Sodium in PDB 7lgd: Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113

Protein crystallography data

The structure of Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113, PDB code: 7lgd 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) 43.55 / 2.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.454, 107.176, 174.19, 90, 90, 90
R / Rfree (%) 20.6 / 26.9

Other elements in 7lgd:

The structure of Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113 (pdb code 7lgd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113, PDB code: 7lgd:

Sodium binding site 1 out of 1 in 7lgd

Go back to Sodium Binding Sites List in 7lgd
Sodium binding site 1 out of 1 in the Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113


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 Sars-Cov-2 Nucleocapsid Peptide N105-113 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na305

b:57.5
occ:1.00
CL C:CL304 3.7 61.1 1.0
CB C:SER88 4.6 48.0 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 15:59:17 2021

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