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Sodium 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:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Without Peptide Bound After Nacl Wash, PDB code: 6tds:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 6tds

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Sodium binding site 1 out of 15 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 Sodium with other atoms in the Na 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:Na503

b:36.2
occ:1.00
 NA A:NA507 2.2 32.3 1.0
N A:THR271 3.1 19.8 1.0
CD1 A:LEU270 3.5 27.2 1.0
O A:THR271 3.7 16.4 1.0
CA A:LEU270 3.8 21.1 1.0
O A:PRO269 3.9 20.4 1.0
C A:LEU270 4.0 20.2 1.0
CA A:THR271 4.0 18.9 1.0
CB A:THR271 4.1 19.9 1.0
C A:THR271 4.3 19.8 1.0
OG1 A:THR271 4.4 18.0 1.0
CG A:LEU270 4.7 23.8 1.0
CB A:LEU270 4.7 23.2 1.0
C A:PRO269 4.7 24.5 1.0
N A:LEU270 4.7 24.3 1.0

Sodium binding site 2 out of 15 in 6tds

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Sodium binding site 2 out of 15 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 Sodium with other atoms in the Na 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:Na504

b:24.5
occ:1.00
 N A:GLY120 2.8 19.6 1.0
OE1 A:GLN96 2.9 12.0 1.0
O A:THR94 3.0 13.3 1.0
N A:ASP119 3.0 16.5 1.0
C A:TYR118 3.4 11.7 1.0
O A:ALA117 3.5 11.8 1.0
CA A:ASP119 3.5 18.4 1.0
C A:THR94 3.6 12.7 1.0
CA A:GLY120 3.6 18.3 1.0
CA A:TYR118 3.6 11.5 1.0
C A:ASP119 3.6 18.7 1.0
C A:ALA117 3.7 11.2 1.0
CB A:THR94 3.7 13.2 1.0
CG2 A:THR94 3.7 14.8 1.0
N A:TYR118 3.7 11.8 1.0
CD A:GLN96 3.8 12.0 1.0
CG A:GLN96 4.0 13.9 1.0
CB A:ALA117 4.0 10.2 1.0
NE2 B:HIS32 4.0 14.9 1.0
N A:GLN96 4.0 11.8 1.0
CE1 B:HIS32 4.1 16.1 1.0
CA A:VAL95 4.1 13.5 1.0
C A:VAL95 4.1 11.1 1.0
O A:TYR118 4.2 10.6 1.0
N A:VAL95 4.2 12.5 1.0
CB A:GLN96 4.3 12.8 1.0
CA A:THR94 4.4 12.8 1.0
CA A:ALA117 4.5 12.0 1.0
C A:GLY120 4.6 19.1 1.0
N A:LYS121 4.6 22.1 1.0
CA A:GLN96 4.8 12.2 1.0
OG1 A:THR94 4.9 13.6 1.0
O A:ASP119 4.9 19.2 1.0

Sodium binding site 3 out of 15 in 6tds

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Sodium binding site 3 out of 15 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 Sodium with other atoms in the Na 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
A:Na505

b:21.2
occ:1.00
 OE1 A:GLU63 2.8 21.0 1.0
OH A:TYR7 2.8 19.8 1.0
OH A:TYR59 2.9 12.8 1.0
CG2 A:VAL34 3.5 15.3 1.0
CD A:GLU63 3.6 18.5 1.0
CG A:GLU63 3.7 17.1 1.0
CZ A:TYR7 3.7 15.8 1.0
CE1 A:TYR7 3.7 13.8 1.0
CZ A:TYR59 3.8 16.5 1.0
CG1 A:VAL34 3.8 13.9 1.0
CE A:MET45 4.0 23.5 1.0
CE1 A:PHE33 4.2 13.4 1.0
CB A:VAL34 4.2 14.6 1.0
CB A:GLU63 4.2 17.0 1.0
C1 A:EDO501 4.2 22.9 1.0
CE2 A:TYR59 4.2 16.4 1.0
O1 A:EDO501 4.5 19.0 1.0
OH A:TYR171 4.5 18.2 1.0
CZ A:PHE33 4.7 15.0 1.0
CE1 A:TYR59 4.7 17.9 1.0
CG A:MET45 4.7 20.5 1.0
OE2 A:GLU63 4.7 20.2 1.0
SD A:MET45 4.9 23.5 1.0
CE2 A:TYR7 5.0 16.5 1.0

Sodium binding site 4 out of 15 in 6tds

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Sodium binding site 4 out of 15 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 Sodium with other atoms in the Na 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
A:Na506

b:40.6
occ:1.00
 O A:GLU177 2.4 18.5 1.0
O A:LYS176 2.9 26.5 1.0
C A:GLU177 2.9 19.9 1.0
O A:GLN180 3.1 21.1 1.0
CB A:ARG181 3.3 19.5 1.0
CA A:GLU177 3.3 25.5 1.0
C A:GLN180 3.5 21.1 1.0
N A:ARG181 3.7 19.9 1.0
C A:LYS176 3.8 26.2 1.0
CA A:ARG181 3.8 17.6 1.0
N A:THR178 3.9 20.5 1.0
N A:GLU177 3.9 25.7 1.0
CG A:ARG181 4.0 19.5 1.0
N A:GLN180 4.4 18.7 1.0
CA A:GLN180 4.5 18.9 1.0
CB A:GLU177 4.6 26.9 1.0
CA A:THR178 4.6 22.1 1.0
C A:THR178 4.7 21.2 1.0
CB A:GLN180 4.8 20.1 1.0
O A:THR178 4.9 25.1 1.0
CD A:ARG181 5.0 18.3 1.0

Sodium binding site 5 out of 15 in 6tds

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Sodium binding site 5 out of 15 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 Sodium with other atoms in the Na 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
A:Na507

b:32.3
occ:1.00
 NA A:NA503 2.2 36.2 1.0
O A:PRO269 2.8 20.4 1.0
C A:PRO269 3.9 24.5 1.0
CA A:LEU270 3.9 21.1 1.0
CD A:LYS268 4.2 31.2 1.0
CD1 A:LEU270 4.2 27.2 1.0
N A:LEU270 4.3 24.3 1.0
N A:THR271 4.5 19.8 1.0
CB A:LYS268 4.5 32.0 1.0
O A:LYS268 4.6 26.6 1.0
CB A:LEU270 4.7 23.2 1.0
C A:LEU270 4.7 20.2 1.0
C A:LYS268 4.8 29.0 1.0
CG A:LYS268 5.0 34.7 1.0

Sodium binding site 6 out of 15 in 6tds

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Sodium binding site 6 out of 15 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 Sodium with other atoms in the Na 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
A:Na508

b:45.2
occ:1.00
 O A:HOH606 3.3 32.1 1.0
OD1 A:ASP77 3.8 29.6 1.0
CG A:ASP77 3.9 25.7 1.0
CG2 A:THR80 4.0 27.2 1.0
CB A:ASP77 4.1 26.2 1.0
OG1 A:THR143 4.1 15.9 1.0
CB A:THR80 4.3 27.1 1.0
CA A:ASP77 4.4 22.6 1.0
CG A:LEU81 4.4 17.9 1.0
CD2 A:LEU81 4.5 18.8 1.0
OD2 A:ASP77 4.5 25.5 1.0
OH A:TYR123 4.7 14.3 1.0
OG1 A:THR80 4.7 34.8 1.0
O A:ASP77 4.8 17.3 1.0
CG2 A:THR143 4.8 14.8 1.0
CE2 A:TYR123 4.9 14.2 1.0
O A:HOH679 4.9 37.5 1.0
CD1 A:LEU81 4.9 18.1 1.0
O A:HOH609 5.0 19.1 1.0

Sodium binding site 7 out of 15 in 6tds

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Sodium binding site 7 out of 15 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 Sodium with other atoms in the Na 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
B:Na203

b:22.8
occ:1.00
 O B:HOH347 2.3 24.9 1.0
N B:GLN3 3.1 12.6 1.0
CA B:ILE2 3.4 16.6 1.0
O B:GLN3 3.5 14.1 1.0
C B:ILE2 3.8 12.7 1.0
CB B:ILE2 4.1 17.4 1.0
CA B:GLN3 4.2 13.7 1.0
CG2 B:ILE2 4.2 17.5 1.0
C B:GLN3 4.2 13.7 1.0
CG1 B:ILE2 4.3 19.8 1.0
O B:MET1 4.4 17.1 1.0
N B:ILE2 4.4 17.9 1.0
CB B:GLN3 4.8 13.1 1.0
C B:MET1 4.9 22.3 1.0

Sodium binding site 8 out of 15 in 6tds

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Sodium binding site 8 out of 15 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 Sodium with other atoms in the Na 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
B:Na204

b:22.0
occ:1.00
 O B:ILE8 2.8 13.5 1.0
O B:HOH348 2.9 28.8 1.0
O B:HOH318 3.0 17.0 1.0
CG1 B:VAL94 3.7 20.8 1.0
C B:ILE8 3.9 12.8 1.0
O B:HOH314 4.0 14.9 1.0
CA B:GLN9 4.1 10.8 1.0
N B:GLN9 4.4 11.5 1.0
CG2 B:VAL94 4.5 19.6 1.0
CB B:VAL94 4.7 19.1 1.0
CG B:GLN9 4.8 11.9 1.0
N B:VAL10 4.9 12.1 0.5
CB B:GLN9 4.9 11.6 1.0
N B:VAL10 4.9 12.8 0.5
O B:HOH334 4.9 21.1 1.0

Sodium binding site 9 out of 15 in 6tds

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Sodium binding site 9 out of 15 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 Sodium with other atoms in the Na binding site number 9 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:Na404

b:19.7
occ:1.00
 O C:HOH573 2.6 19.0 1.0
ND1 C:HIS188 2.6 16.1 1.0
O C:LYS186 2.7 13.7 0.5
O C:LYS186 3.1 13.0 0.5
O C:HOH501 3.1 24.3 1.0
C C:LYS186 3.2 15.1 0.5
C C:LYS186 3.4 16.0 0.5
CE1 C:HIS188 3.4 15.9 1.0
CD1 C:LEU206 3.5 16.4 1.0
CG C:LYS186 3.7 19.6 0.5
N C:THR187 3.7 13.2 1.0
C C:THR187 3.7 14.2 1.0
CG C:HIS188 3.8 14.2 1.0
CB C:LYS186 3.8 18.5 0.5
O C:THR187 3.9 13.8 1.0
CB C:LYS186 3.9 15.5 0.5
CA C:THR187 4.0 14.7 1.0
N C:HIS188 4.1 14.9 1.0
CB C:HIS188 4.2 15.3 1.0
CA C:LYS186 4.2 14.6 0.5
CA C:LYS186 4.2 16.3 0.5
CD C:LYS186 4.2 19.6 0.5
CG C:LEU206 4.3 16.4 1.0
CB C:LEU206 4.6 15.6 1.0
CE C:LYS186 4.6 17.9 0.5
NE2 C:HIS188 4.6 14.5 1.0
CA C:HIS188 4.8 14.1 1.0
CD2 C:HIS188 4.8 14.4 1.0

Sodium binding site 10 out of 15 in 6tds

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Sodium binding site 10 out of 15 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 Sodium with other atoms in the Na binding site number 10 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:Na405

b:21.3
occ:1.00
 OG1 C:THR10 2.8 15.2 1.0
O D:LEU55 2.8 16.5 1.0
O C:ILE23 3.4 15.3 1.0
CB C:THR10 3.5 16.4 1.0
C D:LEU55 3.7 15.9 1.0
N C:THR10 3.7 14.4 1.0
O C:PHE8 3.7 12.1 1.0
C C:PHE9 4.0 14.8 0.6
C C:PHE8 4.0 10.8 1.0
C C:PHE9 4.0 12.9 0.4
CG2 C:ILE23 4.1 13.2 1.0
CA D:SER56 4.1 15.1 1.0
CE2 D:PHE57 4.1 12.6 1.0
C C:ILE23 4.1 13.4 1.0
N C:PHE9 4.2 11.3 0.4
CD2 D:PHE57 4.2 12.0 1.0
CA C:THR10 4.2 15.9 1.0
CA C:PHE9 4.3 14.4 0.6
N D:SER56 4.3 14.2 1.0
CA C:PHE9 4.3 11.6 0.4
N C:PHE9 4.3 12.7 0.6
CB C:PHE8 4.3 11.8 1.0
CB C:ILE23 4.4 14.6 1.0
CG2 C:VAL25 4.4 13.1 1.0
CB D:LEU55 4.5 16.5 1.0
CG D:LEU55 4.6 16.4 1.0
O C:PHE9 4.6 15.9 0.6
O C:PHE9 4.7 13.8 0.4
CA D:LEU55 4.7 17.2 1.0
CG2 C:THR10 4.8 16.2 1.0
CD2 D:LEU55 4.9 17.9 1.0
N C:VAL25 4.9 14.4 1.0
N C:ALA24 4.9 14.8 1.0
CA C:ILE23 4.9 14.3 1.0
CA C:PHE8 4.9 10.4 1.0
C D:SER56 4.9 14.9 1.0
CA C:ALA24 4.9 13.5 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: Tue Oct 8 13:55:25 2024

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