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Zinc in PDB 3d0i: Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2

Enzymatic activity of Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2

All present enzymatic activity of Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2:
3.4.17.23;

Protein crystallography data

The structure of Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2, PDB code: 3d0i was solved by F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.47 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.424, 119.824, 109.772, 90.00, 95.50, 90.00
R / Rfree (%) 22.4 / 27.8

Other elements in 3d0i:

The structure of Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2 (pdb code 3d0i). 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 Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2, PDB code: 3d0i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d0i

Go back to Zinc Binding Sites List in 3d0i
Zinc binding site 1 out of 2 in the Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor 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 Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.3
occ:1.00
NE2 A:HIS378 2.9 58.3 1.0
OE2 A:GLU375 3.1 67.5 1.0
CD2 A:HIS378 3.3 58.1 1.0
OE1 A:GLU402 3.4 70.4 1.0
NE2 A:HIS374 3.5 59.6 1.0
OE1 A:GLU375 3.6 68.7 1.0
CD2 A:HIS374 3.7 58.9 1.0
CD A:GLU375 3.7 67.0 1.0
CE1 A:HIS378 3.9 59.1 1.0
CG A:HIS378 4.4 57.3 1.0
CD A:GLU402 4.4 70.5 1.0
CE1 A:HIS374 4.6 57.7 1.0
ND1 A:HIS378 4.7 58.4 1.0
O A:PRO346 4.7 96.0 1.0
OE2 A:GLU402 4.8 73.3 1.0
CG A:HIS374 4.9 58.2 1.0

Zinc binding site 2 out of 2 in 3d0i

Go back to Zinc Binding Sites List in 3d0i
Zinc binding site 2 out of 2 in the Crystal Structure of Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor 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 Spike Protein Receptor-Binding Domain From the 2005-2006 Sars Coronavirus Civet Strain Complexed with Human-Civet Chimeric Receptor ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:0.3
occ:1.00
OE1 B:GLU402 2.7 60.9 1.0
NE2 B:HIS378 3.1 54.1 1.0
OE2 B:GLU375 3.3 64.0 1.0
NE2 B:HIS374 3.5 58.0 1.0
CD2 B:HIS378 3.6 55.1 1.0
OE1 B:GLU375 3.8 65.8 1.0
CD B:GLU402 3.8 61.8 1.0
CD2 B:HIS374 3.8 56.6 1.0
CD B:GLU375 4.0 63.6 1.0
CE1 B:HIS378 4.0 54.5 1.0
OE2 B:GLU402 4.2 63.0 1.0
CE1 B:HIS374 4.6 57.3 1.0
CG B:HIS378 4.6 53.3 1.0
O B:PRO346 4.7 88.9 1.0
ND1 B:HIS378 4.9 53.5 1.0
CG B:GLU402 5.0 60.0 1.0

Reference:

F.Li, F.Li. N/A N/A.
ISSN: ISSN 0022-538X
PubMed: 18448527
DOI: 10.1128/JVI.00442-08
Page generated: Wed Dec 16 04:11:52 2020

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