Atomistry » Fluorine » PDB 3nlz-3og7 » 3odv
Atomistry »
  Fluorine »
    PDB 3nlz-3og7 »
      3odv »

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: Mon Jul 14 18:17:55 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy