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Magnesium in PDB 6wuu: Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250

Enzymatic activity of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250

All present enzymatic activity of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250, PDB code: 6wuu was solved by Z.Lv, S.K.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.85 / 2.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.425, 189.693, 63.118, 90.00, 98.66, 90.00
R / Rfree (%) 19.5 / 23

Other elements in 6wuu:

The structure of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 (pdb code 6wuu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250, PDB code: 6wuu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6wuu

Go back to Magnesium Binding Sites List in 6wuu
Magnesium binding site 1 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:60.1
occ:1.00
 O D:ASN156 3.2 65.0 1.0
NE2 B:GLN174 3.3 60.3 1.0
O D:CYS155 3.6 66.2 1.0
CG D:LYS157 4.1 81.5 1.0
C D:ASN156 4.2 61.0 1.0
OE2 D:GLU167 4.3 0.9 1.0
CG B:GLU203 4.3 60.3 1.0
CD B:GLN174 4.5 59.1 1.0
CB D:ASN156 4.5 56.2 1.0
CG1 B:VAL202 4.6 55.1 1.0
CB B:VAL202 4.8 58.9 1.0
OE1 B:GLN174 4.8 62.5 1.0
C D:CYS155 4.8 63.2 1.0
CD D:LYS157 4.8 83.3 1.0
CA D:ASN156 4.9 57.6 1.0
OH D:TYR171 4.9 99.4 1.0
ND2 D:ASN156 4.9 80.2 1.0

Magnesium binding site 2 out of 4 in 6wuu

Go back to Magnesium Binding Sites List in 6wuu
Magnesium binding site 2 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:0.3
occ:1.00
 CE2 C:TYR56 3.9 63.6 1.0
CE C:MET84 4.0 72.5 1.0
CZ C:TYR56 4.1 65.9 1.0
CD2 C:TYR56 4.3 59.2 1.0
OH C:TYR56 4.3 67.6 1.0
CD2 C:LEU87 4.5 62.8 1.0
OH C:TYR83 4.8 76.1 1.0
CE1 C:TYR56 4.8 62.9 1.0
N C:GLY38 4.8 0.4 1.0
SD C:MET84 4.9 73.8 1.0
ND2 C:ASN146 4.9 83.9 1.0
CG C:TYR56 5.0 51.5 1.0

Magnesium binding site 3 out of 4 in 6wuu

Go back to Magnesium Binding Sites List in 6wuu
Magnesium binding site 3 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:52.9
occ:1.00
 N D:GLY287 3.1 59.9 1.0
O D:ILE285 3.5 76.8 1.0
O D:TYR273 3.8 62.4 1.0
CB D:ALA114 3.8 53.7 1.0
CA D:ASP286 3.8 77.5 1.0
C D:ASP286 3.9 69.0 1.0
CA D:GLY287 3.9 60.9 1.0
OG1 D:THR115 4.0 70.0 1.0
O D:CYS111 4.1 68.5 1.0
C D:ILE285 4.3 71.3 1.0
OD1 D:ASP286 4.3 92.5 1.0
N D:ASP286 4.4 78.4 1.0
N D:THR115 4.5 71.2 1.0
CA D:LYS274 4.5 64.1 1.0
N D:HIS275 4.6 60.7 1.0
CA D:CYS111 4.7 57.6 1.0
C D:TYR273 4.7 54.9 1.0
C D:ALA114 4.8 69.2 1.0
CB D:CYS111 4.8 59.1 1.0
OG D:SER103 4.8 77.6 1.0
C D:CYS111 4.8 59.8 1.0
CA D:ALA114 4.9 62.3 1.0
CD1 D:LEU118 4.9 51.9 1.0
O D:ASP286 5.0 74.6 1.0

Magnesium binding site 4 out of 4 in 6wuu

Go back to Magnesium Binding Sites List in 6wuu
Magnesium binding site 4 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:0.3
occ:1.00
 OD2 D:ASP61 3.3 0.1 1.0
NE2 D:GLN19 3.9 84.3 1.0
CG D:ASP61 4.2 0.1 1.0
CG D:LEU64 4.3 62.1 1.0
CG D:HIS17 4.3 43.4 1.0
CD1 D:LEU64 4.4 61.8 1.0
CB D:HIS17 4.5 55.5 1.0
CB D:ASP61 4.5 93.1 1.0
O D:HOH604 4.5 0.6 1.0
CD2 D:HIS17 4.6 43.9 1.0
CD2 D:LEU64 4.7 56.2 1.0
ND1 D:HIS17 4.7 42.2 1.0

Reference:

W.Rut, Z.Lv, M.Zmudzinski, S.Patchett, D.Nayak, S.J.Snipas, F.El Oualid, T.T.Huang, M.Bekes, M.Drag, S.K.Olsen. Activity Profiling and Structures of Inhibitor-Bound Sars-Cov-2-Plpro Protease Provides A Framework For Anti-Covid-19 Drug Design To Be Published.
Page generated: Tue Oct 1 23:15:10 2024

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