFA102 2.2 44.5 1.0
F2 B:TFA102 2.2 47.4 1.0
C1 B:TFA102 2.4 40.5 1.0
OXT B:TFA102 2.9 41.4 1.0
O B:TFA102 3.3 45.8 1.0
O B:HOH209 3.5 45.2 1.0
HA2 B:GLY10 5.0 18.1 1.0

Fluorine binding site 8 out of 9 in 8gjc

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Fluorine binding site 8 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:47.4
occ:1.00
 F2 B:TFA102 0.0 47.4 1.0
C2 B:TFA102 1.4 47.8 1.0
O B:HOH209 2.2 45.2 1.0
F3 B:TFA102 2.2 44.5 1.0
F1 B:TFA102 2.2 53.0 1.0
C1 B:TFA102 2.4 40.5 1.0
O B:TFA102 2.6 45.8 1.0
HA2 B:GLY10 3.1 18.1 1.0
OXT B:TFA102 3.5 41.4 1.0
HB2 B:GLU7 3.6 23.4 1.0
CA B:GLY10 3.9 14.9 1.0
C B:GLY10 3.9 19.9 1.0
HB3 B:GLU7 3.9 23.4 1.0
N B:ALA11 4.0 15.7 1.0
H B:ALA11 4.1 19.0 1.0
CB B:GLU7 4.2 19.4 1.0
HB2 B:ALA11 4.2 17.7 1.0
HA B:ALA11 4.3 19.9 1.0
O B:GLY10 4.4 15.2 1.0
O B:HOH208 4.4 51.4 1.0
N B:GLY10 4.5 17.9 1.0
O B:HOH202 4.6 29.2 1.0
HA3 B:GLY10 4.6 18.1 1.0
O B:HOH206 4.6 50.2 1.0
CA B:ALA11 4.6 16.4 1.0
O B:ORN9 4.7 24.6 1.0
HG2 B:GLU7 4.8 27.4 1.0
C B:ORN9 4.9 23.0 1.0
OE1 B:GLU7 4.9 34.4 1.0
H B:GLY10 4.9 21.7 1.0
CB B:ALA11 4.9 14.6 1.0

Fluorine binding site 9 out of 9 in 8gjc

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Fluorine binding site 9 out of 9 in the X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of X-Ray Crystallographic Structure of A Beta-Hairpin Peptide Derived From Abeta 17-35. (Orn)Lvffaed(Orn)Gai(N-Me-Ile)Glm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F102

b:44.5
occ:1.00
 F3 B:TFA102 0.0 44.5 1.0
C2 B:TFA102 1.4 47.8 1.0
F2 B:TFA102 2.2 47.4 1.0
F1 B:TFA102 2.2 53.0 1.0
C1 B:TFA102 2.4 40.5 1.0
OXT B:TFA102 2.9 41.4 1.0
O B:TFA102 3.4 45.8 1.0
HA2 B:GLY10 3.5 18.1 1.0
O B:HOH209 4.2 45.2 1.0
H B:ALA11 4.2 19.0 1.0
HB2 B:ALA11 4.3 17.7 1.0
CA B:GLY10 4.4 14.9 1.0
N B:ALA11 4.6 15.7 1.0
HA3 B:GLY10 4.8 18.1 1.0
C B:GLY10 4.8 19.9 1.0
O B:ORN9 4.9 24.6 1.0

Reference:

S.M.Ruttenberg, A.G.Kreutzer, N.L.Truex, J.S.Nowick. Beta-Hairpin Alignment Alters Oligomer Formation in A Beta-Derived Peptides. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38163326
DOI: 10.1021/ACS.BIOCHEM.3C00526
Page generated: Fri Aug 2 19:55:14 2024

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