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Chlorine in PDB 6hto: Tryptophan Lyase 'Empty State'

Protein crystallography data

The structure of Tryptophan Lyase 'Empty State', PDB code: 6hto was solved by P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.43 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.970, 92.610, 94.460, 90.00, 98.73, 90.00
R / Rfree (%) 16.8 / 19.2

Other elements in 6hto:

The structure of Tryptophan Lyase 'Empty State' also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine atom in the Tryptophan Lyase 'Empty State' (pdb code 6hto). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Tryptophan Lyase 'Empty State', PDB code: 6hto:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 6hto

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Chlorine binding site 1 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:18.8
occ:1.00
 O A:HOH814 3.1 20.3 1.0
O A:HOH1151 3.2 31.5 1.0
OG A:SER281 3.3 12.2 1.0
O A:HOH849 3.4 33.1 1.0
O A:HOH652 3.4 27.1 1.0
CB A:SER281 3.4 10.6 1.0
CG2 A:THR321 3.6 11.5 1.0
CZ A:PHE202 3.7 10.0 1.0
CE2 A:PHE202 3.8 11.5 1.0
CG1 A:VAL319 4.0 11.0 1.0
NH1 A:ARG323 4.1 14.3 1.0
CB A:VAL319 4.2 9.7 1.0
CD A:PRO283 4.3 9.9 1.0
CG A:PRO283 4.5 14.7 1.0
CA A:SER281 4.5 9.3 1.0
CB A:PRO283 4.5 13.8 1.0
O A:VAL319 4.7 15.4 1.0
CZ A:ARG323 4.8 15.1 1.0
O A:HOH756 4.8 21.6 1.0
CE1 A:PHE202 4.8 9.1 1.0
CD2 A:PHE202 5.0 12.8 1.0
CB A:THR321 5.0 11.2 1.0

Chlorine binding site 2 out of 13 in 6hto

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Chlorine binding site 2 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:25.1
occ:0.48
 CL A:CL506 0.0 25.1 0.5
CL A:CL506 1.8 30.2 0.5
O A:HOH756 2.9 21.6 1.0
O A:HOH779 2.9 24.9 1.0
O A:HOH809 3.2 33.3 1.0
NH1 A:ARG323 3.2 14.3 1.0
O A:HOH849 3.7 33.1 1.0
CG A:PRO88 3.9 13.5 1.0
CB A:THR321 4.0 11.2 1.0
O A:HOH1164 4.0 30.8 1.0
CZ A:ARG323 4.0 15.1 1.0
CG2 A:THR321 4.1 11.5 1.0
NH2 A:ARG323 4.2 12.3 1.0
OG1 A:THR321 4.3 11.4 1.0
CB A:PRO88 4.4 10.8 1.0
O A:SER340 4.6 13.6 1.0
O A:HOH1151 4.7 31.5 1.0
CD A:PRO88 4.7 10.9 1.0
CZ A:PHE364 4.7 13.7 1.0
OG A:SER340 4.8 12.2 1.0

Chlorine binding site 3 out of 13 in 6hto

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Chlorine binding site 3 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:30.2
occ:0.52
 CL A:CL506 0.0 30.2 0.5
CL A:CL506 1.8 25.1 0.5
O A:HOH809 2.6 33.3 1.0
O A:SER340 3.1 13.6 1.0
O A:HOH756 3.4 21.6 1.0
CG A:PRO88 3.5 13.5 1.0
CB A:THR321 3.6 11.2 1.0
OG1 A:THR322 3.7 16.3 1.0
N A:GLY342 3.9 13.4 1.0
CD A:PRO88 4.0 10.9 1.0
CG2 A:THR321 4.1 11.5 1.0
C A:SER340 4.1 12.2 1.0
O A:GLY342 4.1 16.9 1.0
OG A:SER340 4.1 12.2 1.0
N A:THR322 4.2 12.1 1.0
OG1 A:THR321 4.3 11.4 1.0
C A:PRO341 4.4 13.4 1.0
NH1 A:ARG323 4.4 14.3 1.0
C A:GLY342 4.4 12.0 1.0
CA A:THR321 4.5 11.4 1.0
CA A:GLY342 4.5 13.8 1.0
CB A:PRO88 4.6 10.8 1.0
O A:HOH779 4.6 24.9 1.0
CA A:PRO341 4.6 12.6 1.0
CB A:SER340 4.7 13.2 1.0
N A:PRO341 4.8 11.5 1.0
C A:THR321 4.9 10.3 1.0
CB A:THR322 4.9 15.3 1.0
O A:PRO341 4.9 14.9 1.0

Chlorine binding site 4 out of 13 in 6hto

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Chlorine binding site 4 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:15.5
occ:1.00
 OE1 A:GLU98 2.5 26.5 0.4
NZ A:LYS100 2.7 22.6 0.3
NH2 A:ARG105 3.4 19.5 1.0
CD A:GLU98 3.4 33.1 0.4
CG A:GLU98 3.5 25.7 0.6
N A:GLY107 3.5 16.0 1.0
CB A:GLU98 3.6 18.3 0.6
CG A:ARG105 3.6 15.6 1.0
O A:HOH700 3.6 31.7 1.0
CD A:ARG105 3.7 14.6 1.0
CA A:GLY107 3.7 18.1 1.0
CB A:GLU98 3.7 13.9 0.4
CB A:ARG105 3.8 12.2 1.0
CE A:LYS100 3.9 13.9 0.3
CA A:GLU98 4.0 13.3 0.6
CA A:GLU98 4.0 12.9 0.4
CD A:LYS100 4.1 14.8 0.3
O A:GLU98 4.1 15.2 1.0
CG A:GLU98 4.2 13.1 0.4
OE2 A:GLU98 4.2 18.2 0.4
C A:GLU98 4.3 11.6 1.0
C A:GLY107 4.4 18.1 1.0
CZ A:ARG105 4.4 18.7 1.0
CD A:LYS100 4.4 28.1 0.7
NE A:ARG105 4.5 14.8 1.0
CE A:LYS100 4.6 21.3 0.7
N A:LYS106 4.6 13.4 1.0
C A:ARG105 4.7 14.2 1.0
N A:ASN108 4.7 16.4 1.0
C A:LYS106 4.8 16.2 1.0
CA A:ARG105 4.8 11.2 1.0
CD A:GLU98 4.9 28.3 0.6
O A:HOH626 5.0 49.8 1.0
NZ A:LYS100 5.0 21.8 0.7
O A:HOH1059 5.0 43.3 1.0

Chlorine binding site 5 out of 13 in 6hto

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Chlorine binding site 5 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:28.5
occ:1.00
 NH1 A:ARG292 3.3 20.8 1.0
O A:HOH700 3.5 31.7 1.0
O A:HOH1059 3.5 43.3 1.0
NH2 A:ARG292 3.6 21.5 1.0
CZ A:ARG292 3.9 20.6 1.0
O A:HOH1007 4.4 43.3 1.0
O A:HOH800 4.6 20.8 1.0

Chlorine binding site 6 out of 13 in 6hto

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Chlorine binding site 6 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:29.0
occ:1.00
 O A:HOH1071 2.9 39.2 1.0
NZ A:LYS290 3.0 38.7 1.0
O A:HOH1119 3.3 42.4 1.0
C A:ARG286 3.5 15.7 1.0
N A:PRO287 3.7 13.8 1.0
O A:HOH927 3.7 32.0 1.0
O A:ARG286 3.8 15.4 1.0
CA A:ARG286 3.8 15.6 1.0
O A:MET285 3.9 14.3 1.0
C A:MET285 4.0 10.8 1.0
N A:ARG286 4.1 14.0 1.0
CA A:PRO287 4.1 16.4 1.0
CD A:PRO287 4.1 15.2 1.0
CG A:MET285 4.2 12.9 0.5
CE A:LYS290 4.2 31.9 1.0
CG A:PRO287 4.3 14.7 1.0
CB A:MET285 4.4 15.1 0.5
CB A:MET285 4.4 15.4 0.5
O A:HOH1017 4.7 23.5 1.0
O A:HOH797 4.7 21.5 1.0
CB A:PRO287 4.8 15.7 1.0
CA A:MET285 4.9 13.3 0.5
CA A:MET285 4.9 13.4 0.5
CE A:MET285 5.0 11.5 0.5
OG1 A:THR294 5.0 22.7 1.0

Chlorine binding site 7 out of 13 in 6hto

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Chlorine binding site 7 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:29.5
occ:1.00
 O A:HOH801 3.3 18.0 1.0
O A:HOH614 3.3 31.8 1.0
O A:HOH909 3.4 32.4 1.0
N A:SER219 3.5 24.3 1.0
O A:VAL222 3.7 14.1 1.0
CA A:THR218 3.7 21.4 1.0
CB A:THR218 3.8 21.6 1.0
CB A:ASP226 4.0 12.9 1.0
CG2 A:THR218 4.0 22.6 1.0
C A:THR218 4.2 29.9 1.0
N A:ASP226 4.3 13.6 1.0
CA A:SER219 4.5 23.7 1.0
O A:HOH645 4.5 32.5 1.0
C A:VAL222 4.6 15.1 1.0
O A:HOH980 4.6 49.8 1.0
CA A:ASP226 4.6 14.8 1.0
O A:PRO223 4.6 13.0 1.0
CB A:ALA225 4.7 14.1 1.0
C A:ALA225 4.8 14.5 1.0
CA A:PRO223 4.8 12.0 1.0
CG A:ASP226 4.9 17.8 1.0
N A:VAL222 4.9 15.4 1.0
OD2 A:ASP226 4.9 20.5 1.0
N A:THR218 4.9 21.5 1.0
O A:LYS217 4.9 21.8 1.0
N A:VAL220 5.0 25.6 1.0
C A:PRO223 5.0 11.1 1.0

Chlorine binding site 8 out of 13 in 6hto

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Chlorine binding site 8 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:21.3
occ:1.00
 O A:HOH716 2.6 14.8 1.0
O A:HOH814 2.8 20.3 1.0
OG1 A:THR321 2.9 11.4 1.0
N A:THR321 3.2 10.2 1.0
CB A:THR321 3.6 11.2 1.0
O A:HOH709 3.7 35.0 1.0
CG2 A:THR321 3.7 11.5 1.0
CA A:THR321 3.8 11.4 1.0
O A:THR321 4.0 10.9 1.0
CA A:PRO283 4.0 12.5 1.0
C A:LEU320 4.1 14.2 1.0
CA A:LEU320 4.1 12.5 1.0
OH A:TYR302 4.1 15.5 1.0
O A:VAL319 4.2 15.4 1.0
CB A:ARG323 4.2 12.6 1.0
C A:THR321 4.2 10.3 1.0
CG A:GLU324 4.3 14.4 1.0
CD A:ARG323 4.4 11.4 1.0
CD1 A:LEU320 4.4 21.2 1.0
CB A:PRO283 4.6 13.8 1.0
NH1 A:ARG323 4.7 14.3 1.0
N A:PRO283 4.8 9.4 1.0
CG A:ARG323 4.8 11.2 1.0
N A:ARG284 4.8 12.8 1.0
OE2 A:GLU324 4.9 19.1 1.0
O A:VAL282 4.9 13.3 1.0
C A:VAL319 5.0 10.1 1.0
O A:HOH621 5.0 26.0 1.0
N A:GLU324 5.0 11.9 1.0
N A:ARG323 5.0 13.4 1.0
C A:PRO283 5.0 13.8 1.0

Chlorine binding site 9 out of 13 in 6hto

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Chlorine binding site 9 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl512

b:24.1
occ:1.00
 O A:HOH638 3.2 20.5 1.0
N A:ARG82 3.4 14.8 1.0
CG A:ARG82 3.5 21.2 1.0
CD A:ARG80 3.8 28.0 1.0
CD A:ARG82 3.9 20.1 1.0
CB A:ARG82 3.9 21.6 1.0
O A:HOH1096 4.0 35.4 1.0
CA A:PRO81 4.1 16.3 1.0
CG A:PRO385 4.2 19.8 1.0
C A:PRO81 4.2 18.0 1.0
NE A:ARG80 4.2 33.1 1.0
CA A:ARG82 4.3 13.9 1.0
O A:HOH1029 4.3 28.3 1.0
CB A:PRO385 4.4 17.9 1.0
CD A:PRO385 4.4 20.2 1.0
CB A:PRO81 4.6 20.8 1.0
CZ A:ARG80 4.9 27.7 1.0
O A:PRO385 4.9 17.8 1.0

Chlorine binding site 10 out of 13 in 6hto

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Chlorine binding site 10 out of 13 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Tryptophan Lyase 'Empty State' within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:19.8
occ:1.00
 O B:HOH1116 2.9 43.4 1.0
O B:HOH700 3.0 20.2 1.0
OG B:SER281 3.2 13.3 1.0
CB B:SER281 3.4 14.3 1.0
CG2 B:THR321 3.6 17.0 1.0
O B:HOH929 3.6 36.7 1.0
O B:HOH673 3.8 26.3 1.0
CZ B:PHE202 3.8 13.6 1.0
CE2 B:PHE202 3.9 14.2 1.0
CG1 B:VAL319 4.0 13.8 1.0
NH1 B:ARG323 4.1 16.4 1.0
CD B:PRO283 4.2 14.2 1.0
CB B:VAL319 4.3 12.5 1.0
CA B:SER281 4.4 12.5 1.0
CB B:PRO283 4.5 12.7 1.0
CG B:PRO283 4.5 16.1 1.0
O B:VAL319 4.6 16.9 1.0
CZ B:ARG323 4.8 15.1 1.0
O B:HOH746 4.9 24.7 1.0
CB B:THR321 4.9 12.9 1.0
CE1 B:PHE202 5.0 14.3 1.0
N B:PRO283 5.0 11.5 1.0

Reference:

P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet. Radical S-Adenosyl-L-Methionine Tryptophan Lyase (Nosl): How the Protein Controls the Carboxyl Radical •CO2-Migration. J.Am.Chem.Soc. V. 140 16661 2018.
ISSN: ESSN 1520-5126
PubMed: 30418774
DOI: 10.1021/JACS.8B09142
Page generated: Sun Jul 28 01:10:03 2024

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