Chlorine in PDB 6tds: Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash

Protein crystallography data

The structure of Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash, PDB code: 6tds was solved by R.Anjanappa, M.Garcia Alai, S.Springer, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.85 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.604, 85.190, 83.848, 90.00, 90.03, 90.00
R / Rfree (%) 19.8 / 24.8

Other elements in 6tds:

The structure of Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash also contains other interesting chemical elements:

Sodium (Na) 15 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash (pdb code 6tds). 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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash, PDB code: 6tds:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6tds

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:33.6
occ:1.00
 O A:HOH700 2.4 26.2 1.0
O B:MET100 2.7 27.5 1.0
NE2 A:HIS188 3.1 14.2 1.0
NE1 A:TRP204 3.4 14.2 1.0
CE2 A:TRP204 3.5 14.3 1.0
CG2 A:THR190 3.6 20.9 1.0
C B:MET100 3.7 23.8 1.0
CD1 A:TRP204 3.8 13.5 1.0
CE1 A:HIS188 3.8 15.1 1.0
OXT B:MET100 3.9 19.8 1.0
CZ2 A:TRP204 4.0 12.5 1.0
CD2 A:TRP204 4.1 14.2 1.0
CG A:TRP204 4.2 12.7 1.0
CD2 A:HIS188 4.2 15.1 1.0
CH2 A:TRP204 4.8 15.0 1.0
CB A:THR190 4.9 16.9 1.0
CE3 A:TRP204 5.0 14.4 1.0

Chlorine binding site 2 out of 8 in 6tds

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:38.8
occ:1.00
 O1 A:EDO502 3.8 41.8 1.0
CZ A:PHE9 3.9 27.6 1.0
ND1 A:HIS70 3.9 24.3 1.0
CB A:VAL67 3.9 17.5 1.0
OH A:TYR99 4.0 28.1 1.0
N A:VAL67 4.0 17.7 1.0
CA A:VAL67 4.0 18.9 1.0
CE A:MET45 4.0 23.5 1.0
CG2 A:VAL67 4.2 17.3 1.0
C2 A:EDO502 4.2 45.6 1.0
CE1 A:HIS70 4.2 25.7 1.0
OE1 A:GLU63 4.3 21.0 1.0
CE1 A:PHE9 4.3 26.7 1.0
CB A:LYS66 4.4 23.8 1.0
C1 A:EDO502 4.4 42.1 1.0
C A:LYS66 4.4 18.8 1.0
O A:GLU63 4.5 16.0 1.0
CD1 A:TYR7 4.8 15.2 1.0
O A:LYS66 4.8 16.2 1.0
CE1 A:TYR7 4.8 13.8 1.0
CE2 A:PHE9 4.9 26.0 1.0

Chlorine binding site 3 out of 8 in 6tds

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:29.3
occ:1.00
 O B:HOH319 2.6 25.2 1.0
N B:THR5 3.2 13.3 1.0
CA B:ARG4 3.7 14.1 1.0
OG1 B:THR5 3.8 20.2 1.0
CB B:THR5 3.9 18.6 1.0
O B:HOH311 3.9 16.2 1.0
CB B:ARG4 3.9 15.5 1.0
C B:ARG4 3.9 13.2 1.0
CA B:THR5 4.0 17.0 1.0
O B:THR5 4.2 14.5 1.0
CG B:ARG4 4.5 16.7 1.0
C B:THR5 4.6 14.9 1.0
O B:GLN3 4.7 14.1 1.0
O B:GLY30 4.8 14.9 1.0
N B:ARG4 4.9 14.1 1.0

Chlorine binding site 4 out of 8 in 6tds

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl410

b:43.8
occ:1.00
 NH2 C:ARG169 2.6 32.9 1.0
NH1 C:ARG169 2.8 30.0 1.0
CZ C:ARG169 3.1 28.1 1.0
CD2 A:LEU110 4.0 34.2 1.0
CD C:ARG108 4.2 45.1 1.0
O C:ASP106 4.2 45.4 1.0
NE C:ARG169 4.4 28.4 1.0
O A:HOH677 4.4 20.0 1.0
CB A:SER2 4.6 31.1 1.0
OG A:SER2 4.9 32.4 1.0
CG C:ARG108 4.9 43.0 1.0

Chlorine binding site 5 out of 8 in 6tds

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl411

b:57.8
occ:1.00
 NH2 C:ARG202 2.6 15.7 1.0
NA C:NA406 3.4 33.2 1.0
CZ C:ARG202 3.7 15.6 1.0
NH1 C:ARG202 3.9 13.7 1.0
CG2 C:THR200 4.1 24.1 1.0
OG1 C:THR200 4.4 19.5 1.0
CB C:THR200 4.6 20.6 1.0
NE C:ARG202 4.8 14.3 1.0

Chlorine binding site 6 out of 8 in 6tds

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl412

b:23.3
occ:1.00
 NH1 C:ARG234 3.2 11.9 1.0
O D:HOH340 3.2 17.8 1.0
NH2 C:ARG234 3.3 14.2 1.0
O D:HOH324 3.3 20.1 1.0
NE1 C:TRP244 3.4 13.7 1.0
CH2 C:TRP204 3.7 17.5 1.0
CZ C:ARG234 3.7 14.0 1.0
CE D:MET100 3.7 27.0 1.0
O D:HOH307 3.8 22.5 1.0
O D:VAL10 4.0 13.3 1.0
SD D:MET100 4.1 23.1 1.0
CD1 C:TRP244 4.1 12.3 1.0
CB D:TYR11 4.1 13.1 1.0
CZ2 C:TRP204 4.3 17.6 1.0
CE2 C:TRP244 4.5 12.6 1.0
CZ3 C:TRP204 4.6 18.3 1.0
O D:HOH336 4.7 14.5 1.0
CB D:MET100 4.8 19.2 1.0
CA D:TYR11 4.9 11.4 1.0
C D:VAL10 4.9 11.3 1.0

Chlorine binding site 7 out of 8 in 6tds

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl413

b:29.9
occ:1.00
 NH2 C:ARG82 2.6 31.7 1.0
O C:LEU78 2.8 20.6 1.0
OH C:TYR118 3.0 17.9 1.0
CZ C:ARG82 3.3 40.4 1.0
CD2 C:LEU78 3.3 20.5 1.0
CB C:HIS93 3.4 15.8 1.0
NE C:ARG82 3.5 36.5 1.0
C C:LEU78 3.5 22.6 1.0
CA C:LEU78 3.5 22.7 1.0
CE1 C:TYR118 3.6 14.3 1.0
CZ C:TYR118 3.7 13.8 1.0
CB C:LEU78 3.7 21.8 1.0
CG C:HIS93 3.8 16.9 1.0
ND1 C:HIS93 4.1 18.0 1.0
CB C:ARG82 4.1 26.0 1.0
CG C:LEU78 4.1 20.1 1.0
N C:ARG82 4.2 21.3 1.0
NH1 C:ARG82 4.3 34.5 1.0
CD C:ARG82 4.4 34.6 1.0
CA C:ARG82 4.5 22.4 1.0
CG C:ARG82 4.5 29.5 1.0
CB C:LEU81 4.6 17.7 1.0
CA C:HIS93 4.6 15.7 1.0
OG C:SER13 4.7 20.4 1.0
OE1 C:GLN87 4.7 22.5 1.0
N C:GLY79 4.8 22.6 1.0
CD2 C:HIS93 4.8 16.5 1.0
CD1 C:TYR118 4.9 13.1 1.0
C C:HIS93 4.9 15.0 1.0
N C:LEU78 4.9 20.3 1.0
CE2 C:TYR118 5.0 14.3 1.0

Chlorine binding site 8 out of 8 in 6tds

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash


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 the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl414

b:48.8
occ:1.00
 CG C:ASP77 3.4 26.3 1.0
OD2 C:ASP77 3.5 30.7 1.0
OD1 C:ASP77 3.5 26.9 1.0
CZ2 C:TRP147 4.0 20.7 1.0
CB C:ASP77 4.0 23.3 1.0
CG2 C:THR143 4.5 15.8 1.0
O C:HOH504 4.6 27.2 1.0
CH2 C:TRP147 4.6 22.3 1.0
CE2 C:TYR123 4.6 15.2 1.0
OG1 C:THR143 4.8 15.2 1.0
CA C:ASP77 4.9 22.4 1.0
CE2 C:TRP147 4.9 19.1 1.0

Reference:

R.Anjanappa, M.Garcia-Alai, J.D.Kopicki, J.Lockhauserbaumer, M.Aboelmagd, J.Hinrichs, I.M.Nemtanu, C.Uetrecht, M.Zacharias, S.Springer, R.Meijers. Structures of Peptide-Free and Partially Loaded Mhc Class I Molecules Reveal Mechanisms of Peptide Selection. Nat Commun V. 11 1314 2020.
ISSN: ESSN 2041-1723
PubMed: 32161266
DOI: 10.1038/S41467-020-14862-4
Page generated: Sat Dec 12 13:43:54 2020

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