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Chlorine in PDB 6dwi: Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog

Protein crystallography data

The structure of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog, PDB code: 6dwi was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.573, 114.097, 128.301, 90.00, 90.46, 90.00
R / Rfree (%) 20.3 / 24.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog (pdb code 6dwi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog, PDB code: 6dwi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6dwi

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Chlorine binding site 1 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:51.0
occ:1.00
 N A:ARG61 3.2 40.6 1.0
N A:ALA60 3.5 43.9 1.0
CB A:ARG61 3.5 38.1 1.0
NH1 A:ARG61 3.6 47.8 1.0
CB A:PRO59 3.7 49.1 1.0
CG A:ARG61 3.7 49.5 1.0
CB A:ALA60 3.9 41.6 1.0
CA A:ARG61 4.0 40.1 1.0
CA A:ALA60 4.0 42.0 1.0
C A:ALA60 4.0 44.2 1.0
C A:PRO59 4.1 49.9 1.0
CD A:ARG61 4.1 54.9 1.0
CA A:PRO59 4.3 47.5 1.0
CZ A:ARG61 4.6 62.1 1.0
NE A:ARG61 4.8 55.0 1.0
O A:PRO59 4.9 49.8 1.0
CG A:PRO59 5.0 53.6 1.0

Chlorine binding site 2 out of 6 in 6dwi

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Chlorine binding site 2 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:38.9
occ:1.00
 O B:HOH477 2.9 66.9 1.0
OH B:TYR148 3.0 27.6 1.0
CA B:PRO152 3.4 28.6 1.0
N B:VAL153 3.5 35.4 1.0
O B:HOH458 3.7 47.9 1.0
CG B:GLU151 3.7 28.8 1.0
CB B:PRO152 3.8 29.2 1.0
CB B:ALA171 3.8 32.1 1.0
CE2 B:TYR148 3.9 24.4 1.0
CZ B:TYR148 3.9 30.4 1.0
CG2 B:VAL153 3.9 35.5 1.0
C B:PRO152 4.0 35.9 1.0
CB B:GLU151 4.1 25.0 1.0
OE2 B:GLU151 4.1 39.7 1.0
O B:VAL153 4.3 36.6 1.0
CD B:GLU151 4.3 40.3 1.0
CD2 B:LEU181 4.3 32.9 1.0
CA B:GLU151 4.4 24.9 1.0
CA B:VAL153 4.5 35.0 1.0
N B:PRO152 4.6 29.9 1.0
CB B:VAL153 4.8 36.4 1.0
C B:VAL153 4.9 40.2 1.0
CA B:ALA171 5.0 31.7 1.0

Chlorine binding site 3 out of 6 in 6dwi

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Chlorine binding site 3 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:35.9
occ:1.00
 O D:HOH402 3.1 50.5 1.0
N C:PHE98 3.4 29.9 1.0
N D:TRP47 3.5 31.9 1.0
CA C:THR97 3.8 31.4 1.0
CA D:GLN46 3.9 32.8 1.0
CD2 C:PHE98 3.9 31.4 1.0
O C:ARG96 4.0 33.0 1.0
CB C:PHE98 4.1 29.1 1.0
C C:THR97 4.1 34.4 1.0
C D:GLN46 4.2 36.0 1.0
CG D:GLN46 4.2 51.0 1.0
CB D:TRP47 4.2 30.2 1.0
CA C:PHE98 4.3 28.6 1.0
O D:LEU45 4.3 31.0 1.0
CA D:TRP47 4.4 31.1 1.0
CB C:THR97 4.5 38.2 1.0
O C:PHE98 4.5 35.0 1.0
CG C:PHE98 4.5 29.3 1.0
O D:TRP47 4.6 29.3 1.0
CG2 C:THR97 4.6 38.2 1.0
CB D:GLN46 4.6 34.2 1.0
N C:THR97 4.7 32.6 1.0
C C:ARG96 4.8 35.9 1.0
C C:PHE98 4.9 36.1 1.0
N D:GLN46 4.9 32.5 1.0

Chlorine binding site 4 out of 6 in 6dwi

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Chlorine binding site 4 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:51.4
occ:1.00
 N F:VAL153 3.2 40.1 1.0
CA F:PRO152 3.3 38.9 1.0
OH F:TYR148 3.6 39.2 1.0
C F:PRO152 3.7 41.6 1.0
CB F:PRO152 3.8 40.0 1.0
CB F:ALA171 3.8 48.0 1.0
CG2 F:VAL153 3.9 45.4 1.0
CG F:GLU151 3.9 37.6 1.0
CE2 F:TYR148 4.0 39.8 1.0
CB F:GLU151 4.1 37.1 1.0
CZ F:TYR148 4.2 42.7 1.0
CD2 F:LEU181 4.2 43.3 1.0
CA F:VAL153 4.3 41.5 1.0
O F:VAL153 4.4 47.4 1.0
CA F:GLU151 4.4 36.6 1.0
CD F:GLU151 4.5 54.8 1.0
N F:PRO152 4.6 39.0 1.0
OE2 F:GLU151 4.6 47.2 1.0
CB F:VAL153 4.6 45.5 1.0
C F:VAL153 4.9 48.3 1.0
O F:PRO152 4.9 39.6 1.0

Chlorine binding site 5 out of 6 in 6dwi

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Chlorine binding site 5 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl301

b:30.1
occ:1.00
 O H:HOH440 2.9 37.4 1.0
O H:HOH455 3.2 37.3 1.0
N G:PHE98 3.2 18.4 1.0
N H:TRP47 3.3 25.1 1.0
CA G:THR97 3.7 20.5 1.0
CD2 G:PHE98 3.7 17.9 1.0
CA H:GLN46 3.8 24.2 1.0
O G:HOH444 3.9 29.4 1.0
C G:THR97 3.9 22.3 1.0
CB G:PHE98 4.0 17.3 1.0
O G:ARG96 4.0 25.0 1.0
C H:GLN46 4.0 26.6 1.0
CB H:TRP47 4.1 21.5 1.0
CA G:PHE98 4.2 16.8 1.0
CG H:GLN46 4.2 54.7 1.0
O H:LEU45 4.2 26.2 1.0
CA H:TRP47 4.2 23.9 1.0
CG G:PHE98 4.3 17.5 1.0
CB G:THR97 4.4 28.5 1.0
O G:PHE98 4.5 22.9 1.0
CG2 G:THR97 4.5 21.1 1.0
O H:HOH474 4.5 43.4 1.0
CB H:GLN46 4.6 26.8 1.0
N G:THR97 4.6 19.9 1.0
O H:TRP47 4.7 28.3 1.0
C G:ARG96 4.7 24.6 1.0
CE2 G:PHE98 4.7 20.0 1.0
N H:GLN46 4.8 23.6 1.0
C G:PHE98 4.8 23.7 1.0
C H:LEU45 4.9 27.6 1.0
C H:TRP47 5.0 28.8 1.0

Chlorine binding site 6 out of 6 in 6dwi

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Chlorine binding site 6 out of 6 in the Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the 4462 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl301

b:43.4
occ:1.00
 O P:HOH347 3.3 38.3 1.0
O P:HOH337 3.4 37.3 1.0
N O:PHE98 3.4 26.9 1.0
O O:ARG96 3.5 30.8 1.0
N P:TRP47 3.5 22.8 1.0
CD2 O:PHE98 3.7 23.3 1.0
CA O:THR97 3.7 29.4 1.0
CA P:GLN46 3.9 24.9 1.0
CB O:PHE98 4.0 24.2 1.0
C O:THR97 4.1 31.1 1.0
CG P:GLN46 4.2 40.3 1.0
C P:GLN46 4.2 27.3 1.0
O P:LEU45 4.3 30.9 1.0
CA O:PHE98 4.3 24.5 1.0
CB P:TRP47 4.3 20.9 1.0
CG O:PHE98 4.3 23.5 1.0
C O:ARG96 4.4 33.0 1.0
CG2 O:THR97 4.5 30.9 1.0
CA P:TRP47 4.5 22.3 1.0
CB O:THR97 4.5 35.0 1.0
N O:THR97 4.5 30.2 1.0
CB P:GLN46 4.6 26.6 1.0
O O:PHE98 4.7 31.9 1.0
CE2 O:PHE98 4.8 24.8 1.0
O P:TRP47 4.8 25.0 1.0
N P:GLN46 5.0 24.4 1.0

Reference:

R.Fong, K.Kajihara, M.Chen, I.Hotzel, S.Mariathasan, W.L.W.Hazenbos, P.J.Lupardus. Structural Investigation of Human S. Aureus-Targeting Antibodies That Bind Wall Teichoic Acid. Mabs V. 10 979 2018.
ISSN: ESSN 1942-0870
PubMed: 30102105
DOI: 10.1080/19420862.2018.1501252
Page generated: Sat Jul 27 21:51:14 2024

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