Zinc in PDB 7dmu: Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39

Enzymatic activity of Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39

All present enzymatic activity of Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39:
3.4.17.23;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39, PDB code: 7dmu was solved by T.Arimori, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 3.20
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 227.800, 227.800, 147.030, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39 (pdb code 7dmu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39, PDB code: 7dmu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7dmu

Go back to Zinc Binding Sites List in 7dmu
Zinc binding site 1 out of 2 in the Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39


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 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.4
occ:1.00
OE2 A:GLU402 2.0 0.5 1.0
O A:HOH1101 2.1 0.4 1.0
OE1 A:GLU402 2.1 0.3 1.0
NE2 A:HIS374 2.1 0.6 1.0
NE2 A:HIS378 2.2 1.0 1.0
OE2 A:GLU375 2.3 0.4 1.0
CD A:GLU402 2.3 0.4 1.0
CD2 A:HIS378 2.7 0.5 1.0
CD2 A:HIS374 3.0 0.3 1.0
CE1 A:HIS374 3.2 0.6 1.0
CE1 A:HIS378 3.3 0.2 1.0
CD A:GLU375 3.5 0.8 1.0
CG A:GLU402 3.8 0.1 1.0
O1 A:SO41003 3.9 0.4 1.0
CG A:HIS378 3.9 0.3 1.0
ND1 A:HIS378 4.2 1.0 1.0
CG A:HIS374 4.2 0.4 1.0
OE1 A:GLU375 4.2 1.0 1.0
ND1 A:HIS374 4.2 0.0 1.0
O4 A:SO41003 4.3 0.2 1.0
CB A:GLU402 4.5 0.9 1.0
CA A:GLU402 4.5 1.0 1.0
CG A:GLU375 4.7 0.5 1.0
S A:SO41003 4.7 0.7 1.0
CE1 A:TYR515 4.9 0.3 1.0
OH A:TYR515 5.0 0.0 1.0

Zinc binding site 2 out of 2 in 7dmu

Go back to Zinc Binding Sites List in 7dmu
Zinc binding site 2 out of 2 in the Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sars-Cov-2 Spike Receptor-Binding Domain Complexed with High Affinity ACE2 Mutant 3N39 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn803

b:0.8
occ:1.00
OE1 C:GLU402 2.0 0.2 1.0
OE2 C:GLU402 2.0 0.5 1.0
O C:HOH901 2.0 0.2 1.0
NE2 C:HIS374 2.1 0.0 1.0
NE2 C:HIS378 2.2 0.5 1.0
OE2 C:GLU375 2.2 0.5 1.0
CD C:GLU402 2.2 0.9 1.0
CE1 C:HIS374 2.4 0.1 1.0
CD2 C:HIS378 2.6 0.8 1.0
CD2 C:HIS374 3.2 0.1 1.0
CE1 C:HIS378 3.4 0.8 1.0
ND1 C:HIS374 3.5 0.1 1.0
CD C:GLU375 3.5 0.7 1.0
CG C:GLU402 3.7 0.2 1.0
CG C:HIS374 3.9 0.9 1.0
CG C:HIS378 3.9 0.1 1.0
OE1 C:GLU375 4.1 0.9 1.0
ND1 C:HIS378 4.2 0.2 1.0
CB C:GLU402 4.5 0.6 1.0
CA C:GLU402 4.5 0.6 1.0
O1 C:SO4804 4.5 0.1 1.0
O3 C:SO4804 4.5 0.2 1.0
O4 C:SO4804 4.6 0.8 1.0
CG C:GLU375 4.7 90.0 1.0
S C:SO4804 4.8 0.9 1.0

Reference:

Y.Higuchi, T.Suzuki, T.Arimori, N.Ikemura, E.Mihara, Y.Kirita, E.Ohgitani, O.Mazda, D.Motooka, S.Nakamura, Y.Matsuura, S.Matoba, T.Okamoto, J.Takagi, A.Hoshino. High Affinity Modified ACE2 Receptors Protects From Sars-Cov-2 Infection in Hamsters To Be Published.
Page generated: Mon Jan 25 16:43:53 2021

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