Chlorine 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
Sodium (Na) 4 atoms
Zinc (Zn) 11 atoms
Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83, PDB code: 7lgt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 7lgt

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Chlorine binding site 1 out of 9 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 Chlorine with other atoms in the Cl 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:Cl307

b:38.8
occ:1.00
 O A:HOH464 3.4 38.0 1.0
OD2 A:ASP129 3.5 43.1 1.0
N A:ASP129 3.5 23.1 1.0
N A:GLU128 3.7 24.0 1.0
CG A:ASP129 3.9 33.0 1.0
CB A:GLU128 3.9 43.0 1.0
CB A:ASN127 3.9 19.8 1.0
CB A:ASP129 4.1 29.6 1.0
CA A:GLU128 4.2 34.4 1.0
C A:GLU128 4.2 29.5 1.0
CA A:ASP129 4.4 30.5 1.0
O A:HOH403 4.5 41.2 1.0
C A:ASN127 4.5 23.1 1.0
OD1 A:ASP129 4.6 31.9 1.0
CG A:ASN127 4.7 26.4 1.0
CA A:ASN127 4.7 25.3 1.0

Chlorine binding site 2 out of 9 in 7lgt

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Chlorine binding site 2 out of 9 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 Chlorine with other atoms in the Cl 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
A:Cl308

b:28.6
occ:1.00
 CD B:PRO14 3.8 40.9 1.0
CG B:PRO14 4.1 39.9 1.0
CD1 A:LEU206 4.6 29.2 1.0
CB A:LYS186 4.7 41.7 1.0
CG A:LYS186 4.8 57.9 1.0

Chlorine binding site 3 out of 9 in 7lgt

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Chlorine binding site 3 out of 9 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 Chlorine with other atoms in the Cl 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
A:Cl309

b:28.5
occ:1.00
 OE2 A:GLU163 3.1 49.9 1.0
O A:HOH416 3.5 35.0 1.0
CD A:GLU163 3.7 50.0 1.0
CD1 A:TYR159 3.7 21.9 1.0
CG A:GLU163 3.9 28.8 1.0
CB A:GLU163 4.2 32.6 1.0
CE1 A:TYR159 4.2 23.6 1.0
CG F:LYS3 4.4 30.4 1.0
NH2 A:ARG62 4.6 42.0 0.6
K F:K101 4.6 35.5 1.0
OE1 A:GLU163 4.7 38.5 1.0
O F:PRO2 4.8 20.7 1.0
CG A:TYR159 4.8 23.3 1.0
CB F:LYS3 4.9 21.8 1.0
NH1 A:ARG62 4.9 32.7 0.6
CA F:LYS3 5.0 20.4 1.0

Chlorine binding site 4 out of 9 in 7lgt

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Chlorine binding site 4 out of 9 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 Chlorine with other atoms in the Cl 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
A:Cl310

b:33.0
occ:1.00
 O A:HOH514 2.7 45.9 1.0
O A:GLY18 2.8 55.9 1.0
CD A:PRO20 3.2 47.3 1.0
CG A:PRO20 3.3 40.8 1.0
N A:ARG14 3.5 27.3 1.0
N A:PRO20 3.6 40.5 1.0
C A:ARG14 3.7 38.6 1.0
N A:PRO15 3.7 35.8 1.0
CA A:PRO15 3.8 48.8 1.0
C A:GLU19 3.9 35.9 1.0
O A:ARG14 3.9 31.6 1.0
C A:GLY18 4.0 55.8 1.0
CA A:PRO20 4.2 36.3 1.0
CA A:SER13 4.2 24.3 1.0
CA A:ARG14 4.3 32.5 1.0
CB A:PRO20 4.3 35.4 1.0
CA A:GLU19 4.3 50.7 1.0
CB A:SER13 4.3 26.3 1.0
C A:SER13 4.3 25.2 1.0
O A:GLU19 4.4 37.6 1.0
CD A:PRO15 4.6 39.8 1.0
CG A:PRO15 4.6 40.3 1.0
N A:GLU19 4.6 59.9 1.0
CB A:PRO15 4.6 41.9 1.0
C A:PRO15 5.0 49.7 1.0

Chlorine binding site 5 out of 9 in 7lgt

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Chlorine binding site 5 out of 9 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl311

b:23.9
occ:1.00
 O A:THR134 3.4 24.1 1.0
O A:HOH474 3.4 22.2 1.0
CA A:ILE124 3.8 19.2 1.0
N A:ALA125 3.8 19.4 1.0
C A:ILE124 3.8 16.8 1.0
N A:ILE124 3.9 15.6 1.0
O A:TYR123 3.9 20.4 1.0
C A:TYR123 4.0 22.7 1.0
CB A:ALA125 4.0 15.3 1.0
CB A:ASP122 4.0 23.0 1.0
CB A:ALA136 4.1 27.1 1.0
N A:ALA136 4.1 24.2 1.0
C A:THR134 4.2 28.7 1.0
CG2 A:THR134 4.2 33.4 1.0
N A:TYR123 4.3 16.0 1.0
O A:ILE124 4.4 19.1 1.0
CA A:ALA136 4.4 25.1 1.0
CA A:ALA125 4.5 18.5 1.0
C A:ALA135 4.5 28.7 1.0
CG A:ASP122 4.6 35.7 1.0
C A:ASP122 4.6 25.3 1.0
CB A:THR134 4.6 28.8 1.0
OD2 A:ASP122 4.7 44.6 1.0
CA A:TYR123 4.8 18.3 1.0
CA A:ALA135 4.8 23.6 1.0
CA A:ASP122 4.8 24.1 1.0
N A:ALA135 4.8 18.2 1.0

Chlorine binding site 6 out of 9 in 7lgt

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Chlorine binding site 6 out of 9 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl312

b:35.5
occ:1.00
 O A:HOH513 2.3 31.1 1.0
NH2 A:ARG131 3.4 24.7 0.3
O A:ARG131 3.5 29.5 1.0
CZ A:ARG131 3.5 26.5 0.3
NH1 A:ARG157 3.5 31.2 1.0
NE A:ARG131 3.5 26.9 0.3
O A:HOH508 3.7 44.3 1.0
CB A:ARG131 3.9 26.4 0.3
CA A:ARG131 3.9 24.9 0.3
CA A:ARG131 3.9 24.9 0.7
CB A:ARG131 4.0 26.5 0.7
CG A:ARG131 4.1 24.0 0.3
C A:ARG131 4.2 30.8 1.0
CB A:ALA153 4.2 27.3 1.0
N A:GLU154 4.2 23.8 1.0
NH1 A:ARG131 4.3 20.4 0.3
CD A:ARG131 4.4 24.9 0.3
CZ A:ARG157 4.5 36.9 1.0
CB A:GLU154 4.5 27.5 1.0
NH2 A:ARG157 4.6 36.1 1.0
CG A:ARG131 4.6 24.0 0.7
CA A:GLU154 4.6 28.4 1.0
C A:ALA153 4.7 26.6 1.0
NH1 A:ARG131 4.9 24.8 0.7
CA A:ALA153 5.0 22.1 1.0

Chlorine binding site 7 out of 9 in 7lgt

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Chlorine binding site 7 out of 9 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 Chlorine with other atoms in the Cl binding site number 7 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
B:Cl103

b:30.4
occ:1.00
 O B:HOH246 3.2 31.4 1.0
N B:ALA15 3.6 35.9 1.0
O B:ASP98 3.9 78.3 1.0
CB B:ALA15 3.9 31.7 1.0
N B:ASP98 4.0 65.1 1.0
OG B:SER11 4.2 26.2 1.0
CA B:ARG97 4.3 51.8 1.0
CA B:ALA15 4.4 39.2 1.0
CA B:PRO14 4.4 39.9 1.0
CZ2 B:TRP95 4.5 29.1 1.0
C B:ARG97 4.5 58.8 1.0
C B:ASP98 4.5 92.7 1.0
C B:PRO14 4.5 32.5 1.0
CB B:ARG97 4.6 48.1 1.0
CA B:ASP98 4.8 70.2 1.0
NE1 B:TRP95 4.9 25.8 1.0
CE2 B:TRP95 5.0 21.4 1.0

Chlorine binding site 8 out of 9 in 7lgt

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Chlorine binding site 8 out of 9 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 Chlorine with other atoms in the Cl binding site number 8 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
B:Cl104

b:35.8
occ:1.00
 O B:HOH255 2.2 35.2 1.0
CE1 B:HIS13 3.6 43.4 1.0
O B:HOH212 3.7 33.0 1.0
CD1 B:PHE22 3.8 26.1 1.0
ND1 B:HIS13 3.8 42.8 1.0
CE1 B:PHE22 3.8 35.9 1.0
CA B:ASN21 4.2 27.1 1.0
O B:SER20 4.3 26.4 1.0
C B:ASN21 4.5 22.3 1.0
N B:ASN21 4.6 27.2 1.0
C B:SER20 4.7 30.1 1.0
CD B:ARG12 4.8 23.3 1.0
O B:ASN21 4.8 21.8 1.0
N B:PHE22 4.9 23.1 1.0
NH1 B:ARG12 4.9 40.8 1.0
NE2 B:HIS13 4.9 37.9 1.0

Chlorine binding site 9 out of 9 in 7lgt

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Chlorine binding site 9 out of 9 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl307

b:28.2
occ:1.00
 O C:HOH492 3.0 35.9 1.0
OE1 C:GLU148 3.5 46.5 1.0
N C:TRP133 3.6 22.1 1.0
OE1 C:GLN144 3.8 52.1 1.0
CB C:GLU148 3.8 30.1 1.0
CD1 C:TRP133 3.9 25.9 1.0
CA C:SER132 4.0 27.0 1.0
CD C:GLU148 4.0 44.0 1.0
CB C:SER132 4.1 25.0 1.0
CG C:GLN144 4.2 20.7 1.0
C C:SER132 4.3 24.2 1.0
CB C:TRP133 4.4 22.4 1.0
O C:TRP133 4.5 25.7 1.0
CD C:GLN144 4.5 31.4 1.0
CA C:TRP133 4.5 24.3 1.0
CG C:TRP133 4.6 23.0 1.0
CG C:GLU148 4.6 37.5 1.0
OE2 C:GLU148 4.6 47.3 1.0
CA C:GLU148 4.9 23.9 1.0
C C:TRP133 5.0 31.5 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: Tue Jul 30 00:02:26 2024

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