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Zinc in PDB 7ekc: Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2

Enzymatic activity of Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2

All present enzymatic activity of Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2:
3.4.17.23;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2, PDB code: 7ekc was solved by P.C.Han, C.Su, Y.F.Zhang, J.X.Qi, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.354, 103.354, 229.784, 90, 90, 90
R / Rfree (%) 21.4 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2 (pdb code 7ekc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2, PDB code: 7ekc:

Zinc binding site 1 out of 1 in 7ekc

Go back to Zinc Binding Sites List in 7ekc
Zinc binding site 1 out of 1 in the Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sars-Cov-2 Gamma Variant Spike Receptor-Binding Domain Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:51.1
occ:1.00
 OE2 A:GLU402 2.2 43.3 1.0
OE1 A:GLU402 2.3 37.7 1.0
NE2 A:HIS378 2.3 33.6 1.0
NE2 A:HIS374 2.3 37.4 1.0
O A:HOH841 2.5 34.9 1.0
CD A:GLU402 2.5 41.0 1.0
CD2 A:HIS374 3.0 37.7 1.0
CE1 A:HIS378 3.2 31.6 1.0
CD2 A:HIS378 3.3 35.4 1.0
CE1 A:HIS374 3.4 38.6 1.0
OE2 A:GLU375 3.9 40.1 1.0
CG A:GLU402 4.0 38.3 1.0
CG A:HIS374 4.3 37.6 1.0
ND1 A:HIS378 4.3 30.9 1.0
CG A:HIS378 4.4 31.9 1.0
ND1 A:HIS374 4.4 37.8 1.0
CD A:GLU375 4.6 39.1 1.0
OE1 A:GLU375 4.7 41.5 1.0
CB A:GLU402 4.8 36.6 1.0
CA A:GLU402 4.9 36.5 1.0

Reference:

P.Han, C.Su, Y.Zhang, C.Bai, A.Zheng, C.Qiao, Q.Wang, S.Niu, Q.Chen, Y.Zhang, W.Li, H.Liao, J.Li, Z.Zhang, H.Cho, M.Yang, X.Rong, Y.Hu, N.Huang, J.Yan, Q.Wang, X.Zhao, G.F.Gao, J.Qi. Molecular Insights Into Receptor Binding of Recent Emerging Sars-Cov-2 Variants. Nat Commun V. 12 6103 2021.
ISSN: ESSN 2041-1723
PubMed: 34671049
DOI: 10.1038/S41467-021-26401-W
Page generated: Tue Oct 29 19:51:12 2024

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