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Zinc in PDB 7wbq: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2

Enzymatic activity of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2

All present enzymatic activity of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2:
3.4.17.23;

Protein crystallography data

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2, PDB code: 7wbq was solved by J.Qi, P.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.70 / 3.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.773, 143.654, 106.414, 90, 95.29, 90
R / Rfree (%) 19.7 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2 (pdb code 7wbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2, PDB code: 7wbq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7wbq

Go back to Zinc Binding Sites List in 7wbq
Zinc binding site 1 out of 2 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:111.5
occ:1.00
OE2 A:GLU402 2.1 126.3 1.0
NE2 A:HIS374 2.1 117.3 1.0
NE2 A:HIS378 2.1 116.1 1.0
CD A:GLU402 3.0 126.7 1.0
CD2 A:HIS374 3.0 116.8 1.0
CE1 A:HIS374 3.0 115.2 1.0
CD2 A:HIS378 3.1 110.2 1.0
CE1 A:HIS378 3.1 105.7 1.0
OE1 A:GLU402 3.2 128.2 1.0
OE2 A:GLU375 3.9 118.0 1.0
ND1 A:HIS374 4.1 114.1 1.0
CG A:HIS374 4.1 116.2 1.0
ND1 A:HIS378 4.2 104.1 1.0
CG A:HIS378 4.2 88.0 1.0
CG A:GLU402 4.4 120.6 1.0
CD A:GLU375 4.5 98.4 1.0
OE1 A:GLU375 4.6 107.7 1.0
O A:HIS374 4.9 119.3 1.0

Zinc binding site 2 out of 2 in 7wbq

Go back to Zinc Binding Sites List in 7wbq
Zinc binding site 2 out of 2 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Delta Variant Spike Glycoprotein in Complex with Its Receptor Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:99.6
occ:1.00
OE2 C:GLU402 2.1 98.4 1.0
NE2 C:HIS374 2.1 119.5 1.0
NE2 C:HIS378 2.1 110.4 1.0
CE1 C:HIS374 2.8 110.9 1.0
CD C:GLU402 2.9 107.8 1.0
CD2 C:HIS378 3.1 102.7 1.0
OE1 C:GLU402 3.1 124.5 1.0
CE1 C:HIS378 3.1 92.3 1.0
CD2 C:HIS374 3.3 107.1 1.0
OE2 C:GLU375 3.8 108.3 1.0
ND1 C:HIS374 4.0 100.8 1.0
ND1 C:HIS378 4.2 82.2 1.0
CG C:HIS378 4.2 81.4 1.0
CG C:HIS374 4.3 104.2 1.0
CG C:GLU402 4.4 121.5 1.0
CD C:GLU375 4.5 103.6 1.0
OE1 C:GLU375 4.6 113.7 1.0

Reference:

P.Han, L.Li, S.Liu, Q.Wang, D.Zhang, Z.Xu, P.Han, X.Li, Q.Peng, C.Su, B.Huang, D.Li, R.Zhang, M.Tian, L.Fu, Y.Gao, X.Zhao, K.Liu, J.Qi, G.F.Gao, P.Wang. Receptor Binding and Complex Structures of Human ACE2 to Spike Rbd From Omicron and Delta Sars-Cov-2. Cell V. 185 630 2022.
ISSN: ISSN 1097-4172
PubMed: 35093192
DOI: 10.1016/J.CELL.2022.01.001
Page generated: Sat Apr 8 05:18:20 2023

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