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Sodium in PDB 6pte: Crystal Structure of Ilnamitki Peptide Bound to Hla-A2

Protein crystallography data

The structure of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2, PDB code: 6pte was solved by A.R.Smith, A.Arbuiso, G.L.J.Keller, B.M.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.82 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.429, 84.106, 85.363, 90.01, 90.06, 90.02
R / Rfree (%) 15.9 / 18.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2 (pdb code 6pte). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2, PDB code: 6pte:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6pte

Go back to Sodium Binding Sites List in 6pte
Sodium binding site 1 out of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2


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 Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:36.5
occ:1.00
 O B:HOH391 2.4 32.0 1.0
O B:LEU88 2.5 25.1 1.0
O B:HOH386 2.5 31.6 1.0
O B:HOH384 2.5 32.3 1.0
OD1 B:ASN84 2.6 22.5 1.0
O B:HIS85 2.6 14.4 1.0
CG B:ASN84 3.4 25.2 1.0
C B:HIS85 3.5 15.0 1.0
C B:LEU88 3.7 24.1 1.0
ND2 B:ASN84 3.7 26.1 1.0
N B:HIS85 3.9 17.2 1.0
CA B:VAL86 4.2 15.0 1.0
N B:VAL86 4.3 14.4 1.0
N B:LEU88 4.4 18.2 1.0
CA B:HIS85 4.4 15.8 1.0
CA B:LEU88 4.4 18.5 1.0
CB B:LEU88 4.5 15.9 1.0
C B:VAL86 4.5 15.0 1.0
O B:VAL86 4.6 18.8 1.0
C B:SER89 4.6 28.8 1.0
CB B:ASN84 4.7 22.5 1.0
O B:SER89 4.7 28.8 1.0
N B:SER89 4.7 23.9 1.0
C B:ASN84 4.8 18.2 1.0
CA B:SER89 4.9 28.5 1.0
N B:GLN90 4.9 25.8 1.0
CA B:ASN84 5.0 14.9 1.0

Sodium binding site 2 out of 4 in 6pte

Go back to Sodium Binding Sites List in 6pte
Sodium binding site 2 out of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2


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 Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:30.4
occ:1.00
 O F:HOH388 2.4 21.9 1.0
O F:LEU88 2.4 28.4 1.0
O F:HIS85 2.4 16.3 1.0
O F:HOH396 2.4 25.6 1.0
OD1 F:ASN84 2.5 19.0 1.0
O F:HOH391 2.6 30.8 1.0
C F:HIS85 3.4 14.8 1.0
CG F:ASN84 3.4 22.5 1.0
C F:LEU88 3.6 24.3 1.0
ND2 F:ASN84 3.7 26.4 1.0
N F:HIS85 3.8 13.9 1.0
CA F:VAL86 4.1 15.1 1.0
N F:VAL86 4.1 13.4 1.0
N F:LEU88 4.2 19.0 1.0
CA F:LEU88 4.2 21.0 1.0
CA F:HIS85 4.2 13.7 1.0
CB F:LEU88 4.3 17.1 1.0
C F:VAL86 4.3 16.5 1.0
O F:VAL86 4.4 17.9 1.0
C F:SER89 4.6 27.2 1.0
O F:SER89 4.6 29.1 1.0
N F:SER89 4.6 25.6 1.0
CB F:ASN84 4.7 16.8 1.0
C F:ASN84 4.8 12.2 1.0
CA F:SER89 4.8 28.1 1.0
N F:GLN90 4.9 24.0 1.0
CA F:ASN84 4.9 12.8 1.0

Sodium binding site 3 out of 4 in 6pte

Go back to Sodium Binding Sites List in 6pte
Sodium binding site 3 out of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2


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 Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:30.3
occ:1.00
 O I:HOH385 2.4 34.0 1.0
O I:HOH381 2.5 30.7 1.0
O I:LEU88 2.5 22.9 1.0
O I:HIS85 2.5 13.9 1.0
OD1 I:ASN84 2.6 22.5 1.0
CG I:ASN84 3.4 24.7 1.0
C I:HIS85 3.5 17.6 1.0
C I:LEU88 3.7 24.5 1.0
ND2 I:ASN84 3.7 28.6 1.0
N I:HIS85 3.8 16.7 1.0
CA I:VAL86 4.2 14.2 1.0
N I:VAL86 4.2 12.5 1.0
CA I:HIS85 4.3 17.5 1.0
N I:LEU88 4.4 18.2 1.0
CA I:LEU88 4.4 19.6 1.0
CB I:LEU88 4.5 17.4 1.0
C I:VAL86 4.5 15.4 1.0
O I:VAL86 4.5 18.9 1.0
CB I:ASN84 4.7 19.9 1.0
C I:SER89 4.7 30.4 1.0
O I:SER89 4.7 31.6 1.0
C I:ASN84 4.8 17.2 1.0
N I:SER89 4.8 26.3 1.0
CA I:ASN84 4.9 14.9 1.0
CA I:SER89 5.0 30.7 1.0
N I:GLN90 5.0 27.2 1.0

Sodium binding site 4 out of 4 in 6pte

Go back to Sodium Binding Sites List in 6pte
Sodium binding site 4 out of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2


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 Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na201

b:26.7
occ:1.00
 O L:HOH392 2.4 28.7 1.0
O L:HOH384 2.4 26.4 1.0
O L:LEU88 2.4 23.6 1.0
OD1 L:ASN84 2.5 19.6 1.0
O L:HIS85 2.5 17.6 1.0
O L:HOH395 2.8 37.4 1.0
CG L:ASN84 3.4 20.7 1.0
C L:HIS85 3.5 15.3 1.0
C L:LEU88 3.6 21.7 1.0
ND2 L:ASN84 3.6 23.5 1.0
N L:HIS85 3.9 11.5 1.0
CA L:VAL86 4.2 14.0 1.0
N L:LEU88 4.2 16.9 1.0
N L:VAL86 4.2 13.1 1.0
CA L:LEU88 4.3 18.0 1.0
CB L:LEU88 4.3 15.3 1.0
CA L:HIS85 4.3 12.9 1.0
C L:VAL86 4.4 15.8 1.0
O L:VAL86 4.5 18.2 1.0
O L:SER89 4.5 28.8 1.0
C L:SER89 4.5 26.6 1.0
N L:SER89 4.6 23.5 1.0
CB L:ASN84 4.7 16.9 1.0
C L:ASN84 4.8 11.8 1.0
CA L:SER89 4.8 27.5 1.0
N L:GLN90 4.9 24.5 1.0
CA L:ASN84 4.9 11.1 1.0

Reference:

T.P.Riley, G.L.J.Keller, A.R.Smith, L.M.Davancaze, A.G.Arbuiso, J.R.Devlin, B.M.Baker. Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol V. 10 2047 2019.
ISSN: ESSN 1664-3224
PubMed: 31555277
DOI: 10.3389/FIMMU.2019.02047
Page generated: Tue Oct 8 12:45:02 2024

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