Chlorine in PDB 5vl2: The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4

Protein crystallography data

The structure of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4, PDB code: 5vl2 was solved by 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) 96.12 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.803, 55.304, 103.426, 90.00, 111.66, 90.00
R / Rfree (%) 21.9 / 26.3

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Chlorine atom in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4 (pdb code 5vl2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 24 binding sites of Chlorine where determined in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4, PDB code: 5vl2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 24 in 5vl2

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Chlorine binding site 1 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:37.9
occ:1.00
 CL2 A:9EG201 0.0 37.9 1.0
C13 A:9EG201 1.8 26.0 1.0
C14 A:9EG201 2.7 27.8 1.0
C12 A:9EG201 2.7 22.6 1.0
CL3 A:9EG201 3.1 37.7 1.0
N A:ALA102 3.3 19.4 1.0
O A:HOH328 3.6 19.1 1.0
C A:ARG101 3.7 18.4 1.0
CB A:ALA102 3.7 19.9 1.0
CD1 A:ILE115 3.8 23.6 1.0
CA A:ARG101 3.8 17.9 1.0
CA A:ALA102 3.9 19.4 1.0
C15 A:9EG201 4.0 24.3 1.0
CG A:PRO114 4.0 15.9 1.0
C11 A:9EG201 4.0 20.8 1.0
N A:ARG101 4.5 16.8 1.0
O A:ARG101 4.5 15.7 1.0
C16 A:9EG201 4.5 21.9 1.0
CG1 A:ILE115 4.6 21.5 1.0
O A:THR100 4.6 16.0 1.0
CD A:PRO114 4.8 15.4 1.0
C A:THR100 4.9 15.7 1.0

Chlorine binding site 2 out of 24 in 5vl2

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Chlorine binding site 2 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:23.7
occ:1.00
 CL1 A:9EG201 0.0 23.7 1.0
C1 A:9EG201 1.8 21.1 1.0
C6 A:9EG201 2.8 20.0 1.0
C2 A:9EG201 2.8 20.3 1.0
C A:ALA79 3.5 18.0 1.0
N A:THR80 3.5 16.4 1.0
CA A:ALA79 3.7 19.9 1.0
CG2 A:VAL81 3.8 15.7 1.0
O A:THR80 3.8 15.4 1.0
CG2 A:THR32 3.9 17.9 1.0
C A:THR80 3.9 15.2 1.0
O A:ALA79 4.0 16.2 1.0
CB A:THR32 4.0 18.6 1.0
C5 A:9EG201 4.0 19.6 1.0
C3 A:9EG201 4.1 19.8 1.0
O A:ASP75 4.2 19.9 1.0
CB A:ARG74 4.2 17.5 1.0
CD A:ARG74 4.2 17.8 1.0
CA A:THR80 4.2 15.3 1.0
N A:VAL81 4.4 15.1 1.0
CA A:THR32 4.4 18.5 1.0
CG A:ARG74 4.6 16.4 1.0
C4 A:9EG201 4.6 19.5 1.0
N A:ALA79 4.6 21.4 1.0
C A:ASP75 4.7 19.2 1.0
OD1 A:ASP76 4.7 24.0 1.0
CB A:ALA79 4.7 20.0 1.0
CA A:ASP76 4.8 19.8 1.0
O A:THR32 4.9 19.3 1.0
CB A:VAL81 5.0 15.7 1.0
CA A:VAL81 5.0 15.5 1.0

Chlorine binding site 3 out of 24 in 5vl2

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Chlorine binding site 3 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:37.7
occ:1.00
 CL3 A:9EG201 0.0 37.7 1.0
C14 A:9EG201 1.8 27.8 1.0
C13 A:9EG201 2.7 26.0 1.0
C15 A:9EG201 2.8 24.3 1.0
CL2 A:9EG201 3.1 37.9 1.0
NE2 A:GLN3 3.2 36.5 1.0
CG A:GLN3 3.3 31.6 1.0
CB A:GLN3 3.4 28.0 1.0
CD A:GLN3 3.5 34.0 1.0
C12 A:9EG201 4.0 22.6 1.0
C16 A:9EG201 4.1 21.9 1.0
OE1 A:GLN3 4.4 45.3 1.0
C11 A:9EG201 4.6 20.8 1.0
CB A:ALA102 4.6 19.9 1.0
CD1 A:ILE115 4.8 23.6 1.0
CA A:GLN3 4.9 26.9 1.0

Chlorine binding site 4 out of 24 in 5vl2

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Chlorine binding site 4 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:47.8
occ:1.00
 CL2 B:9EG201 0.0 47.8 1.0
C13 B:9EG201 1.8 32.6 1.0
C12 B:9EG201 2.7 29.0 1.0
C14 B:9EG201 2.7 32.9 1.0
CL3 B:9EG201 3.1 42.7 1.0
N B:ALA102 3.2 22.7 1.0
O B:HOH318 3.3 22.7 1.0
C B:ARG101 3.5 21.1 1.0
CA B:ARG101 3.6 21.4 1.0
CD1 B:ILE115 3.8 21.1 1.0
CB B:ALA102 3.8 22.3 1.0
CA B:ALA102 4.0 20.9 1.0
CG B:PRO114 4.0 23.8 1.0
C11 B:9EG201 4.0 26.1 1.0
C15 B:9EG201 4.1 28.2 1.0
O B:ARG101 4.3 18.1 1.0
N B:ARG101 4.3 19.4 1.0
C16 B:9EG201 4.6 26.5 1.0
CG1 B:ILE115 4.6 20.4 1.0
O B:THR100 4.6 18.1 1.0
CD B:PRO114 4.7 23.1 1.0
C B:THR100 4.7 19.4 1.0
CB B:ARG101 4.8 22.1 1.0

Chlorine binding site 5 out of 24 in 5vl2

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Chlorine binding site 5 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:24.2
occ:1.00
 CL1 B:9EG201 0.0 24.2 1.0
C1 B:9EG201 1.8 22.4 1.0
C6 B:9EG201 2.8 22.6 1.0
C2 B:9EG201 2.8 20.5 1.0
N B:THR80 3.7 16.8 1.0
C B:ALA79 3.7 17.1 1.0
O B:THR80 3.8 14.4 1.0
CG2 B:VAL81 3.8 16.3 1.0
CA B:ALA79 3.8 17.7 1.0
CG2 B:THR32 3.9 24.0 1.0
CB B:ARG74 3.9 15.8 1.0
CB B:THR32 4.0 23.4 1.0
C B:THR80 4.0 16.5 1.0
CD B:ARG74 4.0 17.5 1.0
O B:ASP75 4.1 17.4 1.0
C5 B:9EG201 4.1 22.7 1.0
C3 B:9EG201 4.1 21.0 1.0
O B:ALA79 4.2 16.6 1.0
CG B:ARG74 4.3 17.2 1.0
CA B:THR80 4.4 15.6 1.0
CA B:THR32 4.4 20.6 1.0
OD1 B:ASP76 4.6 23.1 1.0
N B:VAL81 4.6 16.7 1.0
C B:ASP75 4.6 18.1 1.0
C4 B:9EG201 4.7 22.2 1.0
O B:THR32 4.7 24.5 1.0
CB B:ALA79 4.8 18.5 1.0
CA B:ASP76 4.8 18.5 1.0
N B:ALA79 4.8 19.7 1.0
N B:ASP75 4.8 17.6 1.0
NE B:ARG74 4.9 17.3 1.0
CA B:ARG74 5.0 16.6 1.0
N B:ASP76 5.0 17.2 1.0

Chlorine binding site 6 out of 24 in 5vl2

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Chlorine binding site 6 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


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 T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:42.7
occ:1.00
 CL3 B:9EG201 0.0 42.7 1.0
C14 B:9EG201 1.8 32.9 1.0
C13 B:9EG201 2.8 32.6 1.0
C15 B:9EG201 2.9 28.2 1.0
CL2 B:9EG201 3.1 47.8 1.0
CD B:GLN3 3.4 32.2 1.0
OE1 B:GLN3 3.5 34.0 1.0
NE2 B:GLN3 3.6 31.4 1.0
CB B:GLN3 3.7 25.8 1.0
CG B:GLN3 3.9 28.3 1.0
C12 B:9EG201 4.1 29.0 1.0
C16 B:9EG201 4.2 26.5 1.0
CB B:ALA102 4.4 22.3 1.0
C11 B:9EG201 4.6 26.1 1.0
CD1 B:ILE115 4.8 21.1 1.0

Chlorine binding site 7 out of 24 in 5vl2

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Chlorine binding site 7 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:40.7
occ:1.00
 CL2 C:9EG201 0.0 40.7 1.0
C13 C:9EG201 1.8 29.5 1.0
C12 C:9EG201 2.7 25.3 1.0
C14 C:9EG201 2.7 32.7 1.0
CL3 C:9EG201 3.1 39.5 1.0
CD1 C:ILE115 3.6 27.2 1.0
N C:ALA102 3.6 21.6 1.0
C C:ARG101 3.8 22.7 1.0
CA C:ARG101 3.9 20.6 1.0
CG C:PRO114 3.9 20.2 1.0
C11 C:9EG201 4.0 24.2 1.0
C15 C:9EG201 4.0 26.9 1.0
CB C:ALA102 4.1 24.8 1.0
O C:HOH330 4.2 25.2 1.0
CA C:ALA102 4.2 24.1 1.0
CG1 C:ILE115 4.4 25.7 1.0
N C:ARG101 4.5 18.7 1.0
C16 C:9EG201 4.5 26.1 1.0
O C:ARG101 4.6 20.4 1.0
O C:THR100 4.8 16.0 1.0
CD C:PRO114 4.8 20.8 1.0
C C:THR100 4.9 17.7 1.0

Chlorine binding site 8 out of 24 in 5vl2

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Chlorine binding site 8 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:22.6
occ:1.00
 CL1 C:9EG201 0.0 22.6 1.0
C1 C:9EG201 1.8 19.7 1.0
C2 C:9EG201 2.7 20.4 1.0
C6 C:9EG201 2.8 18.2 1.0
C C:ALA79 3.5 18.1 1.0
N C:THR80 3.6 17.2 1.0
CA C:ALA79 3.7 19.2 1.0
CG2 C:THR32 3.7 24.8 1.0
CG2 C:VAL81 3.8 16.7 1.0
CB C:THR32 3.9 22.8 1.0
O C:ALA79 3.9 16.4 1.0
O C:THR80 4.0 16.1 1.0
CB C:ARG74 4.0 18.8 1.0
C C:THR80 4.0 17.2 1.0
C3 C:9EG201 4.1 19.8 1.0
C5 C:9EG201 4.1 18.7 1.0
CD C:ARG74 4.2 19.1 1.0
CA C:THR80 4.3 17.1 1.0
O C:ASP75 4.3 18.1 1.0
CA C:THR32 4.4 21.6 1.0
CG C:ARG74 4.5 19.4 1.0
N C:VAL81 4.5 16.8 1.0
C4 C:9EG201 4.6 19.2 1.0
CB C:ALA79 4.6 19.8 1.0
OD1 C:ASP76 4.6 23.0 1.0
O C:THR32 4.7 21.9 1.0
CA C:ASP76 4.7 19.9 1.0
C C:ASP75 4.7 18.4 1.0
N C:ALA79 4.7 21.4 1.0
N C:ASP75 4.9 17.3 1.0
N C:ASP76 5.0 19.5 1.0
CB C:VAL81 5.0 16.9 1.0

Chlorine binding site 9 out of 24 in 5vl2

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Chlorine binding site 9 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:39.5
occ:1.00
 CL3 C:9EG201 0.0 39.5 1.0
C14 C:9EG201 1.8 32.7 1.0
C13 C:9EG201 2.8 29.5 1.0
C15 C:9EG201 2.8 26.9 1.0
CL2 C:9EG201 3.1 40.7 1.0
NE2 C:GLN3 3.3 36.2 1.0
CD C:GLN3 3.6 32.2 1.0
CB C:GLN3 3.9 24.6 1.0
C16 C:9EG201 4.1 26.1 1.0
C12 C:9EG201 4.1 25.3 1.0
CG C:GLN3 4.1 28.4 1.0
OE1 C:GLN3 4.1 37.9 1.0
C11 C:9EG201 4.6 24.2 1.0
CB C:ALA102 4.8 24.8 1.0
CD1 C:ILE115 4.9 27.2 1.0

Chlorine binding site 10 out of 24 in 5vl2

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Chlorine binding site 10 out of 24 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:41.1
occ:1.00
 CL2 D:9EG201 0.0 41.1 1.0
C13 D:9EG201 1.8 27.1 1.0
C12 D:9EG201 2.8 24.6 1.0
C14 D:9EG201 2.8 25.6 1.0
CL3 D:9EG201 3.2 35.3 1.0
N D:ALA102 3.2 20.0 1.0
C D:ARG101 3.5 19.9 1.0
CB D:ALA102 3.7 21.3 1.0
CA D:ARG101 3.7 19.4 1.0
CD1 D:ILE115 3.9 21.3 1.0
CA D:ALA102 3.9 21.0 1.0
C11 D:9EG201 4.1 20.7 1.0
C15 D:9EG201 4.1 22.9 1.0
CG D:PRO114 4.1 19.3 1.0
O D:ARG101 4.3 16.2 1.0
N D:ARG101 4.4 17.8 1.0
C16 D:9EG201 4.6 22.4 1.0
CG1 D:ILE115 4.6 19.5 1.0
O D:THR100 4.7 14.4 1.0
C D:THR100 4.8 16.4 1.0
CD D:PRO114 4.9 18.5 1.0
CB D:ARG101 5.0 20.8 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 Dec 12 12:34:28 2020

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