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Chlorine in PDB 7c64: Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)

Protein crystallography data

The structure of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II), PDB code: 7c64 was solved by S.P.Kanaujia, M.Chandravanshi, R.Samanta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.36 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.460, 100.710, 66.260, 90.00, 104.19, 90.00
R / Rfree (%) 13.3 / 16.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) (pdb code 7c64). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II), PDB code: 7c64:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7c64

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Chlorine binding site 1 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:14.8
occ:1.00
 O A:HOH930 3.0 28.2 1.0
NE1 A:TRP188 3.2 7.7 1.0
O A:HOH773 3.3 11.0 1.0
N A:ILE194 3.3 9.6 1.0
CD1 A:ILE194 3.6 16.4 1.0
CB A:GLU193 3.9 13.9 1.0
CB A:ILE194 3.9 10.1 1.0
CD A:PRO367 4.0 9.6 1.0
CE2 A:TRP188 4.0 7.1 1.0
CZ2 A:TRP188 4.1 7.3 1.0
N A:VAL195 4.1 9.3 1.0
CA A:ILE194 4.1 9.5 1.0
CA A:GLU193 4.2 10.7 1.0
O A:VAL195 4.2 13.3 1.0
C A:GLU193 4.2 10.0 1.0
CG1 A:ILE194 4.3 12.4 1.0
CD1 A:TRP188 4.3 7.7 1.0
CD1 A:TYR366 4.4 7.8 1.0
CA A:TYR366 4.6 8.1 1.0
C A:ILE194 4.6 9.7 1.0
NH2 A:ARG364 4.7 11.4 1.0
CG2 A:VAL195 4.8 11.3 1.0
CG A:PRO367 5.0 10.8 1.0
O A:THR365 5.0 8.9 1.0

Chlorine binding site 2 out of 8 in 7c64

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Chlorine binding site 2 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:20.7
occ:1.00
 O A:HOH969 2.7 31.5 1.0
O A:HOH606 2.9 32.3 1.0
O A:HOH974 3.1 35.7 1.0
N A:THR365 3.2 8.4 1.0
OG1 A:THR365 3.4 13.9 1.0
NH1 A:ARG99 3.5 25.6 1.0
O A:THR365 3.6 8.9 1.0
CA A:ARG364 3.7 7.4 1.0
CA A:ALA96 3.7 8.6 1.0
CB A:ALA96 3.7 9.3 1.0
CG A:ARG364 3.8 8.3 1.0
C A:ARG364 3.9 7.7 1.0
CD A:ARG99 4.0 21.8 1.0
CA A:THR365 4.1 9.1 1.0
CB A:ARG364 4.2 7.6 1.0
C A:THR365 4.3 8.1 1.0
CB A:THR365 4.4 11.0 1.0
N A:ALA96 4.5 9.0 1.0
CZ A:ARG99 4.5 19.7 1.0
O A:HOH989 4.6 40.6 1.0
O A:HOH773 4.6 11.0 1.0
NE A:ARG99 4.7 19.5 1.0
O A:GLY363 4.7 7.8 1.0
O A:HOH991 4.8 37.9 1.0
C A:ALA96 4.8 8.1 1.0
O A:ALA96 4.8 10.0 1.0
N A:ARG364 4.9 7.0 1.0
CD A:ARG364 4.9 8.5 1.0

Chlorine binding site 3 out of 8 in 7c64

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Chlorine binding site 3 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:41.8
occ:1.00
 O A:HOH698 3.0 20.9 1.0
N A:GLN108 3.1 14.2 1.0
O A:HOH768 3.1 26.3 1.0
O A:HOH998 3.3 27.8 1.0
N A:ARG107 3.4 14.8 1.0
CB A:ALA106 3.8 15.6 1.0
CB A:GLN108 3.8 14.5 1.0
CG A:GLN108 3.9 17.8 1.0
O A:HOH1082 3.9 36.3 1.0
CA A:GLN108 3.9 13.4 1.0
CB A:ARG107 4.0 18.1 1.0
C A:ARG107 4.0 15.0 1.0
CA A:ARG107 4.0 15.8 1.0
O A:HOH979 4.1 23.4 1.0
C A:ALA106 4.2 14.4 1.0
OE1 A:GLN108 4.3 29.2 1.0
O A:GLN108 4.3 12.5 1.0
CA A:ALA106 4.3 15.6 1.0
CD A:GLN108 4.6 20.0 1.0
C A:GLN108 4.6 11.2 1.0
NE A:ARG107 4.8 30.8 1.0

Chlorine binding site 4 out of 8 in 7c64

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Chlorine binding site 4 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:10.1
occ:1.00
 N B:ILE194 3.2 8.8 1.0
O B:HOH748 3.2 11.0 1.0
O B:HOH864 3.3 23.2 1.0
NE1 B:TRP188 3.3 7.1 1.0
CB B:ILE194 3.8 9.9 1.0
CD1 B:ILE194 3.9 17.4 1.0
CD B:PRO367 3.9 9.4 1.0
CB B:GLU193 3.9 10.2 1.0
CA B:ILE194 4.0 9.6 1.0
N B:VAL195 4.1 8.1 1.0
CE2 B:TRP188 4.1 6.3 1.0
C B:GLU193 4.1 9.1 1.0
CA B:GLU193 4.1 8.4 1.0
CZ2 B:TRP188 4.2 6.9 1.0
CG1 B:ILE194 4.2 12.6 1.0
CD1 B:TRP188 4.4 6.4 1.0
O B:VAL195 4.4 10.4 1.0
CD1 B:TYR366 4.5 7.0 1.0
C B:ILE194 4.6 9.1 1.0
NH2 B:ARG364 4.6 10.9 1.0
CG B:PRO367 4.6 10.7 1.0
CG2 B:VAL195 4.7 11.7 1.0
CA B:TYR366 4.7 7.0 1.0

Chlorine binding site 5 out of 8 in 7c64

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Chlorine binding site 5 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:21.1
occ:1.00
 O B:HOH950 2.8 33.8 1.0
O B:HOH954 2.9 27.4 1.0
N B:THR365 3.2 7.7 1.0
OG1 B:THR365 3.3 13.2 1.0
O B:THR365 3.5 9.1 1.0
NH1 B:ARG99 3.6 21.3 1.0
CA B:ARG364 3.7 6.5 1.0
CB B:ALA96 3.7 9.1 1.0
CA B:ALA96 3.7 8.7 1.0
CG B:ARG364 3.9 7.1 1.0
CD B:ARG99 3.9 19.3 1.0
C B:ARG364 4.0 7.0 1.0
CA B:THR365 4.1 8.3 1.0
C B:THR365 4.2 7.8 1.0
CB B:ARG364 4.3 7.0 1.0
CB B:THR365 4.3 9.7 1.0
O B:HOH1001 4.4 37.8 1.0
N B:ALA96 4.5 7.9 1.0
CZ B:ARG99 4.6 19.3 1.0
O B:HOH625 4.6 31.8 1.0
NE B:ARG99 4.7 20.8 1.0
O B:HOH748 4.7 11.0 1.0
O B:GLY363 4.7 7.3 1.0
O B:ALA96 4.7 8.4 1.0
C B:ALA96 4.8 7.5 1.0
N B:ARG364 4.9 6.3 1.0
CB B:ARG99 4.9 12.4 1.0
CD B:ARG364 4.9 8.0 1.0
CG B:ARG99 5.0 17.8 1.0

Chlorine binding site 6 out of 8 in 7c64

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Chlorine binding site 6 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:41.4
occ:1.00
 O B:HOH706 2.8 27.9 1.0
O B:HOH902 3.0 28.2 1.0
N B:GLN108 3.0 13.4 1.0
N B:ARG107 3.3 16.1 1.0
CB B:GLN108 3.8 13.1 1.0
CB B:ARG107 3.8 20.9 1.0
CA B:ARG107 3.8 17.4 1.0
CG B:GLN108 3.8 14.9 1.0
C B:ARG107 3.9 16.8 1.0
CA B:GLN108 3.9 12.2 1.0
CB B:ALA106 4.0 15.1 1.0
OE1 B:GLN108 4.1 24.6 1.0
O B:HOH1029 4.1 30.8 1.0
C B:ALA106 4.2 14.1 1.0
O B:GLN108 4.2 11.8 1.0
O B:HOH1051 4.3 35.7 1.0
CD B:GLN108 4.4 16.1 1.0
CA B:ALA106 4.4 15.0 1.0
C B:GLN108 4.6 10.7 1.0
CG B:ARG107 4.9 23.1 1.0
NE B:ARG107 5.0 28.4 1.0
O B:HOH1034 5.0 38.8 1.0

Chlorine binding site 7 out of 8 in 7c64

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Chlorine binding site 7 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:35.4
occ:1.00
 O B:HOH1006 2.9 34.5 1.0
O B:HOH900 3.0 22.2 1.0
N B:GLU398 3.0 14.7 1.0
CG B:GLU398 3.2 20.8 1.0
N B:ARG397 3.3 13.4 1.0
CB B:THR396 3.5 15.2 1.0
CB B:GLU398 3.5 16.4 1.0
CB B:ARG397 3.8 14.0 1.0
CA B:ARG397 3.8 12.7 1.0
OG1 B:THR396 3.8 15.4 1.0
CA B:GLU398 3.9 15.4 1.0
C B:ARG397 3.9 12.6 1.0
CD B:GLU398 3.9 23.8 1.0
C B:THR396 4.0 11.9 1.0
CA B:THR396 4.2 13.4 1.0
OE2 B:GLU398 4.2 27.5 1.0
CG2 B:THR396 4.5 15.4 1.0
CG B:ARG397 4.7 16.1 1.0
OE1 B:GLU398 4.8 26.3 1.0
O B:THR396 4.9 12.7 1.0

Chlorine binding site 8 out of 8 in 7c64

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Chlorine binding site 8 out of 8 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in An Open State (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:33.5
occ:1.00
 N B:VAL36 3.1 10.0 1.0
O B:HOH652 3.1 28.6 1.0
CA B:LYS35 3.5 13.7 1.0
O B:HOH755 3.5 15.6 1.0
O B:VAL36 3.6 10.0 1.0
C B:LYS35 3.8 13.1 1.0
CG1 B:VAL36 3.9 10.6 1.0
CD B:LYS35 4.1 26.6 1.0
CA B:VAL36 4.1 9.4 1.0
CB B:LYS35 4.1 16.5 1.0
NZ A:LYS174 4.2 12.8 1.0
CD B:LYS20 4.2 19.5 1.0
O B:VAL34 4.2 19.6 1.0
C B:VAL36 4.3 9.2 1.0
CB B:VAL36 4.5 9.7 1.0
CE B:LYS20 4.6 22.1 1.0
CG B:LYS35 4.7 23.0 1.0
N B:LYS35 4.7 12.9 1.0
NZ B:LYS20 4.7 20.6 1.0
OD1 A:ASP388 4.8 18.8 1.0
CG B:LYS20 4.8 15.8 1.0
CE A:LYS174 4.8 11.4 1.0
C B:VAL34 4.9 14.8 1.0

Reference:

M.Chandravanshi, R.Samanta, S.P.Kanaujia. Conformational Trapping of A Beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of Abc Importers. J.Mol.Biol. V. 432 5711 2020.
ISSN: ESSN 1089-8638
PubMed: 32866452
DOI: 10.1016/J.JMB.2020.08.021
Page generated: Mon Jul 29 19:31:20 2024

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