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Chlorine in PDB 5vm0: The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9

Protein crystallography data

The structure of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9, PDB code: 5vm0 was solved by L.A.Wogulis, M.D.Wogulis, S.Tabares-Da Rosa, G.Gonzalez-Sapienza, D.K.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.47 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.113, 52.485, 57.463, 90.00, 113.74, 90.00
R / Rfree (%) 20.4 / 24.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 (pdb code 5vm0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9, PDB code: 5vm0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5vm0

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Chlorine binding site 1 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:37.7
occ:1.00
 CL2 A:9EG202 0.0 37.7 1.0
C13 A:9EG202 1.8 26.4 1.0
C14 A:9EG202 2.8 27.6 1.0
C12 A:9EG202 2.8 24.6 1.0
CL3 A:9EG202 3.1 30.0 1.0
N A:ALA102 3.6 15.0 1.0
CD1 A:ILE115 3.7 21.9 1.0
CB A:ALA102 3.8 17.9 1.0
CG A:PRO114 3.8 19.9 1.0
C A:ARG101 3.8 14.1 1.0
CA A:ARG101 3.9 12.7 1.0
O A:HOH382 3.9 20.0 1.0
C11 A:9EG202 4.1 21.1 1.0
C15 A:9EG202 4.1 24.8 1.0
CA A:ALA102 4.1 16.6 1.0
CG1 A:ILE115 4.1 20.2 1.0
C16 A:9EG202 4.5 22.7 1.0
N A:ARG101 4.6 12.2 1.0
O A:ARG101 4.7 15.9 1.0
O A:THR100 4.7 13.2 1.0
CD A:PRO114 4.8 18.7 1.0
C A:THR100 4.9 12.6 1.0
CB A:PRO114 5.0 21.2 1.0

Chlorine binding site 2 out of 6 in 5vm0

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Chlorine binding site 2 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:17.6
occ:1.00
 CL1 A:9EG202 0.0 17.6 1.0
C1 A:9EG202 1.8 16.9 1.0
C2 A:9EG202 2.7 16.2 1.0
C6 A:9EG202 2.7 17.1 1.0
C A:LYS79 3.5 16.6 1.0
CA A:LYS79 3.6 15.7 1.0
N A:THR80 3.7 14.6 1.0
CG A:ARG74 3.8 11.2 1.0
CG2 A:THR32 4.0 15.4 1.0
C3 A:9EG202 4.0 17.1 1.0
C5 A:9EG202 4.0 15.2 1.0
CB A:THR32 4.0 14.2 1.0
O A:LYS79 4.0 14.5 1.0
O A:THR80 4.1 13.5 1.0
CD A:ARG74 4.1 11.1 1.0
O A:ASP75 4.2 14.9 1.0
O A:THR32 4.3 11.2 1.0
C A:THR80 4.3 13.3 1.0
CA A:THR32 4.4 13.8 1.0
CA A:SER76 4.4 15.0 1.0
CG2 A:VAL81 4.5 12.7 1.0
CA A:THR80 4.5 13.5 1.0
C4 A:9EG202 4.5 17.1 1.0
N A:LYS79 4.5 15.6 1.0
CB A:LYS79 4.6 18.4 1.0
C A:ASP75 4.7 13.7 1.0
N A:SER76 4.8 14.3 1.0
C A:THR32 4.9 13.0 1.0
O A:SER76 4.9 14.8 1.0
N A:VAL81 4.9 11.2 1.0
OG A:SER76 5.0 16.4 1.0

Chlorine binding site 3 out of 6 in 5vm0

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Chlorine binding site 3 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:30.0
occ:1.00
 CL3 A:9EG202 0.0 30.0 1.0
C14 A:9EG202 1.8 27.6 1.0
C15 A:9EG202 2.8 24.8 1.0
C13 A:9EG202 2.8 26.4 1.0
CL2 A:9EG202 3.1 37.7 1.0
CG A:GLU3 3.5 39.0 1.0
CB A:GLU3 3.7 35.0 1.0
O A:HOH401 3.8 18.9 1.0
O A:HOH330 4.0 22.7 1.0
C16 A:9EG202 4.0 22.7 1.0
CB A:ALA102 4.1 17.9 1.0
C12 A:9EG202 4.1 24.6 1.0
C11 A:9EG202 4.6 21.1 1.0
CD A:GLU3 4.8 45.5 1.0
O A:HOH353 4.8 17.5 1.0

Chlorine binding site 4 out of 6 in 5vm0

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Chlorine binding site 4 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:22.3
occ:1.00
 CL2 B:9EG203 0.0 22.3 1.0
C13 B:9EG203 1.8 19.1 1.0
C12 B:9EG203 2.8 18.7 1.0
C14 B:9EG203 2.8 21.3 1.0
CL3 B:9EG203 3.2 25.1 1.0
N B:ALA102 3.5 11.5 1.0
CD1 B:ILE115 3.7 18.2 1.0
CA B:ARG101 3.9 10.3 1.0
C B:ARG101 3.9 12.4 1.0
CB B:ALA102 3.9 11.5 1.0
CG B:PRO114 4.0 18.4 1.0
CG1 B:ILE115 4.0 16.4 1.0
C11 B:9EG203 4.1 16.9 1.0
C15 B:9EG203 4.1 20.2 1.0
CA B:ALA102 4.2 12.1 1.0
O B:THR100 4.5 10.1 1.0
N B:ARG101 4.5 9.8 1.0
C16 B:9EG203 4.6 17.0 1.0
O B:ARG101 4.7 12.0 1.0
CD B:PRO114 4.7 15.1 1.0
C B:THR100 4.8 10.0 1.0
CB B:ILE115 5.0 16.7 1.0
CB B:PRO114 5.0 15.5 1.0

Chlorine binding site 5 out of 6 in 5vm0

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Chlorine binding site 5 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:16.7
occ:1.00
 CL1 B:9EG203 0.0 16.7 1.0
C1 B:9EG203 1.8 15.0 1.0
C6 B:9EG203 2.8 14.8 1.0
C2 B:9EG203 2.8 14.4 1.0
N B:THR80 3.5 16.0 1.0
C B:LYS79 3.5 18.0 1.0
CG2 B:THR32 3.6 14.0 1.0
CA B:LYS79 3.8 17.3 1.0
O B:THR80 3.8 14.6 1.0
CB B:THR32 3.9 14.4 1.0
C B:THR80 3.9 15.0 1.0
CG2 B:VAL81 4.0 13.8 1.0
O B:LYS79 4.0 16.8 1.0
C3 B:9EG203 4.1 14.9 1.0
C5 B:9EG203 4.1 15.0 1.0
O B:ASP75 4.1 14.7 1.0
CB B:ARG74 4.2 12.6 1.0
CA B:THR80 4.2 15.1 1.0
CD B:ARG74 4.4 12.4 1.0
N B:VAL81 4.4 13.2 1.0
CA B:THR32 4.5 12.8 1.0
C B:ASP75 4.6 14.3 1.0
C4 B:9EG203 4.6 14.9 1.0
CA B:SER76 4.6 14.3 1.0
CG B:ARG74 4.7 12.6 1.0
O B:THR32 4.7 11.2 1.0
N B:LYS79 4.7 16.0 1.0
CB B:LYS79 4.7 19.1 1.0
N B:ASP75 4.8 13.2 1.0
CE B:MET36 4.8 17.6 1.0
N B:SER76 4.8 13.1 1.0

Chlorine binding site 6 out of 6 in 5vm0

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Chlorine binding site 6 out of 6 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:25.1
occ:1.00
 CL3 B:9EG203 0.0 25.1 1.0
C14 B:9EG203 1.8 21.3 1.0
C15 B:9EG203 2.7 20.2 1.0
C13 B:9EG203 2.8 19.1 1.0
CL2 B:9EG203 3.2 22.3 1.0
OE1 B:GLU3 3.4 21.6 1.0
C16 B:9EG203 4.0 17.0 1.0
C12 B:9EG203 4.1 18.7 1.0
CD B:GLU3 4.1 23.8 1.0
CB B:ALA102 4.4 11.5 1.0
CB B:GLU3 4.4 23.8 1.0
CG B:GLU3 4.5 24.9 1.0
C11 B:9EG203 4.6 16.9 1.0
CD1 B:ILE115 4.9 18.2 1.0
OE2 B:GLU3 5.0 27.4 1.0

Reference:

S.Tabares-Da Rosa, L.A.Wogulis, M.D.Wogulis, G.Gonzalez-Sapienza, D.K.Wilson. Structure and Specificity of Several Triclocarban-Binding Single Domain Camelid Antibody Fragments. J. Mol. Recognit. V. 32 E2755 2019.
ISSN: ISSN 1099-1352
PubMed: 30033524
DOI: 10.1002/JMR.2755
Page generated: Sat Jul 12 09:55:01 2025

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