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Chlorine in PDB 4e42: Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4

Protein crystallography data

The structure of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4, PDB code: 4e42 was solved by L.Deng, R.J.Langley, Q.Wang, S.L.Topalian, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.63 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.070, 75.365, 130.859, 90.00, 123.48, 90.00
R / Rfree (%) 20 / 26.3

Other elements in 4e42:

The structure of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 (pdb code 4e42). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4, PDB code: 4e42:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4e42

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Chlorine binding site 1 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:55.5
occ:1.00
 N A:SER139 3.5 42.9 1.0
CB A:ASP138 3.6 42.5 1.0
OG A:SER139 3.7 42.6 1.0
N A:ILE111 3.7 47.6 1.0
O A:PRO109 3.8 42.4 1.0
CB A:SER139 3.8 43.3 1.0
NE2 A:GLN13 4.0 48.9 1.0
CA A:SER139 4.2 43.5 1.0
NE2 A:GLN140 4.2 46.7 1.0
O A:ILE111 4.3 49.4 1.0
CA A:ASP138 4.3 42.1 1.0
C A:ASP138 4.4 42.1 1.0
OD1 A:ASP138 4.4 44.0 1.0
CG A:ASP138 4.4 44.0 1.0
CB A:ILE111 4.4 48.7 1.0
CA A:ILE111 4.5 48.8 1.0
N A:GLN140 4.5 45.5 1.0
CA A:ASP110 4.5 45.7 1.0
CG A:GLN140 4.6 46.8 1.0
C A:ASP110 4.6 46.5 1.0
CG1 A:ILE111 4.7 48.5 1.0
C A:ILE111 4.7 49.7 1.0
OD1 A:ASP110 4.7 47.3 1.0
C A:SER139 4.8 44.5 1.0
C A:PRO109 4.9 42.5 1.0
CD A:GLN140 4.9 47.3 1.0

Chlorine binding site 2 out of 9 in 4e42

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Chlorine binding site 2 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:44.6
occ:1.00
 CG2 B:THR3 3.1 25.3 1.0
OG B:SER5 3.2 28.0 1.0
N B:SER5 3.6 25.7 1.0
O B:THR3 3.8 24.3 1.0
C B:GLN4 3.8 24.8 1.0
CA B:GLN4 3.9 24.6 1.0
C B:THR3 3.9 24.4 1.0
CB B:SER5 3.9 26.1 1.0
O B:ARG20 3.9 27.0 1.0
N B:GLN4 4.0 24.3 1.0
C B:ARG20 4.1 27.5 1.0
N B:SER22 4.2 29.4 1.0
CB B:ARG20 4.3 27.0 1.0
N B:CYS21 4.3 27.7 1.0
CA B:CYS21 4.3 28.6 1.0
CA B:SER5 4.3 26.6 1.0
CB B:THR3 4.4 24.7 1.0
C B:CYS21 4.4 28.8 1.0
O B:GLN4 4.6 24.6 1.0
CB B:SER22 4.6 29.9 1.0
CA B:THR3 4.7 24.3 1.0
CA B:ARG20 4.9 27.4 1.0
O B:SER5 5.0 27.0 1.0

Chlorine binding site 3 out of 9 in 4e42

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Chlorine binding site 3 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:54.3
occ:1.00
 NH1 B:ARG65 3.0 36.9 1.0
CD1 B:PHE67 3.6 28.8 1.0
O B:HOH438 3.6 49.8 1.0
O B:GLN66 3.6 31.8 1.0
CE1 B:PHE67 4.1 28.9 1.0
CA B:PHE67 4.1 31.9 1.0
CD B:ARG65 4.1 33.6 1.0
CZ B:ARG65 4.2 36.0 1.0
CD B:PRO68 4.3 32.5 1.0
C B:GLN66 4.3 31.4 1.0
CG B:PHE67 4.4 30.9 1.0
N B:PHE67 4.6 31.5 1.0
NE B:ARG65 4.6 34.6 1.0
CB B:PHE67 4.7 31.6 1.0

Chlorine binding site 4 out of 9 in 4e42

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Chlorine binding site 4 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:66.6
occ:1.00
 OD1 B:ASN75 3.2 34.5 1.0
OG B:SER63 3.5 35.1 1.0
CA B:GLY64 3.7 30.6 1.0
O B:GLY64 3.7 29.9 1.0
N B:GLY64 3.7 31.1 1.0
C B:GLY64 3.8 30.4 1.0
CG B:ASN75 4.0 34.1 1.0
CB B:ASN75 4.0 32.7 1.0
CB B:SER63 4.1 32.6 1.0
C B:SER63 4.1 32.2 1.0
CG B:ARG65 4.3 31.9 1.0
O B:SER63 4.5 32.5 1.0
N B:ARG65 4.7 30.6 1.0
NE B:ARG65 4.8 34.6 1.0
CA B:SER63 4.8 32.5 1.0
N B:ASN75 4.9 31.6 1.0
CB B:ARG65 4.9 31.1 1.0

Chlorine binding site 5 out of 9 in 4e42

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Chlorine binding site 5 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:46.3
occ:1.00
 NE2 B:HIS8 3.0 38.1 1.0
CD B:ARG105 3.5 29.1 1.0
CD2 B:HIS149 3.7 31.1 1.0
O B:HOH455 3.8 35.5 1.0
CE1 B:HIS8 3.9 36.8 1.0
CD2 B:HIS8 3.9 37.3 1.0
CG B:ARG105 4.1 25.8 1.0
CB B:PRO147 4.1 32.4 1.0
CB B:LEU107 4.2 24.7 1.0
O B:ASP148 4.2 32.3 1.0
CD2 B:LEU107 4.2 24.5 1.0
CG B:PRO147 4.5 32.5 1.0
CG B:HIS149 4.5 30.9 1.0
CG B:LEU107 4.5 25.1 1.0
CB B:HIS149 4.6 30.5 1.0
CD1 B:LEU107 4.6 20.4 1.0
N B:ASP148 4.7 33.0 1.0
NE B:ARG105 4.7 33.1 1.0
C B:ASP148 4.7 32.5 1.0
NE2 B:HIS149 4.8 31.2 1.0
O B:HOH435 5.0 33.4 1.0

Chlorine binding site 6 out of 9 in 4e42

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Chlorine binding site 6 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:55.5
occ:1.00
 CG2 D:THR3 3.0 38.5 1.0
OG D:SER5 3.6 39.8 1.0
N D:SER5 3.6 37.8 1.0
C D:GLN4 3.7 37.2 1.0
O D:THR3 3.8 38.1 1.0
CA D:GLN4 3.8 37.1 1.0
C D:THR3 3.8 37.7 1.0
N D:GLN4 3.9 37.2 1.0
CB D:SER5 4.0 38.2 1.0
O D:ARG20 4.1 36.7 1.0
CB D:THR3 4.1 37.7 1.0
N D:SER22 4.2 39.7 1.0
CA D:CYS21 4.3 38.4 1.0
C D:ARG20 4.4 36.8 1.0
CA D:SER5 4.4 38.3 1.0
O D:GLN4 4.5 37.2 1.0
N D:CYS21 4.5 37.5 1.0
C D:CYS21 4.5 38.9 1.0
CB D:SER22 4.6 40.7 1.0
CA D:THR3 4.6 37.7 1.0
CB D:ARG20 4.7 36.2 1.0

Chlorine binding site 7 out of 9 in 4e42

Go back to Chlorine Binding Sites List in 4e42
Chlorine binding site 7 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:54.7
occ:1.00
 ND2 D:ASN75 3.1 36.8 1.0
CA D:GLY64 3.5 39.0 1.0
O D:GLY64 3.6 38.9 1.0
N D:GLY64 3.7 39.4 1.0
C D:GLY64 3.7 39.0 1.0
C D:SER63 4.1 40.2 1.0
OG D:SER63 4.1 41.5 1.0
CG D:ASN75 4.1 38.7 1.0
CB D:SER63 4.2 40.9 1.0
CB D:ASN75 4.3 38.2 1.0
O D:SER63 4.4 40.1 1.0
N D:ARG65 4.6 39.0 1.0
CG D:ARG65 4.6 41.4 1.0
NE D:ARG65 4.7 47.5 1.0
CA D:SER63 4.8 40.7 1.0
N D:ASN75 4.8 37.9 1.0
CB D:ARG65 4.9 40.2 1.0

Chlorine binding site 8 out of 9 in 4e42

Go back to Chlorine Binding Sites List in 4e42
Chlorine binding site 8 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:54.5
occ:1.00
 NE2 D:HIS8 2.9 42.4 1.0
O D:HOH417 3.5 43.0 1.0
CD D:ARG105 3.7 39.8 1.0
CE1 D:HIS8 3.7 42.8 1.0
CD2 D:HIS8 3.8 43.2 1.0
CB D:LEU107 3.9 37.5 1.0
ND1 D:HIS149 4.0 43.1 1.0
CG D:PRO147 4.0 45.4 1.0
CD2 D:LEU107 4.0 36.5 1.0
CB D:PRO147 4.2 44.9 1.0
CG D:ARG105 4.2 37.5 1.0
CD1 D:LEU107 4.2 36.1 1.0
CG D:LEU107 4.3 37.6 1.0
O D:ASP148 4.5 45.1 1.0
N D:ASP148 4.6 45.4 1.0
CB D:HIS149 4.7 42.5 1.0
CG D:HIS149 4.8 42.6 1.0
C D:ASP148 4.9 44.7 1.0
ND1 D:HIS8 4.9 41.8 1.0
CE1 D:HIS149 4.9 43.2 1.0
CG D:HIS8 5.0 41.0 1.0

Chlorine binding site 9 out of 9 in 4e42

Go back to Chlorine Binding Sites List in 4e42
Chlorine binding site 9 out of 9 in the Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structural Basis For the Recognition of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted T Cell Receptor G4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl305

b:52.1
occ:1.00
 NH1 D:ARG65 3.0 49.1 1.0
O D:HOH420 3.2 43.1 1.0
CD1 D:PHE67 3.4 36.5 1.0
CD D:ARG65 3.6 44.4 1.0
O D:GLN66 3.8 40.3 1.0
CE1 D:PHE67 3.9 34.9 1.0
CZ D:ARG65 4.1 48.8 1.0
CA D:PHE67 4.2 39.7 1.0
NE D:ARG65 4.3 47.5 1.0
CG D:PHE67 4.3 38.0 1.0
C D:GLN66 4.4 39.8 1.0
CD D:PRO68 4.5 40.5 1.0
N D:PHE67 4.6 39.6 1.0
CB D:PHE67 4.6 39.1 1.0
CG D:ARG65 4.7 41.4 1.0
CB D:ARG65 4.8 40.2 1.0
O D:HOH437 4.9 31.1 1.0

Reference:

L.Deng, R.J.Langley, Q.Wang, S.L.Topalian, R.A.Mariuzza. Structural Basis For the Recognition of Mutant Self By A Tumor-Specific, Mhc Class II-Restricted T Cell Receptor G4 Proc.Natl.Acad.Sci.Usa 2012.
ISSN: ESSN 1091-6490
Page generated: Sun Jul 21 12:31:41 2024

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