Chlorine in PDB 8f4y: Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases(Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 2.13
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 171.04, 171.04, 52.029, 90, 90, 120
R / Rfree (%) 15.7 / 18

Other elements in 8f4y:

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 (pdb code 8f4y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 1 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7102

b:112.3
occ:0.50
 CL2 A:XDU7102 0.0 112.3 0.5
CL2 A:XE07103 0.4 45.8 0.5
C10 A:XE07103 1.7 40.4 0.5
C10 A:XDU7102 1.8 97.3 0.5
C5 A:XE07103 2.6 42.4 0.5
C9 A:XDU7102 2.7 101.4 0.5
C5 A:XDU7102 2.8 94.9 0.5
C9 A:XE07103 2.8 40.2 0.5
C4 A:XE07103 2.8 46.1 0.5
C3 A:XDU7102 2.9 77.8 0.5
C4 A:XDU7102 3.2 89.2 0.5
C3 A:XE07103 3.2 49.9 0.5
CA A:CYS6913 3.4 58.3 0.5
CB A:CYS6913 3.6 58.2 0.5
CG2 A:VAL6916 3.7 59.4 1.0
O A:HOH7229 3.7 37.3 0.5
OG A:SER6896 3.7 67.7 1.0
N A:CYS6913 3.7 58.8 0.5
CA A:CYS6913 3.8 63.3 0.5
N A:CYS6913 3.8 59.3 0.5
O A:HOH7371 3.9 58.8 1.0
C6 A:XE07103 3.9 39.2 0.5
C8 A:XDU7102 4.0 105.1 0.5
C8 A:XE07103 4.1 41.6 0.5
CE1 A:PHE6868 4.1 51.5 1.0
C6 A:XDU7102 4.1 100.1 0.5
C2 A:XDU7102 4.1 69.9 0.5
C A:ASP6912 4.1 61.8 0.5
CD1 A:PHE6868 4.1 50.4 1.0
SG A:CYS6913 4.2 59.4 0.5
C2 A:XE07103 4.3 46.5 0.5
CB A:CYS6913 4.3 68.0 0.5
C A:ASP6912 4.3 58.1 0.5
O A:ASP6912 4.3 61.2 0.5
O A:HOH7373 4.3 43.1 1.0
O A:GLY6911 4.4 55.4 1.0
C11 A:XDU7102 4.5 62.0 0.5
C11 A:XE07103 4.5 46.9 0.5
C7 A:XE07103 4.5 42.3 0.5
C7 A:XDU7102 4.6 103.3 0.5
O2 A:FMT7110 4.6 83.3 1.0
O A:ASP6912 4.7 52.6 0.5
CB A:SER6896 4.8 51.1 1.0
C A:CYS6913 4.8 58.6 0.5
CA A:ASP6912 4.9 60.8 0.5
CA A:ASP6912 5.0 66.7 0.5

Chlorine binding site 2 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 2 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7102

b:87.7
occ:0.50
 CL1 A:XDU7102 0.0 87.7 0.5
CL1 A:XE07103 0.4 38.0 0.5
C8 A:XDU7102 1.8 105.1 0.5
C8 A:XE07103 1.8 41.6 0.5
C9 A:XE07103 2.7 40.2 0.5
C7 A:XDU7102 2.8 103.3 0.5
C9 A:XDU7102 2.8 101.4 0.5
C7 A:XE07103 2.9 42.3 0.5
CG A:MET6929 3.4 60.7 1.0
CB A:MET6929 3.5 46.3 1.0
CD1 A:PHE6947 3.7 44.1 1.0
CB A:PHE6947 3.8 45.2 1.0
CE A:MET6929 3.9 65.4 1.0
CG1 A:ILE6951 3.9 49.9 1.0
CG A:PHE6947 4.0 44.4 1.0
C10 A:XE07103 4.0 40.4 0.5
CB A:PHE6868 4.0 40.5 1.0
C6 A:XDU7102 4.0 100.1 0.5
CD1 A:ILE6951 4.1 50.8 1.0
C10 A:XDU7102 4.1 97.3 0.5
C6 A:XE07103 4.2 39.2 0.5
O2 A:FMT7110 4.4 83.3 1.0
CG A:PHE6868 4.4 44.2 1.0
OG A:SER6927 4.4 32.5 1.0
O A:HOH7373 4.5 43.1 1.0
O A:PHE6947 4.5 41.1 1.0
SD A:MET6929 4.5 67.5 1.0
C5 A:XDU7102 4.6 94.9 0.5
CE1 A:PHE6947 4.6 42.6 1.0
C5 A:XE07103 4.6 42.4 0.5
CA A:PHE6947 4.8 43.0 1.0
CD2 A:PHE6868 4.8 48.1 1.0
C A:PHE6947 4.9 40.8 1.0
CA A:MET6929 5.0 38.4 1.0
CD1 A:PHE6868 5.0 50.4 1.0
CD2 A:PHE6947 5.0 47.8 1.0

Chlorine binding site 3 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 3 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7103

b:45.8
occ:0.50
 CL2 A:XE07103 0.0 45.8 0.5
CL2 A:XDU7102 0.4 112.3 0.5
C10 A:XE07103 1.8 40.4 0.5
C10 A:XDU7102 1.9 97.3 0.5
C9 A:XDU7102 2.6 101.4 0.5
C9 A:XE07103 2.7 40.2 0.5
C5 A:XE07103 2.8 42.4 0.5
C5 A:XDU7102 3.0 94.9 0.5
C4 A:XE07103 3.2 46.1 0.5
C3 A:XDU7102 3.3 77.8 0.5
CA A:CYS6913 3.5 58.3 0.5
O A:HOH7371 3.5 58.8 1.0
O A:HOH7229 3.5 37.3 0.5
C4 A:XDU7102 3.5 89.2 0.5
OG A:SER6896 3.6 67.7 1.0
C3 A:XE07103 3.6 49.9 0.5
N A:CYS6913 3.6 58.8 0.5
N A:CYS6913 3.7 59.3 0.5
CB A:CYS6913 3.7 58.2 0.5
CA A:CYS6913 3.8 63.3 0.5
CG2 A:VAL6916 3.9 59.4 1.0
C A:ASP6912 4.0 61.8 0.5
C8 A:XDU7102 4.0 105.1 0.5
C8 A:XE07103 4.0 41.6 0.5
O A:HOH7373 4.1 43.1 1.0
C6 A:XE07103 4.1 39.2 0.5
O A:GLY6911 4.1 55.4 1.0
C A:ASP6912 4.1 58.1 0.5
O A:ASP6912 4.2 61.2 0.5
C6 A:XDU7102 4.2 100.1 0.5
CD1 A:PHE6868 4.2 50.4 1.0
CE1 A:PHE6868 4.3 51.5 1.0
O2 A:FMT7110 4.3 83.3 1.0
CB A:CYS6913 4.3 68.0 0.5
SG A:CYS6913 4.4 59.4 0.5
C2 A:XDU7102 4.5 69.9 0.5
C7 A:XE07103 4.6 42.3 0.5
CA A:ASP6912 4.6 60.8 0.5
C7 A:XDU7102 4.6 103.3 0.5
O A:ASP6912 4.6 52.6 0.5
C2 A:XE07103 4.6 46.5 0.5
CB A:SER6896 4.7 51.1 1.0
CA A:ASP6912 4.7 66.7 0.5
C11 A:XDU7102 4.8 62.0 0.5
C A:CYS6913 4.9 58.6 0.5
C11 A:XE07103 4.9 46.9 0.5

Chlorine binding site 4 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 4 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7103

b:38.0
occ:0.50
 CL1 A:XE07103 0.0 38.0 0.5
CL1 A:XDU7102 0.4 87.7 0.5
C8 A:XDU7102 1.8 105.1 0.5
C8 A:XE07103 1.8 41.6 0.5
C7 A:XDU7102 2.6 103.3 0.5
C9 A:XE07103 2.8 40.2 0.5
C7 A:XE07103 2.8 42.3 0.5
C9 A:XDU7102 2.8 101.4 0.5
CB A:MET6929 3.5 46.3 1.0
CG A:MET6929 3.6 60.7 1.0
CG1 A:ILE6951 3.7 49.9 1.0
CD1 A:ILE6951 3.8 50.8 1.0
CD1 A:PHE6947 3.8 44.1 1.0
CB A:PHE6868 3.9 40.5 1.0
C6 A:XDU7102 3.9 100.1 0.5
CB A:PHE6947 4.0 45.2 1.0
C10 A:XE07103 4.1 40.4 0.5
C6 A:XE07103 4.1 39.2 0.5
C10 A:XDU7102 4.1 97.3 0.5
CG A:PHE6947 4.1 44.4 1.0
CE A:MET6929 4.1 65.4 1.0
OG A:SER6927 4.2 32.5 1.0
CG A:PHE6868 4.2 44.2 1.0
O A:PHE6947 4.5 41.1 1.0
C5 A:XDU7102 4.5 94.9 0.5
CD2 A:PHE6868 4.5 48.1 1.0
C5 A:XE07103 4.6 42.4 0.5
O A:HOH7373 4.6 43.1 1.0
CE1 A:PHE6947 4.6 42.6 1.0
O2 A:FMT7110 4.7 83.3 1.0
SD A:MET6929 4.8 67.5 1.0
CD1 A:PHE6868 4.9 50.4 1.0
C A:PHE6947 4.9 40.8 1.0
CA A:PHE6947 5.0 43.0 1.0

Chlorine binding site 5 out of 8 in 8f4y

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Chlorine binding site 5 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4404

b:102.3
occ:0.80
 CL2 B:XE04404 0.0 102.3 0.8
C10 B:XE04404 1.8 95.3 0.8
C9 B:XE04404 2.7 91.2 0.8
C5 B:XE04404 2.8 93.8 0.8
C4 B:XE04404 3.2 91.8 0.8
OD1 B:ASN4358 3.3 92.7 1.0
CA B:CYS4356 3.6 69.5 0.8
CA B:CYS4356 3.6 63.1 0.2
CB B:CYS4356 3.8 77.6 0.8
ND2 B:ASN4358 3.8 84.4 1.0
O B:CYS4356 3.8 61.7 0.8
CG B:ASN4358 3.9 82.8 1.0
CB B:CYS4356 3.9 62.6 0.2
O B:CYS4356 4.0 62.2 0.2
C8 B:XE04404 4.0 93.2 0.8
C B:CYS4356 4.1 66.0 0.8
C6 B:XE04404 4.1 90.0 0.8
C B:CYS4356 4.1 62.5 0.2
C3 B:XE04404 4.1 92.0 0.8
SG B:CYS4356 4.2 92.5 0.8
O B:THR4355 4.3 69.0 1.0
CB B:ASP4359 4.3 69.2 1.0
SG B:CYS4356 4.5 62.1 0.2
C7 B:XE04404 4.6 91.9 0.8
N B:ASP4359 4.7 63.5 1.0
N B:CYS4356 4.7 67.4 0.8
C11 B:XE04404 4.7 96.6 0.8
N B:CYS4356 4.7 63.7 0.2
C2 B:XE04404 4.9 95.5 0.8
C B:THR4355 5.0 67.5 1.0

Chlorine binding site 6 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 6 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4404

b:104.6
occ:0.80
 CL1 B:XE04404 0.0 104.6 0.8
C8 B:XE04404 1.8 93.2 0.8
C7 B:XE04404 2.8 91.9 0.8
C9 B:XE04404 2.8 91.2 0.8
C B:GLY4362 3.2 72.6 1.0
O B:GLY4362 3.4 78.5 1.0
CA B:GLY4362 3.5 74.2 1.0
N B:PHE4363 3.7 71.1 1.0
OD2 B:ASP4359 3.9 80.1 1.0
C6 B:XE04404 4.1 90.0 0.8
C10 B:XE04404 4.1 95.3 0.8
CD1 B:LEU4284 4.2 121.3 1.0
CA B:PHE4363 4.2 71.0 1.0
CB B:LYS4366 4.5 103.3 1.0
CD B:LYS4366 4.6 119.2 1.0
C5 B:XE04404 4.6 93.8 0.8
CG B:ASP4359 4.7 75.5 1.0
N B:GLY4362 4.8 68.4 1.0
CE B:LYS4281 5.0 163.9 1.0

Chlorine binding site 7 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 7 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4405

b:137.8
occ:0.70
 CL2 B:XE04405 0.0 137.8 0.7
C10 B:XE04405 1.8 116.5 0.7
C9 B:XE04405 2.7 113.3 0.7
C5 B:XE04405 2.8 105.3 0.7
C4 B:XE04405 3.1 103.3 0.7
C3 B:XE04405 3.4 105.0 0.7
C11 B:XE04405 3.7 123.3 0.7
CA B:CYS4332 3.8 83.0 1.0
C2 B:XE04405 4.0 120.4 0.7
C8 B:XE04405 4.1 108.3 0.7
C6 B:XE04405 4.1 97.2 0.7
O B:ARG4331 4.1 80.7 1.0
SG B:CYS4332 4.3 100.3 1.0
CB B:CYS4332 4.3 87.5 1.0
O B:CYS4332 4.4 92.0 1.0
C B:CYS4332 4.5 84.6 1.0
C7 B:XE04405 4.6 95.5 0.7
N B:CYS4332 4.7 76.9 1.0
C B:ARG4331 4.8 74.8 1.0
C12 B:XE04405 4.9 122.3 0.7
F2 B:XE04405 5.0 122.4 0.7

Chlorine binding site 8 out of 8 in 8f4y

Go back to Chlorine Binding Sites List in 8f4y
Chlorine binding site 8 out of 8 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4405

b:122.2
occ:0.70
 CL1 B:XE04405 0.0 122.2 0.7
C8 B:XE04405 1.8 108.3 0.7
C9 B:XE04405 2.8 113.3 0.7
C7 B:XE04405 2.8 95.5 0.7
O B:HOH4519 3.6 60.4 1.0
NH2 B:ARG4331 3.7 64.1 1.0
C10 B:XE04405 4.1 116.5 0.7
C6 B:XE04405 4.1 97.2 0.7
O A:LYS6874 4.4 65.9 1.0
C5 B:XE04405 4.6 105.3 0.7
CZ B:ARG4331 4.6 60.2 1.0
NE B:ARG4331 4.6 62.9 1.0

Reference:

N.L.Inniss, J.Kozic, F.Li, M.Rosas-Lemus, G.Minasov, J.Rybacek, Y.Zhu, R.Pohl, L.Shuvalova, L.Rulisek, J.S.Brunzelle, L.Bednarova, M.Stefek, J.M.Kormanik, E.Andris, J.Sebestik, A.S.M.Li, P.J.Brown, U.Schmitz, K.Saikatendu, E.Chang, R.Nencka, M.Vedadi, K.J.F.Satchell. Discovery of A Druggable, Cryptic Pocket in Sars-Cov-2 NSP16 Using Allosteric Inhibitors. Acs Infect Dis. 2023.
ISSN: ESSN 2373-8227
PubMed: 37728236
DOI: 10.1021/ACSINFECDIS.3C00203
Page generated: Tue Jul 30 09:20:47 2024

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