Sodium in PDB 8ph4: Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor

All present enzymatic activity of Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor:
3.4.22.69;

The structure of Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor, PDB code: 8ph4 was solved by T.Barthel, N.Altincekic, N.Jores, J.Wollenhaupt, M.S.Weiss, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.28 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.69, 100.04, 103.37, 90, 90, 90
R / Rfree (%)	22.3 / 24.9

The binding sites of Sodium atom in the Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor (pdb code 8ph4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor, PDB code: 8ph4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.1 occ:1.00 O A:HOH637 2.2 29.9 1.0 O A:GLY120 2.4 24.9 1.0 O A:HOH579 2.4 27.4 1.0 O A:HOH570 2.5 26.1 1.0 O A:MET17 2.5 24.4 1.0 N17 A:YQN402 2.8 31.5 1.0 C16 A:YQN402 3.3 31.5 1.0 C A:GLY120 3.5 24.7 1.0 C A:MET17 3.6 24.0 1.0 C18 A:YQN402 3.9 31.5 1.0 N A:GLY71 4.0 32.1 1.0 CA A:GLY120 4.3 24.4 1.0 CA A:VAL18 4.3 24.6 1.0 N A:VAL18 4.3 23.7 1.0 N A:SER121 4.3 23.6 1.0 CA A:SER121 4.4 24.2 1.0 CD A:PRO122 4.4 24.2 1.0 O A:HOH615 4.5 26.5 1.0 CB A:MET17 4.5 23.1 1.0 CA A:MET17 4.5 23.2 1.0 C15 A:YQN402 4.6 31.5 1.0 CA A:GLY71 4.7 33.5 1.0 O A:GLU14 4.8 23.2 1.0 C A:ALA70 4.9 40.1 1.0 CA A:ALA70 4.9 38.5 1.0 C A:VAL18 5.0 24.9 1.0 N A:MET17 5.0 23.3 1.0

Sodium binding site 2 out of 2 in the Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of the Sars-COV2 Main Protease NSP5 with An Uracil-Carrying X77-Like Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:30.8 occ:1.00 O B:GLY120 2.3 26.4 1.0 O B:MET17 2.3 23.8 1.0 O B:HOH569 2.4 27.8 1.0 O B:HOH586 2.5 32.5 1.0 O B:HOH520 2.7 26.0 1.0 N17 B:YQN401 2.8 32.1 1.0 C B:MET17 3.3 23.7 1.0 C B:GLY120 3.3 26.4 1.0 C16 B:YQN401 3.5 32.1 1.0 C18 B:YQN401 3.8 32.1 1.0 N B:VAL18 4.0 24.0 1.0 CA B:VAL18 4.0 24.7 1.0 CA B:GLY120 4.1 25.9 1.0 N B:GLY71 4.1 32.2 1.0 CB B:MET17 4.2 22.9 1.0 CA B:MET17 4.2 22.9 1.0 N B:SER121 4.3 25.4 1.0 CA B:SER121 4.4 26.2 1.0 CD B:PRO122 4.5 24.7 1.0 N B:MET17 4.7 22.4 1.0 C B:VAL18 4.8 25.1 1.0 O B:HOH582 4.8 29.6 1.0 C15 B:YQN401 4.8 32.1 1.0 CA B:ALA70 4.8 30.9 1.0 O B:GLU14 4.8 22.4 1.0 CA B:GLY71 4.9 33.6 1.0 C B:ALA70 5.0 32.0 1.0

N.Altincekic, N.Jores, F.Lohr, C.Richter, C.Ehrhardt, M.J.J.Blommers, H.Berg, S.Ozturk, S.L.Gande, V.Linhard, J.Orts, M.J.Abi Saad, M.Butikofer, J.Kaderli, B.G.Karlsson, U.Brath, M.Hedenstrom, G.Grobner, U.H.Sauer, A.Perrakis, J.Langer, L.Banci, F.Cantini, M.Fragai, D.Grifagni, T.Barthel, J.Wollenhaupt, M.S.Weiss, A.Robertson, A.Bax, S.Sreeramulu, H.Schwalbe. Targeting the Main Protease (M Pro , NSP5) By Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies. Acs Chem.Biol. 2024.
ISSN: ESSN 1554-8937
PubMed: 38232960
DOI: 10.1021/ACSCHEMBIO.3C00720