Sodium in PDB 7gqu: Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide, PDB code: 7gqu was solved by M.Classen, J.Benz, D.Brugger, O.Tagliente, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.255, 83.802, 119.624, 90, 90, 90
R / Rfree (%)	18 / 20.9

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide (pdb code 7gqu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide, PDB code: 7gqu:

Sodium binding site 1 out of 1 in the Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Werner Helicase Fragment 517-945 in Covalent Complex with N-[(E,1S)-1-Cyclopropyl-3-Methylsulfonylprop-2-Enyl]-2- (1,1-Difluoroethyl)-4-Phenoxypyrimidine-5-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:51.0 occ:1.00 O A:HOH1246 2.2 45.7 1.0 O A:GLY545 2.5 32.5 1.0 O A:HOH1268 2.5 40.3 1.0 O A:HOH1179 2.6 33.3 1.0 O1 A:GOL1003 2.8 39.4 1.0 C A:GLY545 3.7 30.3 1.0 O A:HOH1199 3.7 35.6 1.0 C1 A:GOL1003 4.1 48.3 1.0 CA A:HIS546 4.3 26.5 1.0 N A:HIS546 4.4 25.2 1.0 O2 A:GOL1003 4.5 45.4 1.0 ND1 A:HIS546 4.6 28.3 1.0 O A:HOH1150 4.6 43.8 1.0 O A:HOH1281 4.7 42.5 1.0 CA A:GLY545 4.8 28.5 1.0 C2 A:GOL1003 4.8 51.9 1.0 N A:SER547 5.0 26.1 1.0

K.A.Baltgalvis, K.N.Lamb, K.T.Symons, C.C.Wu, M.A.Hoffman, A.N.Snead, X.Song, T.Glaza, S.Kikuchi, J.C.Green, D.C.Rogness, B.Lam, M.E.Rodriguez-Aguirre, D.R.Woody, C.L.Eissler, S.Rodiles, S.M.Negron, S.M.Bernard, E.Tran, J.Pollock, A.Tabatabaei, V.Contreras, H.N.Williams, M.K.Pastuszka, J.J.Sigler, P.Pettazzoni, M.G.Rudolph, M.Classen, D.Brugger, C.Claiborne, J.M.Plancher, I.Cuartas, J.Seoane, L.E.Burgess, R.T.Abraham, D.S.Weinstein, G.M.Simon, M.P.Patricelli, T.M.Kinsella. Chemoproteomic Discovery of A Covalent Allosteric Inhibitor of Wrn Helicase Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07318-Y