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Chlorine in PDB 6eq8: Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58

Protein crystallography data

The structure of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58, PDB code: 6eq8 was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.06 / 2.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 355.260, 73.660, 108.080, 90.00, 105.49, 90.00
R / Rfree (%) 18.4 / 21.7

Other elements in 6eq8:

The structure of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 also contains other interesting chemical elements:

Calcium (Ca) 13 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Chlorine atom in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 (pdb code 6eq8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 35 binding sites of Chlorine where determined in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58, PDB code: 6eq8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 35 in 6eq8

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Chlorine binding site 1 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl715

b:78.0
occ:1.00
 CG D:MET267 3.1 61.5 1.0
O D:PRO264 3.5 50.7 1.0
CB D:TYR280 3.7 44.3 1.0
N D:TYR280 3.7 45.7 1.0
C D:SER279 3.7 48.9 1.0
CA D:MET267 3.8 52.0 1.0
O D:TYR266 3.8 54.9 1.0
N D:SER279 3.9 45.2 1.0
CA D:SER279 3.9 46.3 1.0
CB D:MET267 3.9 56.2 1.0
C D:VAL278 4.1 47.6 1.0
O D:SER279 4.2 45.9 1.0
N D:MET267 4.2 52.6 1.0
C D:TYR266 4.2 55.3 1.0
O D:VAL278 4.2 48.1 1.0
CA D:TYR280 4.3 44.0 1.0
O D:GLU265 4.3 52.4 1.0
CE D:MET267 4.4 65.6 1.0
C D:GLU265 4.5 52.8 1.0
SD D:MET267 4.5 69.3 1.0
C D:PRO264 4.6 50.9 1.0
CZ2 D:TRP100 4.7 41.2 1.0
CA D:GLU265 4.8 49.6 1.0
CA D:VAL278 4.9 40.8 1.0
O D:PRO277 4.9 44.1 1.0
CG D:TYR280 4.9 44.9 1.0
N D:VAL278 4.9 40.0 1.0
C D:PRO277 4.9 43.9 1.0

Chlorine binding site 2 out of 35 in 6eq8

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Chlorine binding site 2 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl716

b:83.8
occ:1.00
 CG D:ARG96 3.9 37.6 1.0
NE D:ARG96 4.0 39.0 1.0
O D:HOH950 4.0 60.9 1.0
CZ D:ARG96 4.1 47.8 1.0
NH2 D:ARG96 4.2 35.2 1.0
OD1 D:ASP283 4.3 60.6 1.0
CD D:ARG96 4.6 39.4 1.0
NH1 D:ARG96 4.7 34.0 1.0

Chlorine binding site 3 out of 35 in 6eq8

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Chlorine binding site 3 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl717

b:74.3
occ:1.00
 ND2 D:ASN516 3.4 90.8 1.0
O D:HOH961 3.6 49.3 1.0
CB D:ARG96 3.9 34.9 1.0
N D:ARG96 4.2 36.8 1.0
CB D:ASP514 4.2 53.2 1.0
CG D:ARG96 4.3 37.6 1.0
O D:HOH950 4.4 60.9 1.0
OD1 D:ASP514 4.4 76.6 1.0
CG D:ASP514 4.4 75.0 1.0
CA D:ARG96 4.6 36.8 1.0
O D:ARG96 4.6 39.5 1.0
CG D:ASN516 4.7 89.6 1.0

Chlorine binding site 4 out of 35 in 6eq8

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Chlorine binding site 4 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl718

b:63.1
occ:1.00
 N D:ILE634 3.0 32.1 1.0
O D:GLY617 3.1 37.2 1.0
N D:GLY359 3.4 41.9 1.0
CA D:PRO633 3.5 34.6 1.0
CA D:GLY359 3.5 41.4 1.0
C D:PRO633 3.7 37.8 1.0
C D:GLY617 3.7 38.5 1.0
CG2 D:ILE634 3.8 32.2 1.0
CG1 D:ILE634 3.8 32.3 1.0
O D:HOH805 3.8 42.2 1.0
CB D:ILE634 4.0 32.6 1.0
CA D:ILE634 4.0 30.3 1.0
CB D:PRO633 4.1 35.9 1.0
N D:ALA618 4.3 34.1 1.0
C D:GLY359 4.4 45.5 1.0
C D:PHE358 4.4 44.8 1.0
O D:THR632 4.4 39.9 1.0
CA D:GLY617 4.4 37.9 1.0
CA D:ALA618 4.5 34.9 1.0
N D:GLY617 4.5 39.0 1.0
O D:ALA357 4.5 41.7 1.0
N D:PRO633 4.7 35.9 1.0
N D:LEU619 4.7 38.2 1.0
CD D:PRO360 4.8 43.7 1.0
N D:PRO360 4.8 42.8 1.0
C D:ALA618 4.8 39.8 1.0
O D:PRO633 4.9 38.2 1.0
CA D:PHE358 5.0 38.7 1.0
N D:PHE635 5.0 32.6 1.0

Chlorine binding site 5 out of 35 in 6eq8

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Chlorine binding site 5 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl719

b:63.0
occ:1.00
 N D:TYR255 3.1 54.4 1.0
CB D:THR254 3.5 65.7 1.0
CA D:THR254 3.5 57.5 1.0
CD2 D:TYR255 3.7 56.7 1.0
C D:THR254 3.8 58.1 1.0
CB D:TYR255 4.1 51.9 1.0
CG2 D:THR254 4.1 67.8 1.0
CA D:TYR255 4.2 52.1 1.0
CG D:TYR255 4.4 54.3 1.0
OG1 D:THR254 4.6 63.9 1.0
CE2 D:TYR255 4.7 58.1 1.0
N D:THR254 4.9 59.5 1.0
N D:ASN256 5.0 53.6 1.0
O D:THR254 5.0 56.0 1.0

Chlorine binding site 6 out of 35 in 6eq8

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Chlorine binding site 6 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl720

b:48.3
occ:1.00
 OH D:TYR280 3.0 53.9 1.0
N D:ASP283 3.1 47.2 1.0
CD D:ARG96 3.6 39.4 1.0
CA D:PRO282 3.7 45.4 1.0
C D:PRO282 3.8 50.5 1.0
CZ D:TYR280 3.9 51.9 1.0
CE1 D:TYR280 3.9 44.8 1.0
CA D:ASP283 3.9 47.1 1.0
CD1 D:LEU314 3.9 40.8 1.0
CD D:PRO97 4.0 38.7 1.0
OD1 D:ASP283 4.1 60.6 1.0
CB D:PRO282 4.1 48.1 1.0
CG D:ASP283 4.1 61.8 1.0
CG D:ARG96 4.2 37.6 1.0
CB D:ARG96 4.3 34.9 1.0
OD2 D:ASP283 4.4 72.3 1.0
NE D:ARG96 4.4 39.0 1.0
CG D:PRO97 4.5 43.8 1.0
CB D:ASP283 4.6 50.3 1.0
N D:PRO282 4.9 46.0 1.0
N D:PRO97 4.9 36.9 1.0
CA D:ARG96 4.9 36.8 1.0

Chlorine binding site 7 out of 35 in 6eq8

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Chlorine binding site 7 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl721

b:46.4
occ:1.00
 N D:GLY76 3.2 41.1 1.0
CA D:GLY76 3.5 41.1 1.0
OE1 D:GLU299 3.8 64.8 1.0
CB D:LYS74 4.0 42.7 1.0
N D:THR75 4.2 41.8 1.0
C D:THR75 4.4 45.3 1.0
C D:LYS74 4.4 44.1 1.0
CG2 D:THR75 4.5 51.0 1.0
CE D:LYS74 4.6 60.0 1.0
CA D:LYS74 4.6 40.5 1.0
CG D:LYS74 4.7 42.0 1.0
C D:GLY76 4.7 43.4 1.0
CA D:THR75 4.7 41.6 1.0
O D:HOH876 4.8 35.0 1.0
CD D:GLU299 4.9 74.8 1.0
NZ D:LYS74 5.0 78.7 1.0
N D:ASN77 5.0 38.3 1.0

Chlorine binding site 8 out of 35 in 6eq8

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Chlorine binding site 8 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl711

b:55.5
occ:1.00
 O B:HOH909 3.1 38.1 1.0
N B:GLY76 3.2 49.0 1.0
CA B:GLY76 3.5 48.9 1.0
CB B:LYS74 3.8 48.5 1.0
OE1 B:GLU299 3.9 55.7 1.0
N B:THR75 4.2 47.2 1.0
CE B:LYS74 4.4 80.9 1.0
C B:THR75 4.4 51.6 1.0
C B:LYS74 4.5 49.9 1.0
CA B:LYS74 4.6 45.8 1.0
CG B:LYS74 4.6 53.6 1.0
NZ B:LYS74 4.7 0.4 1.0
C B:GLY76 4.7 49.8 1.0
CA B:THR75 4.8 47.3 1.0
N B:ASN77 4.9 44.9 1.0
O B:THR33 5.0 50.0 1.0
CD B:GLU299 5.0 77.2 1.0

Chlorine binding site 9 out of 35 in 6eq8

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Chlorine binding site 9 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl712

b:76.7
occ:1.00
 OE1 B:GLN384 3.7 43.0 1.0
CG B:GLN384 3.9 43.1 1.0
CD B:GLN384 4.0 52.7 1.0
CB B:GLN384 4.2 43.4 1.0
O B:PRO379 4.3 54.3 1.0
NE2 B:GLN384 4.8 43.9 1.0

Chlorine binding site 10 out of 35 in 6eq8

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Chlorine binding site 10 out of 35 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl713

b:78.8
occ:1.00
 ND2 B:ASN378 3.6 53.6 1.0
O B:ASN378 3.7 51.5 1.0
OD1 B:ASN378 3.7 62.5 1.0
CG B:ASN378 3.8 66.7 1.0
O B:PRO379 3.9 54.3 1.0
C B:PRO379 4.3 54.4 1.0
C B:ASN378 4.5 52.4 1.0
N B:ASP380 4.5 51.9 1.0
CA B:ASP380 4.5 52.1 1.0
CB B:ASN378 4.9 48.4 1.0
CB B:ASP380 4.9 54.7 1.0

Reference:

T.Meyer, A.Vigouroux, M.Aumont-Nicaise, G.Comte, L.Vial, C.Lavire, S.Morera. The Plant Defense Signal Galactinol Is Specifically Used As A Nutrient By the Bacterial Pathogenagrobacterium Fabrum. J. Biol. Chem. V. 293 7930 2018.
ISSN: ESSN 1083-351X
PubMed: 29602905
DOI: 10.1074/JBC.RA118.001856
Page generated: Sat Jul 27 22:32:09 2024

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