Sodium in PDB 7jyw: Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope

Protein crystallography data

The structure of Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope, PDB code: 7jyw was solved by S.Gras, A.T.Nguyen, C.Szeto, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.16 / 2.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.295, 87.295, 312.441, 90, 90, 120
R / Rfree (%) 24.1 / 27.5

Other elements in 7jyw:

The structure of Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Nickel (Ni) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope (pdb code 7jyw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope, PDB code: 7jyw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7jyw

Go back to Sodium Binding Sites List in 7jyw
Sodium binding site 1 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope


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 A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:93.2
occ:1.00
OE2 A:GLU19 3.1 136.9 1.0
NH2 A:ARG79 3.1 135.1 1.0
CZ A:ARG79 3.9 148.7 1.0
NE A:ARG79 4.0 127.0 1.0
NE A:ARG75 4.0 125.8 1.0
CD A:PRO20 4.2 92.7 1.0
CD A:GLU19 4.3 142.9 1.0
CD A:ARG75 4.3 111.2 1.0
CA A:GLU19 4.7 99.3 1.0
CZ A:ARG75 4.8 138.3 1.0
CG A:GLU19 5.0 114.3 1.0
O A:GLY18 5.0 107.3 1.0

Sodium binding site 2 out of 2 in 7jyw

Go back to Sodium Binding Sites List in 7jyw
Sodium binding site 2 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope


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 A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:102.3
occ:1.00
N A:ALA135 3.1 97.9 1.0
CE A:LYS144 3.4 138.6 1.0
CA A:THR134 3.7 98.8 1.0
CD A:LYS144 3.7 127.3 1.0
O A:TRP133 3.9 105.2 1.0
C A:THR134 3.9 101.6 1.0
O A:ALA135 3.9 101.6 1.0
NZ A:LYS144 4.0 147.7 1.0
CA A:ALA135 4.1 97.8 1.0
CB A:ALA135 4.1 98.6 1.0
CG2 A:THR134 4.3 100.5 1.0
C A:ALA135 4.5 101.9 1.0
CB A:THR134 4.5 103.9 1.0
N A:THR134 4.6 99.7 1.0
NZ A:LYS127 4.6 144.4 1.0
C A:TRP133 4.6 104.9 1.0

Reference:

A.T.Nguyen, C.Szeto, J.Rossjohn, S.Gras. Crystal Structure of Hla A*2402 in Complex with Iyfspirvtf, An 10-Mer Influenza B Epitope Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Sat Apr 17 17:08:57 2021

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