Magnesium in PDB 6ywk: Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes

All present enzymatic activity of Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes, PDB code: 6ywk was solved by X.Ni, M.Schroeder, V.Olieric, E.M.Sharpe, J.A.Wojdyla, M.Wang, S.Knapp, A.Chaikuad, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.09 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.227, 111.765, 196.369, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes (pdb code 6ywk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes, PDB code: 6ywk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:13.2 occ:1.00 OE2 C:GLU120 2.0 39.3 1.0 ND1 C:HIS1 2.0 33.5 1.0 N C:HIS1 2.0 36.8 1.0 N C:GLY0 2.0 36.7 1.0 OE1 C:GLU120 2.2 35.1 1.0 CD C:GLU120 2.3 36.8 1.0 C C:GLY0 2.8 38.2 1.0 CA C:GLY0 2.9 37.3 1.0 CE1 C:HIS1 3.0 33.7 1.0 CG C:HIS1 3.0 36.6 1.0 CA C:HIS1 3.1 38.5 1.0 CB C:HIS1 3.3 38.1 1.0 N C:MET2 3.7 41.9 1.0 CG C:GLU120 3.9 35.8 1.0 C C:HIS1 3.9 39.1 1.0 O C:GLY0 4.0 40.0 1.0 NE2 C:HIS1 4.1 33.5 1.0 CD2 C:HIS1 4.1 34.9 1.0 O C:HOH324 4.6 54.7 1.0 O1 C:EDO204 4.8 60.1 1.0 O C:HOH305 4.8 56.9 1.0 CB C:GLU120 4.9 33.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:12.5 occ:1.00 O E:HOH305 1.7 38.2 1.0 N E:HIS1 1.9 37.0 1.0 ND1 E:HIS1 2.0 36.9 1.0 N E:GLY0 2.0 36.4 1.0 C E:GLY0 2.7 39.0 1.0 CA E:GLY0 2.8 36.5 1.0 CG E:HIS1 2.9 38.7 1.0 CE1 E:HIS1 3.0 38.2 1.0 CA E:HIS1 3.0 40.6 1.0 CB E:HIS1 3.2 40.3 1.0 N E:MET2 3.7 42.5 1.0 O E:GLY0 3.9 41.9 1.0 C E:HIS1 3.9 41.9 1.0 CD2 E:HIS1 4.0 39.9 1.0 NE2 E:HIS1 4.1 39.5 1.0 O E:HOH325 4.2 35.6 1.0

X.Ni, M.Schroeder, V.Olieric, E.M.Sharpe, J.A.Wojdyla, M.Wang, S.Knapp, A.Chaikuad, Structural Genomics Consortium (Sgc). Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Hepes To Be Published.