Sodium in PDB 7kgp: Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324

Protein crystallography data

The structure of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324, PDB code: 7kgp was solved by C.Szeto, D.S.M.Chatzileontiadou, A.Riboldi-Tunnicliffe, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.192, 79.546, 111.578, 90, 90, 90
R / Rfree (%) 19.4 / 20.4

Other elements in 7kgp:

The structure of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 (pdb code 7kgp). 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-A*0201 in Complex with Sars-Cov-2 N316-324, PDB code: 7kgp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7kgp

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Sodium binding site 1 out of 4 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


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*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:39.3
occ:1.00
O A:HOH766 2.4 46.0 1.0
O A:HOH651 2.8 33.2 1.0
NE2 A:HIS3 2.9 23.6 1.0
N A:GLY1 3.1 31.7 1.0
NE1 A:TRP107 3.1 27.0 1.0
O A:GLY1 3.3 29.7 1.0
CD2 A:HIS3 3.6 22.6 1.0
CE2 A:TRP107 4.1 26.5 1.0
CE1 A:HIS3 4.1 22.9 1.0
CD1 A:TRP107 4.1 27.1 1.0
C A:GLY1 4.1 29.2 1.0
CA A:GLY1 4.2 31.1 1.0
CZ2 A:TRP107 4.3 26.9 1.0
OE1 A:GLN180 4.6 28.3 1.0
O A:SER105 4.6 33.2 1.0
CG A:HIS3 4.9 20.8 1.0
CG A:GLN180 5.0 24.6 1.0

Sodium binding site 2 out of 4 in 7kgp

Go back to Sodium Binding Sites List in 7kgp
Sodium binding site 2 out of 4 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


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*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:31.4
occ:1.00
OG B:SER28 2.8 17.1 1.0
O B:HOH264 2.9 22.7 1.0
CB A:GLU232 3.1 18.8 1.0
CG A:GLU232 3.3 27.3 1.0
O B:HOH206 3.3 35.7 1.0
O B:HOH275 3.4 35.5 1.0
CB B:SER28 3.7 17.1 1.0
CE2 B:TYR26 3.9 16.9 1.0
O A:HOH715 4.1 33.5 1.0
O B:HOH250 4.2 18.9 1.0
O B:HOH329 4.2 36.8 1.0
O A:HOH724 4.3 61.5 1.0
CD A:GLU232 4.5 38.2 1.0
O B:HOH320 4.5 32.8 1.0
CA A:GLU232 4.6 16.1 1.0
CD2 B:TYR26 4.6 16.1 1.0
OE1 A:GLU232 4.7 40.8 1.0
CZ B:TYR26 4.8 18.1 1.0
OH B:TYR26 4.8 21.6 1.0
O A:THR233 4.8 16.4 1.0
CE B:LYS6 4.9 46.4 1.0

Sodium binding site 3 out of 4 in 7kgp

Go back to Sodium Binding Sites List in 7kgp
Sodium binding site 3 out of 4 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


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-A*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:35.7
occ:1.00
OE1 A:GLN224 2.5 30.1 1.0
NE A:ARG219 2.9 26.6 1.0
NH2 A:ARG219 3.5 28.4 1.0
CD A:GLN224 3.6 29.1 1.0
CZ A:ARG219 3.6 25.5 1.0
CB A:ARG219 3.6 20.9 1.0
O A:HOH890 3.7 36.8 1.0
CG A:ARG219 3.8 23.9 1.0
CD A:ARG219 3.9 26.4 1.0
NE2 A:GLN224 4.0 30.0 1.0
OH A:TYR257 4.8 17.5 1.0
CG A:GLN224 4.8 28.4 1.0
CB A:GLN224 4.9 28.3 1.0
NH1 A:ARG219 4.9 17.7 1.0

Sodium binding site 4 out of 4 in 7kgp

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Sodium binding site 4 out of 4 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


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-A*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:34.9
occ:1.00
O B:LEU87 2.2 36.8 1.0
O B:HOH266 2.3 36.3 1.0
O B:HOH314 2.4 35.5 1.0
O B:HIS84 2.5 24.4 1.0
OD1 B:ASN83 2.6 31.3 1.0
C B:LEU87 3.4 36.6 1.0
CG B:ASN83 3.5 30.8 1.0
C B:HIS84 3.5 23.8 1.0
ND2 B:ASN83 3.8 33.4 1.0
N B:HIS84 4.0 22.8 1.0
CA B:LEU87 4.1 34.8 1.0
N B:LEU87 4.1 33.2 1.0
CB B:LEU87 4.2 34.5 1.0
CA B:VAL85 4.2 25.9 1.0
N B:VAL85 4.3 24.3 1.0
O B:VAL85 4.3 28.8 1.0
C B:VAL85 4.4 28.3 1.0
N B:SER88 4.4 38.1 1.0
CA B:HIS84 4.4 22.6 1.0
C B:SER88 4.6 39.3 1.0
O B:SER88 4.6 40.2 1.0
CA B:SER88 4.7 39.3 1.0
CB B:ASN83 4.8 26.4 1.0
C B:ASN83 4.9 22.7 1.0
N B:GLN89 5.0 38.2 1.0

Reference:

C.Szeto, D.S.M.Chatzileontiadou, A.T.Nguyen, H.Sloane, C.A.Lobos, D.Jayasinghe, H.Halim, C.Smith, A.Riboldi-Tunnicliffe, E.J.Grant, S.Gras. The Presentation of Sars-Cov-2 Peptides By the Common Hla-A*02:01 Molecule To Be Published.
Page generated: Mon Jan 25 15:54:07 2021

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