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Fluorine in PDB 7mpb: Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate

Enzymatic activity of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate

All present enzymatic activity of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate:
3.4.22.69;

Protein crystallography data

The structure of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate, PDB code: 7mpb was solved by S.Pandey, T.N.Malla, E.A.Stojkovic, M.Schmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.35, 67.46, 157.509, 90, 90, 90
R / Rfree (%) 21 / 24.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate (pdb code 7mpb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate, PDB code: 7mpb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7mpb

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Fluorine binding site 1 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:57.3
occ:0.62
 F1 A:ETF402 0.0 57.3 0.6
C1 A:ETF402 1.3 54.8 0.6
F2 A:ETF402 2.1 54.0 0.6
F3 A:ETF402 2.2 54.5 0.6
C2 A:ETF402 2.3 57.8 0.6
O A:ETF402 2.7 58.5 0.6
CG A:MET49 3.1 60.3 1.0
ND1 A:HIS41 3.6 47.7 1.0
O A:THR45 3.8 71.3 1.0
CE1 A:HIS41 4.0 43.2 1.0
SD A:MET49 4.1 60.7 1.0
CE A:MET49 4.2 53.0 1.0
CB A:MET49 4.2 63.2 1.0
O A:CYS44 4.3 56.1 1.0
C A:THR45 4.3 67.2 1.0
O A:HIS41 4.6 44.5 1.0
CA A:SER46 4.6 69.7 1.0
N A:SER46 4.7 69.3 1.0
CG A:HIS41 4.8 48.1 1.0
C A:CYS44 4.9 57.6 1.0
CB A:CYS44 4.9 56.0 1.0

Fluorine binding site 2 out of 6 in 7mpb

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Fluorine binding site 2 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:54.0
occ:0.62
 F2 A:ETF402 0.0 54.0 0.6
C1 A:ETF402 1.3 54.8 0.6
F1 A:ETF402 2.1 57.3 0.6
F3 A:ETF402 2.2 54.5 0.6
C2 A:ETF402 2.3 57.8 0.6
O A:HIS41 2.8 44.5 1.0
ND1 A:HIS41 3.0 47.7 1.0
O A:CYS44 3.0 56.1 1.0
O A:ETF402 3.6 58.5 0.6
CE1 A:HIS41 3.6 43.2 1.0
CG2 A:THR25 3.6 46.4 1.0
OG1 A:THR25 3.9 54.3 1.0
C A:CYS44 3.9 57.6 1.0
C A:HIS41 3.9 42.1 1.0
CG A:HIS41 4.1 48.1 1.0
CB A:CYS44 4.2 56.0 1.0
CG A:MET49 4.3 60.3 1.0
O A:THR45 4.4 71.3 1.0
CB A:THR25 4.4 51.9 1.0
CA A:CYS44 4.4 57.2 1.0
N A:CYS44 4.5 52.1 1.0
CB A:HIS41 4.6 43.7 1.0
CA A:VAL42 4.7 43.3 1.0
N A:VAL42 4.7 43.6 1.0
SD A:MET49 4.7 60.7 1.0
C A:THR45 4.7 67.2 1.0
NE2 A:HIS41 4.8 44.6 1.0
N A:THR45 4.8 62.7 1.0
CA A:HIS41 4.9 45.9 1.0
C A:VAL42 4.9 46.0 1.0

Fluorine binding site 3 out of 6 in 7mpb

Go back to Fluorine Binding Sites List in 7mpb
Fluorine binding site 3 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:54.5
occ:0.62
 F3 A:ETF402 0.0 54.5 0.6
C1 A:ETF402 1.3 54.8 0.6
F1 A:ETF402 2.2 57.3 0.6
F2 A:ETF402 2.2 54.0 0.6
C2 A:ETF402 2.3 57.8 0.6
O A:ETF402 2.8 58.5 0.6
CE1 A:HIS41 3.1 43.2 1.0
ND1 A:HIS41 3.3 47.7 1.0
CG2 A:THR25 4.3 46.4 1.0
O5 A:ASC401 4.4 60.6 0.6
NE2 A:HIS41 4.4 44.6 1.0
O A:HIS41 4.6 44.5 1.0
CG A:HIS41 4.7 48.1 1.0
C5 A:ASC401 4.7 60.0 0.6
OG1 A:THR25 4.9 54.3 1.0
O A:CYS44 4.9 56.1 1.0

Fluorine binding site 4 out of 6 in 7mpb

Go back to Fluorine Binding Sites List in 7mpb
Fluorine binding site 4 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:56.8
occ:0.72
 F1 B:ETF402 0.0 56.8 0.7
C1 B:ETF402 1.3 55.1 0.7
F3 B:ETF402 2.2 56.3 0.7
F2 B:ETF402 2.2 55.1 0.7
C2 B:ETF402 2.3 53.5 0.7
O B:ETF402 2.7 57.1 0.7
CG B:MET49 3.4 44.0 1.0
ND1 B:HIS41 3.8 43.3 1.0
SD B:MET49 4.2 41.6 1.0
CE B:MET49 4.3 50.9 1.0
CE1 B:HIS41 4.3 45.1 1.0
CB B:MET49 4.6 50.6 1.0
O B:THR45 4.7 61.6 1.0
O B:HIS41 4.7 33.7 1.0
O B:CYS44 4.7 55.0 1.0
CG B:HIS41 4.9 41.7 1.0
C B:THR45 5.0 60.1 1.0

Fluorine binding site 5 out of 6 in 7mpb

Go back to Fluorine Binding Sites List in 7mpb
Fluorine binding site 5 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:55.1
occ:0.72
 F2 B:ETF402 0.0 55.1 0.7
C1 B:ETF402 1.3 55.1 0.7
F3 B:ETF402 2.2 56.3 0.7
F1 B:ETF402 2.2 56.8 0.7
C2 B:ETF402 2.3 53.5 0.7
O B:CYS44 2.6 55.0 1.0
O B:HIS41 3.2 33.7 1.0
C B:CYS44 3.4 51.6 1.0
O B:ETF402 3.5 57.1 0.7
CB B:CYS44 3.7 46.9 1.0
CG B:MET49 3.8 44.0 1.0
O B:THR45 3.9 61.6 1.0
ND1 B:HIS41 3.9 43.3 1.0
C B:THR45 4.1 60.1 1.0
OG1 B:THR25 4.1 47.1 1.0
CG2 B:THR25 4.1 46.0 1.0
CA B:CYS44 4.1 48.5 1.0
N B:THR45 4.2 51.9 1.0
CA B:THR45 4.2 58.6 1.0
SD B:MET49 4.3 41.6 1.0
N B:CYS44 4.4 46.6 1.0
C B:HIS41 4.4 37.0 1.0
CB B:THR25 4.7 41.7 1.0
N B:SER46 4.8 63.2 1.0
CE1 B:HIS41 4.8 45.1 1.0
CG B:HIS41 4.8 41.7 1.0
CB B:HIS41 4.8 36.4 1.0

Fluorine binding site 6 out of 6 in 7mpb

Go back to Fluorine Binding Sites List in 7mpb
Fluorine binding site 6 out of 6 in the Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars Coronavirus-2 Main Protease 3CL-Pro Binding Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:56.3
occ:0.72
 F3 B:ETF402 0.0 56.3 0.7
C1 B:ETF402 1.3 55.1 0.7
F2 B:ETF402 2.2 55.1 0.7
F1 B:ETF402 2.2 56.8 0.7
C2 B:ETF402 2.3 53.5 0.7
O B:ETF402 2.9 57.1 0.7
ND1 B:HIS41 2.9 43.3 1.0
CE1 B:HIS41 3.3 45.1 1.0
CG2 B:THR25 3.4 46.0 1.0
O B:HIS41 3.6 33.7 1.0
CG B:HIS41 4.2 41.7 1.0
O B:CYS44 4.4 55.0 1.0
C B:HIS41 4.5 37.0 1.0
NE2 B:HIS41 4.6 42.2 1.0
OG1 B:THR25 4.6 47.1 1.0
CB B:THR25 4.7 41.7 1.0
CB B:HIS41 4.9 36.4 1.0

Reference:

T.N.Malla, S.Pandey, I.Poudyal, L.Aldama, D.Feliz, M.Noda, G.N.Phillips, E.A.Stojkovic, M.Schmidt. Vitamin C Inhibits Sars Coronavirus-2 Main Protease Essential For Viral Replication Biorxiv 2021.
DOI: 10.1101/2021.05.02.442358
Page generated: Fri Aug 2 09:43:41 2024

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