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

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

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

Sodium

(Na)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hla-B*07:02 in Complex with Sars-Cov-2 Nucleocapsid Peptide N105-113, PDB code: 7lgd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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 A:Cl301 b:67.4 occ:1.00 NH2 A:ARG21 3.8 78.8 1.0 NH1 A:ARG21 4.1 76.8 1.0 CE1 B:HIS51 4.1 73.6 1.0 CZ A:ARG21 4.5 79.6 1.0 NE2 B:HIS51 4.6 76.2 1.0

Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl binding site number 2 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 A:Cl302 b:75.5 occ:1.00 NH2 A:ARG239 3.4 69.7 1.0 CZ A:ARG239 4.5 80.6 1.0 CD A:PRO50 4.5 46.9 1.0 NE A:ARG239 4.6 71.3 1.0 CG A:PRO50 4.8 48.6 1.0

Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl binding site number 3 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 B:Cl101 b:72.6 occ:1.00 NH1 B:ARG12 3.4 74.2 1.0 CE1 B:HIS13 3.5 86.7 1.0 NE2 B:HIS13 4.0 85.6 1.0 CE1 B:PHE22 4.1 73.1 1.0 CD B:ARG12 4.2 71.9 1.0 CZ B:ARG12 4.5 73.6 1.0 ND1 B:HIS13 4.6 78.4 1.0 CD1 B:PHE22 4.7 78.3 1.0 NE B:ARG12 4.8 70.6 1.0 CZ B:PHE22 4.9 74.8 1.0

Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl304 b:61.1 occ:1.00 N C:SER88 3.3 43.2 1.0 NA C:NA305 3.7 57.5 1.0 CB C:SER88 3.9 48.0 1.0 CA C:GLN87 3.9 37.6 1.0 CG C:GLN87 4.0 43.6 1.0 CB C:GLN87 4.1 37.5 1.0 C C:GLN87 4.1 34.3 1.0 CA C:SER88 4.2 38.5 1.0

Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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 D:Cl102 b:71.8 occ:1.00 NH1 D:ARG12 3.7 51.8 1.0 NE2 D:HIS13 3.8 58.3 1.0 CE2 D:PHE22 4.0 68.6 1.0 CD D:ARG12 4.5 53.6 1.0 CD2 D:HIS13 4.6 52.5 1.0 CD2 D:PHE22 4.7 58.1 1.0 CE1 D:HIS13 4.8 60.5 1.0 CZ D:ARG12 4.9 51.5 1.0 CZ D:PHE22 5.0 63.2 1.0

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