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Magnesium in PDB 7tlt: Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02

Protein crystallography data

The structure of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02, PDB code: 7tlt was solved by L.D.Murdolo, C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.812, 64.467, 76.422, 106.53, 92.43, 97.51
R / Rfree (%) 19.2 / 23.8

Other elements in 7tlt:

The structure of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 (pdb code 7tlt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02, PDB code: 7tlt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7tlt

Go back to Magnesium Binding Sites List in 7tlt
Magnesium binding site 1 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:42.2
occ:1.00
N E:LEU4 3.3 35.4 1.0
ND2 A:ASN66 3.4 30.4 1.0
OH E:TYR1 3.5 51.4 1.0
CE2 E:TYR1 3.7 46.1 1.0
CA E:PRO3 3.8 32.8 1.0
CB E:LEU4 3.9 35.1 1.0
C E:PRO3 4.0 37.7 1.0
CZ E:TYR1 4.1 53.0 1.0
CB E:PRO3 4.2 34.8 1.0
CA E:LEU4 4.2 35.3 1.0
CG A:ASN66 4.2 42.7 1.0
NH2 A:ARG65 4.3 58.4 1.0
OD1 A:ASN66 4.3 34.2 1.0
OH A:TYR159 4.6 49.2 1.0
CE1 A:TYR159 4.8 42.7 1.0
CD2 E:TYR1 4.9 45.5 1.0
CZ A:TYR159 5.0 49.3 1.0

Magnesium binding site 2 out of 2 in 7tlt

Go back to Magnesium Binding Sites List in 7tlt
Magnesium binding site 2 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:71.6
occ:1.00
OG A:SER207 3.6 57.0 1.0
CD2 B:HIS13 3.6 49.5 1.0
NZ A:LYS186 3.6 99.5 1.0
CD B:PRO14 4.1 43.8 1.0
CG B:HIS13 4.4 46.7 1.0
CD A:LYS186 4.5 71.5 1.0
NE2 B:HIS13 4.5 49.7 1.0
CE A:LYS186 4.7 90.4 1.0
CB B:HIS13 4.7 42.5 1.0
CB A:SER207 4.8 46.2 1.0
CA B:HIS13 4.9 40.6 1.0
CG B:PRO14 5.0 47.4 1.0

Reference:

L.D.Murdolo, C.Szeto, S.Gras. Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 To Be Published.
Page generated: Thu Oct 3 09:21:00 2024

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