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Chlorine in PDB 5whu: Crystal Structure of 3'Sl Bound Artb

Protein crystallography data

The structure of Crystal Structure of 3'Sl Bound Artb, PDB code: 5whu was solved by X.Gao, J.E.Galan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.915, 94.213, 123.964, 90.00, 102.60, 90.00
R / Rfree (%) 17.4 / 23

Other elements in 5whu:

The structure of Crystal Structure of 3'Sl Bound Artb also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of 3'Sl Bound Artb (pdb code 5whu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 23 binding sites of Chlorine where determined in the Crystal Structure of 3'Sl Bound Artb, PDB code: 5whu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 23 in 5whu

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Chlorine binding site 1 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:57.9
occ:1.00
 O A:HOH347 2.7 33.8 1.0
O A:HOH310 3.0 20.2 1.0
CA A:TYR91 3.7 18.3 1.0
N A:TYR91 3.8 11.0 1.0
CG A:ARG90 3.9 23.7 1.0
CD A:ARG90 4.0 27.1 1.0
C A:ARG90 4.1 14.9 1.0
O A:ARG90 4.2 11.7 1.0
CB A:TYR91 4.3 16.1 1.0
CB A:ARG90 4.4 17.8 1.0
CE1 C:TYR91 4.5 26.3 1.0
CB A:ALA94 4.5 12.7 1.0
CD1 C:TYR91 4.6 21.8 1.0
CD2 A:TYR91 4.7 11.2 1.0
CA A:ARG90 4.9 17.3 1.0
C A:TYR91 4.9 16.9 1.0
CG A:TYR91 4.9 12.7 1.0
O A:HOH346 5.0 33.5 1.0

Chlorine binding site 2 out of 23 in 5whu

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Chlorine binding site 2 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:58.3
occ:1.00
 O A:HOH330 2.9 33.3 1.0
N A:ASN27 3.0 23.4 1.0
CB A:ASN27 3.0 29.4 1.0
CA A:ASN27 3.4 23.8 1.0
CG A:ASN27 3.5 41.7 1.0
ND2 A:ASN27 3.5 52.6 1.0
N A:THR28 3.6 20.3 1.0
C A:ASN27 3.7 22.8 1.0
OG1 A:THR28 3.7 29.5 1.0
C A:ASP25 3.7 27.5 1.0
CA A:ASP25 3.8 29.4 1.0
N A:TYR26 3.8 17.9 1.0
N A:ASP25 4.0 28.1 1.0
O A:HOH304 4.0 22.8 1.0
C A:TYR26 4.2 25.1 1.0
O A:ASP25 4.2 27.1 1.0
OD1 A:ASN27 4.5 37.4 1.0
CB A:THR28 4.5 24.4 1.0
CA A:TYR26 4.5 24.6 1.0
O A:ASN27 4.5 21.6 1.0
O A:HOH340 4.7 26.4 1.0
CA A:THR28 4.7 21.1 1.0
OD1 A:ASP25 5.0 52.4 1.0

Chlorine binding site 3 out of 23 in 5whu

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Chlorine binding site 3 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:39.5
occ:1.00
 O A:HOH334 3.0 35.2 1.0
N A:THR68 3.5 23.5 1.0
N A:HIS67 3.5 34.8 1.0
ND1 A:HIS67 3.6 44.2 1.0
CE1 A:HIS67 3.7 46.3 1.0
ND2 A:ASN120 3.8 24.2 1.0
CB A:THR68 3.9 25.6 1.0
O A:THR68 4.0 29.7 1.0
CG1 A:VAL66 4.1 30.4 1.0
CB A:SER118 4.1 23.8 1.0
CA A:THR68 4.2 23.9 1.0
CA A:VAL66 4.2 39.6 1.0
OG1 A:THR68 4.2 22.0 1.0
CG A:HIS67 4.3 34.7 1.0
C A:VAL66 4.3 36.5 1.0
C A:HIS67 4.3 23.8 1.0
CA A:HIS67 4.4 28.3 1.0
NE2 A:HIS67 4.4 47.1 1.0
C A:THR68 4.5 25.5 1.0
O A:HOH342 4.6 36.6 1.0
CB A:VAL66 4.7 36.3 1.0
CD2 A:HIS67 4.7 41.5 1.0
OG A:SER118 4.8 24.5 1.0
O A:PHE117 5.0 21.6 1.0
CB A:HIS67 5.0 29.0 1.0

Chlorine binding site 4 out of 23 in 5whu

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Chlorine binding site 4 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:53.1
occ:1.00
 O A:HOH319 2.9 27.6 1.0
O D:HOH311 2.9 17.0 1.0
ND2 D:ASN112 3.8 18.2 1.0
O D:HOH329 3.8 15.7 1.0
CB A:ALA24 4.3 22.3 1.0
O A:ASN22 4.3 27.5 1.0
N A:ALA24 4.6 20.1 1.0
CG D:ASN112 4.8 19.5 1.0
CA A:ALA24 5.0 20.7 1.0

Chlorine binding site 5 out of 23 in 5whu

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Chlorine binding site 5 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:43.6
occ:1.00
 O B:HOH333 3.1 24.7 1.0
N B:HIS67 3.4 47.1 1.0
N B:THR68 3.4 26.3 1.0
CE1 B:HIS67 3.7 59.9 1.0
NE2 B:HIS67 3.8 58.2 1.0
ND1 B:HIS67 3.8 59.4 1.0
ND2 B:ASN120 3.8 23.3 1.0
CD2 B:HIS67 3.9 55.5 1.0
CG B:HIS67 3.9 56.1 1.0
O B:THR68 3.9 27.5 1.0
CB B:THR68 4.0 32.4 1.0
CB B:SER118 4.1 21.4 1.0
CA B:VAL66 4.1 47.5 1.0
CA B:THR68 4.1 25.4 1.0
C B:VAL66 4.2 46.9 1.0
CG1 B:VAL66 4.2 50.6 1.0
CA B:HIS67 4.2 50.0 1.0
C B:HIS67 4.2 49.5 1.0
C B:THR68 4.5 28.2 1.0
OG1 B:THR68 4.5 35.8 1.0
O B:ASN65 4.6 57.1 1.0
CB B:HIS67 4.7 52.2 1.0
OG B:SER118 4.7 28.5 1.0
CB B:VAL66 4.8 51.9 1.0
O B:PHE117 5.0 36.6 1.0

Chlorine binding site 6 out of 23 in 5whu

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Chlorine binding site 6 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:49.2
occ:1.00
 O B:CYS128 2.5 31.4 1.0
O B:HOH308 2.7 20.1 1.0
C B:CYS128 3.6 28.4 1.0
OH C:TYR93 4.1 25.8 1.0
O B:HOH320 4.1 28.3 1.0
CA B:THR129 4.1 41.1 1.0
OE2 B:GLU97 4.3 16.2 1.0
N B:THR129 4.3 36.0 1.0
N B:CYS128 4.4 22.4 1.0
CA B:CYS128 4.6 24.4 1.0
O B:ASP98 4.7 28.2 1.0
CG2 B:THR129 4.8 35.5 1.0
C B:THR129 4.9 48.4 1.0

Chlorine binding site 7 out of 23 in 5whu

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Chlorine binding site 7 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:64.7
occ:1.00
 OE2 F:GLU105 3.5 44.5 1.0
O B:HOH337 3.8 47.1 1.0
OE1 F:GLU105 3.9 47.0 1.0
O B:HOH325 4.1 27.7 1.0
CD F:GLU105 4.2 40.8 1.0
CA B:GLY96 4.4 22.5 1.0
O B:THR95 4.4 22.5 1.0
N B:GLY96 4.7 30.0 1.0
O B:ALA94 4.7 19.4 1.0
C B:THR95 4.7 28.2 1.0

Chlorine binding site 8 out of 23 in 5whu

Go back to Chlorine Binding Sites List in 5whu
Chlorine binding site 8 out of 23 in the Crystal Structure of 3'Sl Bound Artb


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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl205

b:40.5
occ:1.00
 O C:HOH328 2.4 38.7 1.0
N C:HIS67 3.5 32.4 1.0
N C:THR68 3.7 31.9 1.0
ND2 C:ASN120 3.7 25.8 1.0
CA C:VAL66 3.9 43.2 1.0
CG1 C:VAL66 3.9 32.9 1.0
O C:THR68 4.1 21.1 1.0
NE2 C:HIS67 4.2 50.1 1.0
CB C:SER118 4.2 18.7 1.0
C C:VAL66 4.2 35.7 1.0
CD2 C:HIS67 4.2 49.4 1.0
CB C:THR68 4.2 24.0 1.0
CE1 C:HIS67 4.3 47.6 1.0
CG C:HIS67 4.4 45.6 1.0
ND1 C:HIS67 4.4 46.6 1.0
CA C:THR68 4.4 28.2 1.0
CB C:VAL66 4.4 37.7 1.0
CA C:HIS67 4.5 33.1 1.0
O C:ASN65 4.5 56.4 1.0
O C:HOH327 4.5 30.8 1.0
C C:HIS67 4.5 27.7 1.0
OG1 C:THR68 4.7 24.2 1.0
C C:THR68 4.7 25.4 1.0
CG2 C:VAL66 4.9 38.2 1.0
OG C:SER118 5.0 18.1 1.0

Chlorine binding site 9 out of 23 in 5whu

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Chlorine binding site 9 out of 23 in the Crystal Structure of 3'Sl Bound Artb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl205

b:46.9
occ:1.00
 O D:HOH318 3.0 26.0 1.0
N D:HIS67 3.3 30.5 1.0
N D:THR68 3.3 22.8 1.0
ND2 D:ASN120 3.5 20.1 1.0
CE1 D:HIS67 3.5 47.1 1.0
O D:THR68 3.6 21.9 1.0
ND1 D:HIS67 3.6 47.6 1.0
NE2 D:HIS67 3.7 46.2 1.0
CA D:VAL66 3.9 35.9 1.0
CG D:HIS67 3.9 41.0 1.0
CD2 D:HIS67 3.9 44.8 1.0
CB D:THR68 4.0 22.1 1.0
CA D:THR68 4.0 21.9 1.0
CB D:SER118 4.1 23.7 1.0
C D:VAL66 4.1 34.2 1.0
CG1 D:VAL66 4.1 28.6 1.0
C D:HIS67 4.2 30.3 1.0
CA D:HIS67 4.2 29.9 1.0
C D:THR68 4.3 32.1 1.0
OG1 D:THR68 4.4 22.5 1.0
O D:ASN65 4.6 38.7 1.0
OG D:SER118 4.6 17.4 1.0
CB D:VAL66 4.6 30.3 1.0
CB D:HIS67 4.7 35.6 1.0
CG D:ASN120 4.8 27.1 1.0

Chlorine binding site 10 out of 23 in 5whu

Go back to Chlorine Binding Sites List in 5whu
Chlorine binding site 10 out of 23 in the Crystal Structure of 3'Sl Bound Artb


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl208

b:34.9
occ:1.00
 O E:HOH336 2.6 41.4 1.0
N E:HIS67 3.6 24.7 1.0
N E:THR68 3.6 23.3 1.0
CG1 E:VAL66 3.8 34.1 1.0
ND2 E:ASN120 3.9 19.7 1.0
CA E:VAL66 4.1 28.9 1.0
O E:THR68 4.1 26.9 1.0
CE1 E:HIS67 4.1 45.3 1.0
ND1 E:HIS67 4.1 42.1 1.0
CB E:THR68 4.2 21.7 1.0
C E:VAL66 4.2 27.8 1.0
CB E:SER118 4.3 25.5 1.0
CA E:THR68 4.3 22.9 1.0
NE2 E:HIS67 4.4 44.9 1.0
CG E:HIS67 4.4 35.6 1.0
C E:HIS67 4.5 30.1 1.0
CA E:HIS67 4.5 30.2 1.0
OG1 E:THR68 4.5 20.9 1.0
CB E:VAL66 4.5 32.0 1.0
CD2 E:HIS67 4.6 40.5 1.0
C E:THR68 4.7 24.9 1.0
O E:ASN65 4.8 37.9 1.0
O E:HOH328 4.9 33.6 1.0

Reference:

X.Gao, L.Deng, G.Stack, H.Yu, X.Chen, Y.Naito-Matsui, A.Varki, J.E.Galan. Evolution of Host Adaptation in the Salmonella Typhoid Toxin. Nat Microbiol V. 2 1592 2017.
ISSN: ESSN 2058-5276
PubMed: 28993610
DOI: 10.1038/S41564-017-0033-2
Page generated: Fri Jul 26 19:23:11 2024

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