Sodium in PDB 7lgt: Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83

Protein crystallography data

The structure of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83, PDB code: 7lgt was solved by S.Gras, C.Szeto, D.S.M.Chatzileontiadou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.06 / 1.97
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.144, 62.854, 63.01, 77.15, 77, 77.86
R / Rfree (%) 18.9 / 24.6

Other elements in 7lgt:

The structure of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 also contains other interesting chemical elements:

Potassium (K) 12 atoms
Chlorine (Cl) 9 atoms
Zinc (Zn) 11 atoms
Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 (pdb code 7lgt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83, PDB code: 7lgt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7lgt

Go back to Sodium Binding Sites List in 7lgt
Sodium binding site 1 out of 4 in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:44.4
occ:1.00
CA A:SER195 3.8 41.4 1.0
C A:SER195 3.9 46.0 1.0
O A:SER195 4.0 37.6 1.0
N A:SER195 4.0 36.0 1.0
CB A:PRO193 4.1 41.1 1.0
C A:ILE194 4.2 45.0 1.0
O A:ILE194 4.3 45.7 1.0
N A:ASP196 4.5 34.1 1.0
O A:PRO193 4.6 39.3 1.0
C A:PRO193 4.7 36.1 1.0
OD1 A:ASP196 4.8 44.5 1.0

Sodium binding site 2 out of 4 in 7lgt

Go back to Sodium Binding Sites List in 7lgt
Sodium binding site 2 out of 4 in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:43.0
occ:1.00
OE2 C:GLU53 3.0 69.4 1.0
N C:ALA49 3.5 36.9 1.0
C C:ARG48 3.7 30.6 1.0
C C:ALA49 3.7 42.7 1.0
CD C:GLU53 3.9 61.0 1.0
CA C:ALA49 3.9 35.0 1.0
N C:PRO50 3.9 48.2 1.0
O C:ALA49 4.0 42.6 1.0
CA C:ARG48 4.1 32.7 1.0
O C:ARG48 4.3 36.8 1.0
CA C:PRO50 4.3 48.2 1.0
O C:PRO47 4.3 30.3 1.0
N C:ARG48 4.3 29.8 1.0
CG C:GLU53 4.5 51.0 1.0
C C:PRO47 4.5 34.9 1.0
CD C:PRO50 4.6 44.8 1.0
OE1 C:GLU53 4.7 69.7 1.0
NH1 C:ARG239 4.9 38.0 1.0
CB C:PRO50 5.0 42.4 1.0
CB C:PRO47 5.0 43.9 1.0

Sodium binding site 3 out of 4 in 7lgt

Go back to Sodium Binding Sites List in 7lgt
Sodium binding site 3 out of 4 in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na305

b:43.5
occ:1.00
O C:HOH496 2.6 54.2 1.0
CA C:SER195 3.8 40.5 1.0
N C:SER195 3.9 38.7 1.0
C C:SER195 3.9 41.4 1.0
O C:SER195 4.0 31.5 1.0
C C:ILE194 4.1 41.2 1.0
O C:ILE194 4.3 41.9 1.0
N C:ASP196 4.5 41.6 1.0
O C:PRO193 4.6 33.9 1.0
CB C:PRO193 4.6 30.1 1.0
OD1 C:ASP196 4.7 46.6 1.0
C C:PRO193 4.7 35.2 1.0
CA C:ILE194 4.9 33.7 1.0
N C:ILE194 4.9 33.1 1.0
CG C:PRO193 5.0 34.0 1.0

Sodium binding site 4 out of 4 in 7lgt

Go back to Sodium Binding Sites List in 7lgt
Sodium binding site 4 out of 4 in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na306

b:35.3
occ:1.00
NE2 D:GLN8 3.6 43.7 1.0
CD D:GLN8 3.9 33.5 1.0
N C:GLU232 4.0 38.4 1.0
CB C:VAL231 4.1 43.7 1.0
CG D:GLN8 4.1 30.5 1.0
CG1 C:VAL231 4.1 34.6 1.0
CA C:VAL231 4.2 35.7 1.0
CB D:LYS6 4.5 33.9 1.0
OE1 D:GLN8 4.6 34.1 1.0
CB C:GLU232 4.6 51.6 1.0
C C:VAL231 4.7 38.8 1.0
CD D:LYS6 4.7 57.5 1.0
CA C:GLU232 4.9 40.4 1.0
CG D:LYS6 5.0 47.1 1.0

Reference:

K.E.Lineburg, E.J.Grant, S.Swaminathan, D.S.Chatzileontiadou, C.Szeto, H.Sloane, A.Panikkar, J.Raju, P.Crooks, S.Rehan, A.T.Nguyen, L.Lekieffre, M.A.Neller, Z.W.M.Tong, D.Jayasinghe, K.Y.Chew, C.A.Lobos, H.Halim, J.M.Burrows, A.Riboldi-Tunnicliffe, W.Chen, L.D'orsogna, R.Khanna, K.R.Short, C.Smith, S.Gras. CD8+ T Cells Specific For An Immunodominant Sars-Cov-2 Nucleocapsid Epitope Cross-React with Selective Seasonal Coronaviruses Immunity 2021.
ISSN: ISSN 1074-7613
DOI: 10.1016/J.IMMUNI.2021.04.006
Page generated: Mon Jul 12 15:59:18 2021

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