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Fluorine in PDB 3odv: X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography

Protein crystallography data

The structure of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography, PDB code: 3odv was solved by B.L.Pentelute, K.Mandal, Z.P.Gates, M.R.Sawaya, T.O.Yeates, S.B.H.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.13 / 0.95
Space group P -1
Cell size a, b, c (Å), α, β, γ (°) 25.150, 30.511, 41.097, 109.39, 97.39, 97.09
R / Rfree (%) 18.8 / 20.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography (pdb code 3odv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography, PDB code: 3odv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 1 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F39

b:18.4
occ:0.50
 F1 A:TFA39 0.0 18.4 0.5
C2 A:TFA39 1.3 14.2 0.5
F2 A:TFA39 2.2 17.5 0.5
F3 A:TFA39 2.2 17.5 0.5
C1 A:TFA39 2.3 14.6 0.5
O A:TFA39 2.6 16.7 0.5
O A:HOH55 2.8 26.2 1.0
OXT A:TFA39 3.4 10.7 0.5
CB A:LYS27 3.4 8.3 0.5
O A:HOH60 3.5 47.0 1.0
CG A:LYS27 3.6 12.1 0.5
C A:GLY26 3.7 8.7 1.0
N A:LYS27 3.8 8.3 0.5
N A:LYS27 3.8 9.0 0.5
CA A:GLY26 3.8 8.7 1.0
CD A:LYS27 3.9 16.6 0.5
CB A:LYS27 4.1 10.0 0.5
O A:GLY26 4.1 10.3 1.0
O A:HIS34 4.2 8.6 1.0
CA A:LYS27 4.2 8.6 0.5
OG1 A:THR36 4.3 14.4 1.0
CD A:LYS27 4.4 12.0 0.5
CG A:LYS27 4.5 9.3 0.5
CA A:LYS27 4.5 9.4 0.5
N A:GLY26 4.6 8.1 1.0
CE A:LYS27 4.8 19.1 0.5
C A:HIS34 4.8 6.5 1.0
CB A:HIS34 4.9 7.2 1.0

Fluorine binding site 2 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 2 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F39

b:17.5
occ:0.50
 F2 A:TFA39 0.0 17.5 0.5
C2 A:TFA39 1.3 14.2 0.5
F1 A:TFA39 2.2 18.4 0.5
F3 A:TFA39 2.2 17.5 0.5
C1 A:TFA39 2.2 14.6 0.5
O A:TFA39 2.8 16.7 0.5
OXT A:TFA39 3.0 10.7 0.5
CB A:HIS34 3.3 7.2 1.0
CE A:MET29 3.4 12.6 0.5
CG A:LYS27 3.6 12.1 0.5
CB A:LYS27 3.6 8.3 0.5
CD A:LYS27 4.0 16.6 0.5
O A:HIS34 4.0 8.6 1.0
CE A:MET29 4.1 15.6 0.5
CG A:HIS34 4.2 7.8 1.0
C A:HIS34 4.2 6.5 1.0
CE A:LYS27 4.2 19.1 0.5
N A:GLY1 4.3 9.1 1.0
CA A:HIS34 4.4 6.7 1.0
N A:LYS27 4.4 8.3 0.5
N A:LYS27 4.4 9.0 0.5
CD A:LYS27 4.5 12.0 0.5
CA A:GLY1 4.6 9.4 1.0
CA A:LYS27 4.6 8.6 0.5
CB A:LYS27 4.6 10.0 0.5
O A:LYS27 4.6 11.0 0.5
CG A:LYS27 4.6 9.3 0.5
SD A:MET29 4.8 12.0 0.5
O A:HOH55 4.8 26.2 1.0
O A:LYS27 4.8 10.1 0.5
N A:CYS35 4.8 6.5 1.0
C A:GLY26 4.9 8.7 1.0
CD2 A:HIS34 4.9 9.7 1.0
CA A:LYS27 4.9 9.4 0.5
ND1 A:HIS34 5.0 9.2 1.0
O A:HOH60 5.0 47.0 1.0

Fluorine binding site 3 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 3 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F39

b:17.5
occ:0.50
 F3 A:TFA39 0.0 17.5 0.5
C2 A:TFA39 1.3 14.2 0.5
F1 A:TFA39 2.2 18.4 0.5
F2 A:TFA39 2.2 17.5 0.5
C1 A:TFA39 2.4 14.6 0.5
OXT A:TFA39 2.6 10.7 0.5
CA A:GLY1 3.2 9.4 1.0
N A:GLY1 3.4 9.1 1.0
O A:TFA39 3.5 16.7 0.5
O A:HOH55 3.6 26.2 1.0
OG1 A:THR36 3.6 14.4 1.0
C A:CYS35 3.8 6.6 1.0
O A:HIS34 3.8 8.6 1.0
N A:THR36 3.9 7.0 1.0
C A:HIS34 3.9 6.5 1.0
N A:CYS35 4.0 6.5 1.0
O A:CYS35 4.1 7.2 1.0
CB A:HIS34 4.1 7.2 1.0
CA A:CYS35 4.1 6.8 1.0
CA A:THR36 4.3 7.7 1.0
O A:HOH60 4.3 47.0 1.0
CA A:GLY26 4.4 8.7 1.0
C A:GLY1 4.5 8.6 1.0
CB A:THR36 4.6 9.6 1.0
CA A:HIS34 4.7 6.7 1.0
N A:LYS27 4.9 8.3 0.5
N A:LYS27 4.9 9.0 0.5
C A:GLY26 4.9 8.7 1.0
N A:VAL2 5.0 8.3 1.0

Fluorine binding site 4 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 4 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F39

b:19.3
occ:0.50
 F1 B:TFA39 0.0 19.3 0.5
C2 B:TFA39 1.3 15.6 0.5
F3 B:TFA39 2.1 18.4 0.5
F2 B:TFA39 2.2 18.0 0.5
C1 B:TFA39 2.3 15.4 0.5
O B:TFA39 2.8 17.6 0.5
OXT B:TFA39 3.3 13.8 0.5
CB B:HIS34 3.3 8.4 1.0
CE B:MET29 3.4 15.0 0.5
CD B:LYS27 3.8 19.8 0.7
CB B:LYS27 3.8 12.0 0.7
SD B:MET29 3.9 22.1 0.5
CB B:LYS27 4.0 11.4 0.3
O B:HIS34 4.0 9.3 1.0
CE B:LYS27 4.1 21.1 0.7
CD B:LYS27 4.1 13.0 0.3
NZ B:LYS27 4.1 23.4 0.7
CG B:HIS34 4.2 8.4 1.0
CG B:LYS27 4.3 15.9 0.7
CG B:LYS27 4.4 12.2 0.3
C B:HIS34 4.4 7.9 1.0
O B:HOH54 4.5 16.2 1.0
CA B:HIS34 4.5 7.8 1.0
N B:GLY1 4.5 12.7 1.0
SD B:MET29 4.7 12.6 0.5
CA B:GLY1 4.8 12.5 1.0
CG B:MET29 4.8 16.2 0.5
ND1 B:HIS34 4.9 10.6 1.0
CA B:LYS27 5.0 10.4 0.7
O B:LYS27 5.0 10.4 0.3
O B:LYS27 5.0 10.4 0.7

Fluorine binding site 5 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 5 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F39

b:18.0
occ:0.50
 F2 B:TFA39 0.0 18.0 0.5
C2 B:TFA39 1.3 15.6 0.5
F1 B:TFA39 2.2 19.3 0.5
F3 B:TFA39 2.2 18.4 0.5
C1 B:TFA39 2.4 15.4 0.5
OXT B:TFA39 2.6 13.8 0.5
CA B:GLY1 3.2 12.5 1.0
N B:GLY1 3.3 12.7 1.0
O B:HOH54 3.4 16.2 1.0
O B:TFA39 3.5 17.6 0.5
O B:HIS34 3.7 9.3 1.0
OG1 B:THR36 3.9 12.6 0.5
C B:HIS34 4.0 7.9 1.0
CB B:HIS34 4.0 8.4 1.0
O B:CYS35 4.0 11.1 1.0
OG1 B:THR36 4.1 13.8 0.5
C B:CYS35 4.1 9.5 1.0
O B:HOH60 4.2 21.2 1.0
N B:THR36 4.3 11.1 0.5
C B:GLY1 4.3 12.4 1.0
N B:CYS35 4.4 7.9 1.0
N B:THR36 4.5 9.4 0.5
CA B:HIS34 4.6 7.8 1.0
CA B:CYS35 4.7 8.4 1.0
CA B:THR36 4.7 9.4 0.5
CA B:THR36 4.8 11.6 0.5
N B:VAL2 4.8 12.0 1.0
O B:HOH80 4.9 32.8 1.0
CB B:LYS27 4.9 12.0 0.7
CB B:THR36 4.9 9.5 0.5
O B:HOH79 5.0 26.0 1.0

Fluorine binding site 6 out of 6 in 3odv

Go back to Fluorine Binding Sites List in 3odv
Fluorine binding site 6 out of 6 in the X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F39

b:18.4
occ:0.50
 F3 B:TFA39 0.0 18.4 0.5
C2 B:TFA39 1.3 15.6 0.5
F1 B:TFA39 2.1 19.3 0.5
F2 B:TFA39 2.2 18.0 0.5
C1 B:TFA39 2.3 15.4 0.5
O B:TFA39 2.8 17.6 0.5
O B:HOH54 3.1 16.2 1.0
O B:HOH79 3.3 26.0 1.0
OXT B:TFA39 3.3 13.8 0.5
CE B:LYS27 3.3 21.1 0.7
NZ B:LYS27 3.4 23.4 0.7
CB B:LYS27 3.6 12.0 0.7
CB B:LYS27 3.7 11.4 0.3
CD B:LYS27 3.8 19.8 0.7
CD B:LYS27 4.0 13.0 0.3
O B:HOH80 4.1 32.8 1.0
O B:HOH60 4.2 21.2 1.0
OG1 B:THR36 4.2 13.8 0.5
O B:HIS34 4.2 9.3 1.0
CG B:LYS27 4.3 15.9 0.7
OG1 B:THR36 4.3 12.6 0.5
CG B:LYS27 4.5 12.2 0.3
N B:LYS27 4.7 9.7 0.3
N B:LYS27 4.8 10.0 0.7
CA B:LYS27 4.8 10.4 0.7
CA B:LYS27 4.9 10.2 0.3
CB B:HIS34 5.0 8.4 1.0

Reference:

B.L.Pentelute, K.Mandal, Z.P.Gates, M.R.Sawaya, T.O.Yeates, S.B.Kent. Total Chemical Synthesis and X-Ray Structure of Kaliotoxin By Racemic Protein Crystallography. Chem.Commun.(Camb.) V. 46 8174 2010.
ISSN: ISSN 1359-7345
PubMed: 20877851
DOI: 10.1039/C0CC03148H
Page generated: Sun Dec 13 11:52:13 2020

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