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Chlorine in PDB 8dv3: Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1

Protein crystallography data

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1, PDB code: 8dv3 was solved by R.Farquhar, J.Rossjohn, A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.58 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.816, 78.628, 92.725, 90, 90, 90
R / Rfree (%) 19.2 / 25.3

Other elements in 8dv3:

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Iodine (I) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 (pdb code 8dv3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1, PDB code: 8dv3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8dv3

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Chlorine binding site 1 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1202

b:33.5
occ:1.00
 O A:HOH1456 2.8 46.9 1.0
O A:HOH1422 3.1 29.5 1.0
NH1 A:ARG71 3.3 36.6 1.0
CG A:ARG71 3.7 28.0 1.0
CD A:ARG71 3.9 32.0 1.0
CL A:CL1215 4.1 26.1 1.0
CZ A:ARG71 4.3 40.2 1.0
NE A:ARG71 4.5 30.7 1.0
O A:HOH1475 4.5 33.3 1.0
CA A:GLY45 4.9 25.2 1.0

Chlorine binding site 2 out of 6 in 8dv3

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Chlorine binding site 2 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1213

b:35.1
occ:1.00
 O A:TYR169 2.8 18.0 1.0
OD1 A:ASN57 2.8 19.4 1.0
N A:ASN57 3.0 20.8 1.0
CA A:GLY172 3.2 23.6 1.0
N A:VAL173 3.3 16.4 1.0
CD1 A:TYR169 3.4 16.8 1.0
CA A:GLY56 3.4 19.1 1.0
C A:GLY172 3.4 17.2 1.0
CA A:TYR169 3.4 14.8 1.0
C A:TYR169 3.5 25.1 1.0
C A:GLY56 3.7 20.3 1.0
O A:ARG168 3.7 16.2 1.0
CG A:ASN57 3.7 20.8 1.0
N A:GLY172 3.7 21.6 1.0
CD1 A:PHE58 3.8 16.5 1.0
CE1 A:TYR169 3.8 19.0 1.0
CE1 A:PHE58 3.9 21.0 1.0
CG A:TYR169 4.0 18.8 1.0
CA A:ASN57 4.0 24.1 1.0
O A:LYS55 4.1 20.5 1.0
N A:PHE58 4.2 17.4 1.0
CA A:VAL173 4.2 17.2 1.0
O A:GLY172 4.2 23.6 1.0
CB A:ASN57 4.3 21.9 1.0
CB A:TYR169 4.3 16.2 1.0
CB A:VAL173 4.3 15.8 1.0
N A:TYR169 4.4 15.1 1.0
C A:ASN57 4.4 21.5 1.0
C A:ARG168 4.5 20.1 1.0
N A:GLY56 4.5 17.4 1.0
CG A:PHE58 4.6 20.2 1.0
C A:LYS55 4.7 19.8 1.0
ND2 A:ASN57 4.7 23.3 1.0
CZ A:TYR169 4.8 20.5 1.0
N A:LEU170 4.8 17.2 1.0
CZ A:PHE58 4.8 19.4 1.0
O A:GLY56 4.9 22.9 1.0
CD2 A:TYR169 4.9 15.7 1.0
C A:LEU171 5.0 22.2 1.0

Chlorine binding site 3 out of 6 in 8dv3

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Chlorine binding site 3 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1214

b:19.5
occ:1.00
 O A:HOH1466 3.1 32.1 1.0
O A:HOH1472 3.3 32.2 1.0
N A:LYS214 3.7 16.9 1.0
CB A:LYS214 3.9 22.9 1.0
CD A:PRO7 4.0 23.8 1.0
CE2 A:TYR212 4.0 21.5 1.0
CA A:GLY6 4.1 29.7 1.0
CB A:PRO213 4.1 21.1 1.0
N A:PRO7 4.2 21.2 1.0
C A:GLY6 4.2 28.7 1.0
CA A:PRO213 4.3 20.6 1.0
OH A:TYR212 4.3 21.4 1.0
CG A:PRO7 4.3 25.0 1.0
CZ A:TYR212 4.4 20.6 1.0
CA A:LYS214 4.4 26.9 1.0
C A:PRO213 4.5 21.8 1.0
CD2 A:TYR212 4.7 23.0 1.0
O A:GLY6 4.9 19.6 1.0
NE1 A:TRP243 4.9 28.1 1.0
CA A:PRO7 4.9 22.2 1.0
OD2 A:ASP33 5.0 35.7 1.0
O A:HOH1367 5.0 21.9 1.0
CD A:PRO215 5.0 24.6 1.0
N A:GLY6 5.0 31.2 1.0

Chlorine binding site 4 out of 6 in 8dv3

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Chlorine binding site 4 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1215

b:26.1
occ:1.00
 O A:HOH1441 3.0 39.1 1.0
O A:HOH1422 3.0 29.5 1.0
NE1 A:TRP40 3.4 28.6 1.0
O A:HOH1456 3.6 46.9 1.0
CA A:GLY45 3.7 25.2 1.0
CL A:CL1202 4.1 33.5 1.0
O A:HOH1475 4.1 33.3 1.0
O A:SER42 4.2 26.6 0.6
O A:SER42 4.2 26.5 0.4
CE2 A:TRP40 4.2 21.5 1.0
CA A:SER42 4.3 27.2 0.6
CA A:SER42 4.3 27.2 0.4
N A:GLY45 4.3 22.1 1.0
CG2 A:ILE74 4.3 30.6 1.0
CZ2 A:TRP40 4.4 24.0 1.0
CD1 A:TRP40 4.4 24.8 1.0
C A:SER42 4.7 27.7 0.6
C A:SER42 4.7 27.6 0.4
CG A:ARG71 4.7 28.0 1.0
O A:ASP41 4.8 20.5 1.0
CB A:SER42 4.8 26.0 0.4
CB A:SER42 4.8 26.1 0.6
CD1 A:ILE74 4.9 25.6 1.0
C A:GLY45 5.0 26.6 1.0
CB A:ILE74 5.0 24.6 1.0
O A:HOH1408 5.0 28.8 1.0
OG A:SER42 5.0 26.0 0.6

Chlorine binding site 5 out of 6 in 8dv3

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Chlorine binding site 5 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:19.3
occ:1.00
 N B:GLY45 3.1 49.9 1.0
CB B:ALA81 3.6 31.1 1.0
O B:HOH305 3.6 59.8 1.0
CA B:GLY45 3.7 48.0 1.0
O B:GLU79 3.9 41.2 1.0
N B:ASN44 4.0 44.1 1.0
C B:ASN44 4.1 49.7 1.0
CB B:GLU79 4.1 42.4 1.0
C B:GLU79 4.1 40.0 1.0
CB B:LEU42 4.2 32.4 1.0
CA B:ASN44 4.2 46.5 1.0
N B:ALA81 4.2 33.3 1.0
C B:TYR80 4.2 37.4 1.0
N B:TYR80 4.4 39.3 1.0
OE1 B:GLU79 4.4 63.5 1.0
CA B:TYR80 4.5 31.1 1.0
CA B:ALA81 4.5 32.0 1.0
O B:LEU42 4.6 31.4 1.0
O B:TYR80 4.6 36.3 1.0
CE B:LYS96 4.7 52.3 1.0
CD1 B:LEU42 4.7 33.5 1.0
C B:LEU42 4.8 29.5 1.0
CA B:GLU79 4.8 40.4 1.0
C B:LYS43 4.8 46.0 1.0
CG B:LYS96 4.9 47.7 1.0
C B:GLY45 5.0 54.0 1.0

Chlorine binding site 6 out of 6 in 8dv3

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Chlorine binding site 6 out of 6 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:29.5
occ:1.00
 N B:SER90 3.8 38.3 1.0
CB B:SER90 4.1 40.9 1.0
OG B:SER90 4.3 43.8 1.0
N B:GLN91 4.4 42.6 1.0
CD2 B:LEU89 4.4 32.2 1.0
CA B:SER90 4.5 40.8 1.0
O B:HOH365 4.5 45.5 1.0
O B:GLN91 4.6 37.0 1.0
CA B:LEU89 4.7 39.9 1.0
C B:LEU89 4.7 40.1 1.0
C B:SER90 4.9 48.0 1.0
CB B:LEU89 4.9 41.1 1.0

Reference:

R.Farquhar, I.Van Rhijn, D.B.Moody, J.Rossjohn, A.Shahine. Alpha Beta T-Cell Receptor Recognition of Self-Phosphatidylinositol Presented By CD1B. J.Biol.Chem. V. 299 02849 2023.
ISSN: ESSN 1083-351X
PubMed: 36587766
DOI: 10.1016/J.JBC.2022.102849
Page generated: Tue Jul 30 08:54:09 2024

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