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Chlorine in PDB 4lfs: High Resolution X-Ray Structure of Racemic Shk Toxin

Protein crystallography data

The structure of High Resolution X-Ray Structure of Racemic Shk Toxin, PDB code: 4lfs was solved by B.Dang, T.Kubota, K.Mandal, F.Bezanilla, S.B.H.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.83 / 0.97
Space group P 1 21/C 1
Cell size a, b, c (Å), α, β, γ (°) 30.912, 51.653, 21.065, 90.00, 104.51, 90.00
R / Rfree (%) 14.4 / 15.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the High Resolution X-Ray Structure of Racemic Shk Toxin (pdb code 4lfs). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the High Resolution X-Ray Structure of Racemic Shk Toxin, PDB code: 4lfs:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4lfs

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Chlorine binding site 1 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:6.3
occ:0.50
 CL A:CL101 0.0 6.3 0.5
CL A:CL101 0.5 6.1 0.5
HH21 A:ARG1 2.4 10.1 0.5
HE A:ARG1 2.5 12.5 0.5
HH11 A:ARG1 2.7 18.1 0.5
HG2 A:ARG1 3.0 4.2 0.5
HD2 A:ARG1 3.1 9.3 0.5
O A:HOH245 3.2 6.7 0.6
HG3 A:ARG1 3.2 13.4 0.5
NH2 A:ARG1 3.2 8.7 0.5
NE A:ARG1 3.3 7.1 0.5
NH1 A:ARG1 3.4 9.4 0.5
CG A:ARG1 3.4 6.7 0.5
HB2 A:ARG1 3.5 12.9 0.5
HH22 A:ARG1 3.5 3.6 0.5
CD A:ARG1 3.7 7.0 0.5
O A:HOH260 3.8 16.3 0.7
CZ A:ARG1 3.9 8.3 0.5
HH12 A:ARG1 4.1 15.7 0.5
H1 A:ARG1 4.2 10.6 0.5
CZ A:ARG1 4.3 8.6 0.5
H32 A:GOL104 4.4 11.0 0.5
HD2 A:ARG1 4.4 6.8 0.5
NE A:ARG1 4.5 7.5 0.5
CD A:ARG1 4.5 6.7 0.5
CB A:ARG1 4.5 6.7 0.5
HD3 A:ARG1 4.5 7.1 0.5
H1 A:ARG1 4.6 6.7 0.5
O A:HOH240 4.7 4.0 0.8
O1 A:GOL104 4.8 6.4 0.5
HB3 A:ARG1 4.9 2.1 0.5
CB A:ARG1 4.9 6.7 0.5
HO2 A:GOL104 4.9 13.2 0.5
CG A:ARG1 5.0 6.6 0.5

Chlorine binding site 2 out of 8 in 4lfs

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Chlorine binding site 2 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:6.1
occ:0.50
 CL A:CL101 0.0 6.1 0.5
CL A:CL101 0.5 6.3 0.5
HE A:ARG1 2.4 12.5 0.5
HH21 A:ARG1 2.5 10.1 0.5
HD2 A:ARG1 2.8 9.3 0.5
HG3 A:ARG1 2.8 13.4 0.5
HG2 A:ARG1 2.9 4.2 0.5
HH11 A:ARG1 2.9 18.1 0.5
O A:HOH245 3.1 6.7 0.6
CG A:ARG1 3.1 6.7 0.5
NE A:ARG1 3.2 7.1 0.5
HB2 A:ARG1 3.2 12.9 0.5
NH2 A:ARG1 3.3 8.7 0.5
CD A:ARG1 3.4 7.0 0.5
NH1 A:ARG1 3.6 9.4 0.5
HH22 A:ARG1 3.8 3.6 0.5
O A:HOH260 3.8 16.3 0.7
CZ A:ARG1 3.9 8.3 0.5
H1 A:ARG1 4.0 10.6 0.5
H32 A:GOL104 4.0 11.0 0.5
HD2 A:ARG1 4.1 6.8 0.5
HD3 A:ARG1 4.1 7.1 0.5
CB A:ARG1 4.2 6.7 0.5
CD A:ARG1 4.2 6.7 0.5
CZ A:ARG1 4.3 8.6 0.5
NE A:ARG1 4.3 7.5 0.5
HH12 A:ARG1 4.4 15.7 0.5
H1 A:ARG1 4.4 6.7 0.5
O1 A:GOL104 4.5 6.4 0.5
HB3 A:ARG1 4.5 2.1 0.5
CB A:ARG1 4.6 6.7 0.5
O A:HOH240 4.6 4.0 0.8
HO2 A:GOL104 4.7 13.2 0.5
HO1 A:GOL104 4.7 25.6 0.5
CG A:ARG1 4.8 6.6 0.5
N A:ARG1 4.8 6.7 0.5
H3 A:ARG1 5.0 11.1 0.5
HG3 A:ARG1 5.0 5.3 0.5

Chlorine binding site 3 out of 8 in 4lfs

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Chlorine binding site 3 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:6.8
occ:0.50
 CL A:CL102 0.0 6.8 0.5
CL A:CL102 0.4 6.0 0.5
HB2 A:CYS3 2.8 4.2 1.0
HB2 A:CYS35 3.1 6.5 1.0
O A:HOH241 3.1 7.6 1.0
O A:HOH242 3.1 7.4 1.0
CB A:CYS3 3.7 5.1 1.0
CB A:CYS35 3.9 5.2 1.0
HB3 A:CYS35 3.9 6.1 1.0
H A:CYS3 4.1 9.1 1.0
HB3 A:CYS3 4.1 6.3 1.0
O A:ARG1 4.1 6.6 0.5
O A:ARG1 4.1 6.3 0.5
N A:CYS3 4.3 4.8 1.0
HO3 A:GOL104 4.4 14.2 0.5
CA A:CYS3 4.5 4.9 1.0
HA A:CYS3 4.6 4.6 1.0
HH21 A:ARG29 4.6 20.6 1.0
SG A:CYS3 4.7 5.3 1.0
SG A:CYS35 4.7 5.8 1.0
HA A:SER2 4.9 4.2 1.0
OXT A:CYS35 4.9 5.3 1.0
O3 A:GOL104 5.0 6.4 0.5
HA A:CYS35 5.0 5.8 1.0

Chlorine binding site 4 out of 8 in 4lfs

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Chlorine binding site 4 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:6.0
occ:0.50
 CL A:CL102 0.0 6.0 0.5
CL A:CL102 0.4 6.8 0.5
HB2 A:CYS3 2.7 4.2 1.0
HB2 A:CYS35 2.8 6.5 1.0
O A:HOH241 3.2 7.6 1.0
O A:HOH242 3.4 7.4 1.0
CB A:CYS35 3.7 5.2 1.0
CB A:CYS3 3.7 5.1 1.0
HB3 A:CYS35 3.8 6.1 1.0
HB3 A:CYS3 4.0 6.3 1.0
H A:CYS3 4.2 9.1 1.0
O A:ARG1 4.4 6.6 0.5
O A:ARG1 4.4 6.3 0.5
SG A:CYS3 4.5 5.3 1.0
N A:CYS3 4.5 4.8 1.0
OXT A:CYS35 4.5 5.3 1.0
CA A:CYS3 4.6 4.9 1.0
SG A:CYS35 4.6 5.8 1.0
HO3 A:GOL104 4.7 14.2 0.5
HA A:CYS3 4.7 4.6 1.0
HA A:CYS35 4.7 5.8 1.0
HH21 A:ARG29 4.8 20.6 1.0
CA A:CYS35 4.8 4.9 1.0

Chlorine binding site 5 out of 8 in 4lfs

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Chlorine binding site 5 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:6.7
occ:0.50
 CL A:CL103 0.0 6.7 0.5
CL A:CL103 0.4 9.1 0.5
HG1 A:THR13 2.3 12.6 1.0
HD1 A:PHE15 2.8 15.9 1.0
HG2 A:GLN16 3.1 6.1 1.0
OG1 A:THR13 3.1 5.2 1.0
HG21 A:THR13 3.2 8.0 1.0
HB3 A:PHE15 3.2 3.4 1.0
O A:HOH253 3.5 15.7 0.7
CD1 A:PHE15 3.7 8.1 1.0
CG2 A:THR13 3.9 6.2 1.0
CB A:THR13 3.9 5.1 1.0
CG A:GLN16 4.0 5.3 1.0
HG3 A:GLN16 4.0 6.5 1.0
HB A:THR13 4.0 5.8 1.0
HG23 A:THR13 4.1 10.8 1.0
CB A:PHE15 4.1 5.5 1.0
H A:GLN16 4.3 4.5 1.0
HE21 A:GLN16 4.3 6.7 1.0
CG A:PHE15 4.3 5.8 1.0
O A:HOH239 4.4 6.1 1.0
HB2 A:PHE15 4.5 6.9 1.0
CD A:GLN16 4.5 5.3 1.0
HE1 A:PHE15 4.6 27.7 1.0
NE2 A:GLN16 4.6 5.9 1.0
CE1 A:PHE15 4.6 9.3 1.0
HG22 A:THR13 4.8 6.8 1.0
N A:GLN16 4.8 4.3 1.0
H A:PHE15 4.9 6.6 1.0

Chlorine binding site 6 out of 8 in 4lfs

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Chlorine binding site 6 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:9.1
occ:0.50
 CL A:CL103 0.0 9.1 0.5
CL A:CL103 0.4 6.7 0.5
HG1 A:THR13 2.2 12.6 1.0
HG21 A:THR13 3.0 8.0 1.0
OG1 A:THR13 3.1 5.2 1.0
HD1 A:PHE15 3.1 15.9 1.0
HG2 A:GLN16 3.2 6.1 1.0
O A:HOH253 3.2 15.7 0.7
HB3 A:PHE15 3.5 3.4 1.0
CG2 A:THR13 3.6 6.2 1.0
HG23 A:THR13 3.8 10.8 1.0
CB A:THR13 3.8 5.1 1.0
HG3 A:GLN16 3.9 6.5 1.0
CG A:GLN16 3.9 5.3 1.0
HB A:THR13 4.0 5.8 1.0
CD1 A:PHE15 4.0 8.1 1.0
O A:HOH239 4.1 6.1 1.0
HE21 A:GLN16 4.2 6.7 1.0
H A:GLN16 4.4 4.5 1.0
CB A:PHE15 4.4 5.5 1.0
HG22 A:THR13 4.5 6.8 1.0
NE2 A:GLN16 4.5 5.9 1.0
CD A:GLN16 4.6 5.3 1.0
CG A:PHE15 4.7 5.8 1.0
HB2 A:PHE15 4.8 6.9 1.0
HE1 A:PHE15 4.9 27.7 1.0
H A:THR13 4.9 4.5 1.0
N A:GLN16 4.9 4.3 1.0
CE1 A:PHE15 4.9 9.3 1.0
O A:HOH226 5.0 13.7 0.6

Chlorine binding site 7 out of 8 in 4lfs

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Chlorine binding site 7 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl105

b:8.5
occ:0.50
 CL A:CL105 0.0 8.5 0.5
CL A:CL105 0.3 8.6 0.5
O A:HOH206 3.0 7.4 0.9
HE3 A:LYS22 3.1 24.6 1.0
O A:HOH216 3.2 10.4 0.7
O A:HOH213 3.4 7.9 0.6
HB2 A:LYS22 3.4 6.4 1.0
CE A:LYS22 4.1 11.9 1.0
HZ2 A:LYS22 4.3 27.5 1.0
CB A:LYS22 4.4 5.7 1.0
HZ3 A:LYS22 4.4 18.1 1.0
H A:LYS22 4.5 5.8 1.0
NZ A:LYS22 4.5 13.6 1.0
HE2 A:LYS22 4.6 22.4 1.0
O A:HOH205 4.6 7.4 1.0
HB3 A:LYS22 4.6 3.4 1.0
HB3 A:MET21 4.7 4.2 0.1
HB3 A:MET21 4.8 5.8 0.9
HD2 A:LYS22 4.9 11.6 1.0
CD A:LYS22 4.9 8.6 1.0

Chlorine binding site 8 out of 8 in 4lfs

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Chlorine binding site 8 out of 8 in the High Resolution X-Ray Structure of Racemic Shk Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of High Resolution X-Ray Structure of Racemic Shk Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl105

b:8.6
occ:0.50
 CL A:CL105 0.0 8.6 0.5
CL A:CL105 0.3 8.5 0.5
HE3 A:LYS22 3.0 24.6 1.0
O A:HOH216 3.1 10.4 0.7
O A:HOH213 3.1 7.9 0.6
O A:HOH206 3.3 7.4 0.9
HB2 A:LYS22 3.4 6.4 1.0
CE A:LYS22 3.9 11.9 1.0
HZ2 A:LYS22 4.1 27.5 1.0
HZ3 A:LYS22 4.2 18.1 1.0
NZ A:LYS22 4.3 13.6 1.0
CB A:LYS22 4.4 5.7 1.0
HE2 A:LYS22 4.4 22.4 1.0
H A:LYS22 4.6 5.8 1.0
HB3 A:LYS22 4.7 3.4 1.0
O A:HOH205 4.7 7.4 1.0
HD2 A:LYS22 4.8 11.6 1.0
CD A:LYS22 4.8 8.6 1.0
HB3 A:MET21 4.9 4.2 0.1

Reference:

B.Dang, T.Kubota, K.Mandal, F.Bezanilla, S.B.Kent. Native Chemical Ligation at Asx-Cys, Glx-Cys: Chemical Synthesis and High-Resolution X-Ray Structure of Shk Toxin By Racemic Protein Crystallography. J.Am.Chem.Soc. V. 135 11911 2013.
ISSN: ISSN 0002-7863
PubMed: 23919482
DOI: 10.1021/JA4046795
Page generated: Sun Jul 21 18:53:28 2024

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