Atomistry » Sodium » PDB 9dpp-9ewc » 9dy8
Atomistry »
  Sodium »
    PDB 9dpp-9ewc »
      9dy8 »

Sodium in PDB 9dy8: Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B

Enzymatic activity of Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B

All present enzymatic activity of Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B, PDB code: 9dy8 was solved by L.D.Murdolo, J.C.Maddumage, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.16 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.821, 81.423, 110.345, 90, 90, 90
R / Rfree (%) 19.6 / 24.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B (pdb code 9dy8). 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 Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B, PDB code: 9dy8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 9dy8

Go back to Sodium Binding Sites List in 9dy8
Sodium binding site 1 out of 4 in the Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B


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 Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:18.3
occ:1.00
 OE1 A:GLN96 2.8 13.5 1.0
N A:GLY120 2.9 17.2 1.0
O A:THR94 3.1 16.5 1.0
N A:ASP119 3.1 13.9 1.0
O A:ALA117 3.1 13.9 1.0
C A:ALA117 3.4 18.8 1.0
C A:TYR118 3.4 18.2 1.0
CA A:TYR118 3.5 21.6 1.0
N A:TYR118 3.6 12.0 1.0
C A:THR94 3.7 13.5 1.0
CD A:GLN96 3.7 12.0 1.0
CA A:GLY120 3.7 21.3 1.0
CA A:ASP119 3.8 15.1 1.0
C A:ASP119 3.8 16.1 1.0
CG2 A:THR94 3.8 11.4 1.0
CG A:GLN96 3.8 12.7 1.0
N A:GLN96 3.9 11.0 1.0
CB A:THR94 3.9 13.2 1.0
CB A:ALA117 4.0 9.2 1.0
NE2 B:HIS32 4.1 21.0 1.0
CB A:GLN96 4.1 8.1 1.0
CE1 B:HIS32 4.1 18.3 1.0
CA A:LEU95 4.2 11.4 1.0
N A:LEU95 4.2 12.4 1.0
O A:TYR118 4.2 12.9 1.0
CA A:ALA117 4.3 10.7 1.0
C A:LEU95 4.4 14.9 1.0
CA A:THR94 4.5 8.1 1.0
CA A:GLN96 4.6 9.9 1.0
C A:GLY120 4.6 17.6 1.0
N A:LYS121 4.7 11.5 1.0
NE2 A:GLN96 5.0 10.8 1.0
O A:ASP119 5.0 19.0 1.0

Sodium binding site 2 out of 4 in 9dy8

Go back to Sodium Binding Sites List in 9dy8
Sodium binding site 2 out of 4 in the Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B


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 Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:20.8
occ:1.00
 N A:ARG14 2.6 9.3 1.0
O A:HOH470 2.8 26.4 1.0
O A:GLY18 3.0 19.0 1.0
N A:PRO20 3.4 17.3 1.0
CD A:PRO20 3.4 14.7 1.0
C A:ARG14 3.4 14.6 1.0
CA A:SER13 3.5 11.4 1.0
C A:GLU19 3.5 19.3 1.0
C A:SER13 3.5 13.8 1.0
CA A:ARG14 3.5 11.0 1.0
CG A:PRO20 3.5 15.5 1.0
CG A:ARG14 3.6 13.6 1.0
O A:ARG14 3.6 19.7 1.0
CB A:SER13 3.8 14.3 1.0
CA A:PRO20 3.8 9.4 1.0
CA A:GLU19 3.9 16.8 1.0
N A:PRO15 3.9 19.1 1.0
C A:GLY18 4.0 23.6 1.0
O A:GLU19 4.0 13.7 1.0
CB A:ARG14 4.2 12.6 1.0
O A:HOH437 4.2 18.3 1.0
CB A:PRO20 4.3 14.7 1.0
N A:GLU19 4.4 18.3 1.0
CA A:PRO15 4.5 16.8 1.0
CD A:PRO15 4.7 16.2 1.0
O A:SER13 4.7 12.6 1.0
O A:VAL12 4.7 15.1 1.0
N A:SER13 4.8 14.6 1.0
CD A:ARG14 4.9 22.8 1.0
OG A:SER13 4.9 15.9 1.0

Sodium binding site 3 out of 4 in 9dy8

Go back to Sodium Binding Sites List in 9dy8
Sodium binding site 3 out of 4 in the Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B


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 Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:46.3
occ:1.00
 CD A:PRO47 3.9 15.1 1.0
CE2 A:TRP60 4.1 17.4 1.0
CG A:PRO47 4.1 11.9 1.0
NE1 A:TRP60 4.1 27.9 1.0
CD2 A:TRP60 4.2 22.3 1.0
CD1 A:TRP60 4.3 24.0 1.0
CG A:TRP60 4.4 26.1 1.0
CZ2 A:TRP60 4.5 18.7 1.0
CE3 A:TRP60 4.8 25.6 1.0

Sodium binding site 4 out of 4 in 9dy8

Go back to Sodium Binding Sites List in 9dy8
Sodium binding site 4 out of 4 in the Crystal Structure of Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B


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 Hla-B*18:01 in Complex with Pemtffsvk, An 9-Mer Epitope From Influenza B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:27.6
occ:1.00
 OH A:TYR118 2.7 14.3 1.0
O A:LEU78 2.7 14.5 1.0
O A:HOH461 2.7 23.8 1.0
CD2 A:LEU78 3.5 10.6 1.0
CZ A:TYR118 3.5 13.5 1.0
CB A:HIS93 3.6 13.8 1.0
CE1 A:TYR118 3.6 10.9 1.0
C A:LEU78 3.6 11.9 1.0
CA A:LEU78 3.8 16.3 1.0
CB A:LEU78 3.8 14.3 1.0
CG A:HIS93 3.9 12.2 1.0
CB A:ARG82 3.9 23.0 1.0
N A:ARG82 3.9 13.1 1.0
CD2 A:HIS93 4.0 15.1 1.0
CA A:ARG82 4.2 19.8 1.0
CG A:LEU78 4.3 8.9 1.0
CG A:ARG82 4.4 30.9 1.0
CB A:LEU81 4.5 10.6 1.0
CD A:ARG82 4.5 44.8 1.0
OE1 A:GLN87 4.5 19.6 1.0
C A:LEU81 4.7 21.0 1.0
N A:ARG79 4.7 13.6 1.0
CE2 A:TYR118 4.8 12.6 1.0
CA A:HIS93 4.9 14.2 1.0
CD1 A:TYR118 4.9 13.6 1.0
OG A:SER13 4.9 15.9 1.0
ND1 A:HIS93 4.9 19.1 1.0

Reference:

L.D.Murdolo, S.Liwei Leong, J.C.Maddumage, N.A.Mifsud, D.S.M.Chatzileontiadou, E.J.Grant, S.Gras. Characterisation of An Influenza B Virus-Derived Peptide Presented By Hla-B*18:01. Biochem.J. V. 482 811 2025.
ISSN: ESSN 1470-8728
PubMed: 40587260
DOI: 10.1042/BCJ20240739
Page generated: Mon Aug 18 16:46:58 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy