Atomistry » Sodium » PDB 6p9k-6puk » 6pte
Atomistry »
  Sodium »
    PDB 6p9k-6puk »
      6pte »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy