Zinc 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
Chlorine (Cl) 9 atoms
Bromine (Br) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 11 binding sites of Zinc where determined in the Hla-B*07:02 in Complex with 229E-Derived Coronavirus Nucleocapsid Peptide N75-83, PDB code: 7lgt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 7lgt

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Zinc binding site 1 out of 11 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 Zinc with other atoms in the Zn 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:Zn301

b:51.6
occ:1.00
NH2 A:ARG151 4.0 49.8 1.0

Zinc binding site 2 out of 11 in 7lgt

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Zinc binding site 2 out of 11 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 Zinc with other atoms in the Zn 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:Zn302

b:50.6
occ:1.00
OE2 A:GLU53 2.3 61.1 1.0
CD A:GLU53 3.5 60.7 1.0
N A:ALA49 3.5 28.6 1.0
C A:ALA49 3.7 36.5 1.0
O A:ALA49 3.7 32.7 1.0
C A:ARG48 3.8 25.3 1.0
N A:PRO50 4.0 33.8 1.0
CA A:ALA49 4.0 22.9 1.0
CA A:ARG48 4.1 26.1 1.0
O A:PRO47 4.2 25.9 1.0
OE1 A:GLU53 4.2 64.4 1.0
N A:ARG48 4.3 23.4 1.0
CA A:PRO50 4.3 38.8 1.0
O A:ARG48 4.3 29.4 1.0
NH2 A:ARG239 4.3 27.1 0.6
C A:PRO47 4.4 25.3 1.0
CD A:PRO50 4.5 38.2 1.0
CG A:GLU53 4.5 39.6 1.0
CB A:PRO47 4.8 29.3 1.0
CG A:PRO50 4.8 41.6 1.0

Zinc binding site 3 out of 11 in 7lgt

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Zinc binding site 3 out of 11 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 Zinc with other atoms in the Zn 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:Zn303

b:31.8
occ:1.00
O A:HOH426 3.2 33.4 1.0
CD A:ARG239 3.5 34.8 0.6
CD A:ARG239 3.6 34.3 0.4
NE1 A:TRP51 3.6 32.7 1.0
CD1 A:TRP51 3.9 31.6 1.0
CD A:PRO50 3.9 38.2 1.0
NE A:ARG239 4.0 29.1 0.6
CB A:LYS178 4.1 56.4 1.0
CG2 A:THR31 4.2 22.3 1.0
NE A:ARG239 4.3 31.1 0.4
NH1 A:ARG239 4.5 29.1 0.6
CZ A:ARG239 4.5 33.7 0.6
CB A:ALA49 4.6 28.3 1.0
CG A:LYS178 4.7 55.8 1.0
CG A:PRO50 4.8 41.6 1.0
CZ A:ARG239 4.8 29.4 0.4
NH2 A:ARG239 4.9 32.1 0.4
CG A:ARG239 4.9 24.4 0.6
N A:LEU179 4.9 56.3 1.0
CG A:ARG239 4.9 27.8 0.4
CE2 A:TRP51 4.9 31.7 1.0
N A:PRO50 4.9 33.8 1.0
NH1 A:ARG181 5.0 56.1 1.0
OG1 A:THR31 5.0 26.9 1.0

Zinc binding site 4 out of 11 in 7lgt

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Zinc binding site 4 out of 11 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 Zinc with other atoms in the Zn 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:Zn304

b:31.0
occ:1.00
O A:HOH470 2.9 37.2 1.0
CG A:LYS68 4.0 30.8 1.0
NH2 A:ARG75 4.0 43.0 0.6
CB A:SER38 4.0 19.9 1.0
CZ A:PHE36 4.0 21.5 1.0
CA A:SER38 4.3 25.2 1.0
CE1 A:PHE36 4.4 22.7 1.0
CG A:PRO43 4.4 38.0 1.0
CB A:ALA71 4.4 21.4 1.0
CA A:LYS68 4.5 23.3 1.0
CB A:PRO43 4.6 34.6 1.0
CB A:LYS68 4.6 31.8 1.0
O A:SER38 4.8 41.0 1.0
O A:LYS68 4.9 19.9 1.0
CD A:LYS68 5.0 36.3 1.0

Zinc binding site 5 out of 11 in 7lgt

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Zinc binding site 5 out of 11 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 Zinc with other atoms in the Zn 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:Zn305

b:39.1
occ:1.00
N A:GLY16 3.3 40.8 1.0
NE A:ARG17 3.6 66.0 1.0
C A:ARG14 3.7 38.6 1.0
NH1 A:ARG17 3.7 65.8 1.0
CA A:ARG14 3.8 32.5 1.0
N A:PRO15 3.8 35.8 1.0
CD A:PRO15 3.8 39.8 1.0
CA A:GLY16 3.8 51.3 1.0
CZ A:ARG17 4.0 71.4 1.0
O A:ARG14 4.1 31.6 1.0
CB A:ARG14 4.2 36.2 1.0
N A:ARG17 4.2 57.8 1.0
C A:GLY16 4.3 58.4 1.0
C A:PRO15 4.4 49.7 1.0
CB A:SER92 4.4 23.8 1.0
CG A:ARG17 4.6 64.3 1.0
CA A:PRO15 4.6 48.8 1.0
O A:ALA90 4.6 29.9 1.0
CD A:ARG17 4.6 65.9 1.0
N A:SER92 4.8 23.1 1.0
CA A:SER92 5.0 25.1 1.0

Zinc binding site 6 out of 11 in 7lgt

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Zinc binding site 6 out of 11 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 Zinc with other atoms in the Zn 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
B:Zn101

b:44.6
occ:1.00
CE B:LYS19 2.8 48.2 1.0
CD B:LYS19 3.0 32.0 1.0
O B:HOH261 3.4 38.9 1.0
NZ B:LYS19 3.8 41.0 1.0
CG B:LYS19 4.5 39.1 1.0

Zinc binding site 7 out of 11 in 7lgt

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Zinc binding site 7 out of 11 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 Zinc with other atoms in the Zn 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:Zn102

b:33.0
occ:1.00
O B:HOH235 3.2 31.9 1.0
N B:GLY18 3.7 28.3 1.0
CA B:GLY18 3.7 29.1 1.0
C B:ASN17 3.9 35.5 1.0
O B:ASN17 4.1 35.7 1.0
CB B:ASN17 4.2 32.3 1.0
CG2 B:THR73 4.6 26.4 1.0
CA B:ASN17 4.6 31.8 1.0
CB B:THR73 4.8 34.6 1.0
O B:PRO72 4.9 30.6 1.0

Zinc binding site 8 out of 11 in 7lgt

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Zinc binding site 8 out of 11 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 Zinc with other atoms in the Zn 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
C:Zn301

b:32.7
occ:1.00
NE1 C:TRP51 3.6 36.0 1.0
CB C:LYS178 3.8 48.5 1.0
CG C:LYS178 3.8 57.0 1.0
NE C:ARG239 3.9 38.1 1.0
CG2 C:THR31 4.0 28.6 1.0
CD1 C:TRP51 4.0 41.5 1.0
CD C:PRO50 4.1 44.8 1.0
CZ C:ARG239 4.1 47.8 1.0
CB C:ALA49 4.3 28.9 1.0
CD C:ARG239 4.3 45.2 1.0
NH1 C:ARG239 4.4 38.0 1.0
NH2 C:ARG239 4.7 36.5 1.0
CG C:PRO50 4.7 43.1 1.0
CG C:ARG239 4.8 42.4 1.0
CE2 C:TRP51 4.9 32.2 1.0
CA C:ALA49 5.0 35.0 1.0

Zinc binding site 9 out of 11 in 7lgt

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Zinc binding site 9 out of 11 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 Zinc with other atoms in the Zn 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:Zn302

b:41.2
occ:1.00
O C:HOH474 3.2 41.8 1.0
NZ C:LYS68 3.3 59.0 1.0
CB C:SER38 3.8 31.3 1.0
NH1 C:ARG75 4.1 56.6 1.0
CG C:PRO43 4.2 50.7 1.0
CZ C:PHE36 4.2 25.6 1.0
CG C:LYS68 4.3 35.6 1.0
CA C:SER38 4.3 37.4 1.0
CE C:LYS68 4.4 44.2 1.0
CA C:LYS68 4.5 22.7 1.0
CB C:ALA71 4.5 30.6 1.0
CE1 C:PHE36 4.5 28.5 1.0
CB C:LYS68 4.5 32.0 1.0
O C:SER38 4.8 38.3 1.0
CB C:PRO43 4.8 45.2 1.0
CD C:LYS68 4.9 32.4 1.0
O C:LYS68 5.0 21.3 1.0
OG C:SER38 5.0 29.6 1.0

Zinc binding site 10 out of 11 in 7lgt

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Zinc binding site 10 out of 11 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 Zinc with other atoms in the Zn binding site number 10 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:Zn303

b:60.9
occ:1.00
NZ C:LYS178 2.6 65.2 1.0
CD C:LYS178 3.2 59.4 1.0
CE C:LYS178 3.4 74.0 1.0
CB C:TRP51 4.0 37.3 1.0
CD1 C:TRP51 4.1 41.5 1.0
CG C:LYS178 4.2 57.0 1.0
CA C:GLY175 4.3 40.0 1.0
CB C:ASP177 4.3 49.1 1.0
CG C:TRP51 4.4 42.3 1.0
N C:LYS178 4.5 50.3 1.0
CB C:LYS178 4.5 48.5 1.0
O C:GLY175 4.5 39.1 1.0
O C:ASN174 4.5 37.8 1.0
C C:GLY175 4.6 38.9 1.0
CA C:TRP51 4.8 39.1 1.0
CG C:PRO50 4.8 43.1 1.0
N C:TRP51 4.8 40.0 1.0
OD2 C:ASP177 4.8 65.1 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 17:22:46 2021

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