Sodium in PDB 7udq: Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1

The structure of Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1, PDB code: 7udq was solved by C.A.Bingman, N.Murray, R.W.Smith, D.J.Pagliarini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.72 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.273, 54.859, 80.012, 109.79, 94.62, 92.11
R / Rfree (%)	19.2 / 23.9

The binding sites of Sodium atom in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1 (pdb code 7udq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1, PDB code: 7udq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1


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 COQ8A-CA157 Inhibitor Complex in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:69.2 occ:1.00 H A:ILE341 2.1 51.2 1.0 HG12 A:ILE341 2.1 57.2 1.0 OE1 A:GLU405 2.2 66.2 1.0 OG A:SER340 2.3 69.3 1.0 H A:SER340 2.5 63.3 1.0 O A:HOH814 2.7 42.8 1.0 N A:ILE341 2.7 42.6 1.0 HG13 A:ILE341 2.7 57.2 1.0 CG1 A:ILE341 2.8 47.6 1.0 N A:SER340 3.1 52.7 1.0 HB1 A:ALA339 3.1 63.8 1.0 HG23 A:ILE341 3.1 57.6 1.0 HB3 A:GLU405 3.2 54.6 1.0 CB A:SER340 3.3 60.7 1.0 C A:SER340 3.4 55.7 1.0 CA A:SER340 3.4 58.2 1.0 CD A:GLU405 3.5 60.5 1.0 CB A:ILE341 3.6 49.9 1.0 HB2 A:SER340 3.6 72.9 1.0 HB3 A:ALA339 3.6 63.8 1.0 CA A:ILE341 3.6 48.0 1.0 CB A:ALA339 3.8 53.1 1.0 CG2 A:ILE341 3.8 48.0 1.0 H A:GLY342 3.8 59.2 1.0 HB2 A:GLU405 3.9 54.6 1.0 CB A:GLU405 3.9 45.5 1.0 HD11 A:ILE341 4.0 58.0 1.0 CD1 A:ILE341 4.0 48.3 1.0 C A:ALA339 4.1 54.3 1.0 HB3 A:SER340 4.1 72.9 1.0 HG21 A:ILE341 4.2 57.6 1.0 CG A:GLU405 4.3 53.5 1.0 N A:GLY342 4.3 49.3 1.0 OE2 A:GLU405 4.3 66.5 1.0 C A:ILE341 4.4 47.3 1.0 HA A:SER340 4.4 69.9 1.0 HD13 A:ILE341 4.4 58.0 1.0 HA A:ILE341 4.4 57.7 1.0 O A:SER340 4.5 63.9 1.0 HB A:ILE341 4.5 60.0 1.0 OH A:TYR408 4.5 40.9 1.0 HB2 A:ALA339 4.5 63.8 1.0 CA A:ALA339 4.6 62.6 1.0 HG22 A:ILE341 4.6 57.6 1.0 HE1 A:TYR408 4.7 47.1 1.0 HD12 A:ILE341 4.7 58.0 1.0 HG3 A:GLU405 4.9 64.2 1.0 HD23 A:LEU402 4.9 53.5 1.0 HH A:TYR408 4.9 49.2 1.0 HG2 A:GLU405 4.9 64.2 1.0 O A:ALA339 4.9 57.3 1.0 HA A:ALA339 5.0 75.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:59.5 occ:1.00 OD1 A:ASP420 2.2 68.9 1.0 O A:HOH924 2.3 60.2 1.0 CG A:ASP420 2.8 70.4 1.0 O A:ARG416 2.8 43.3 1.0 OD2 A:ASP420 3.0 72.7 1.0 HB3 A:ARG419 3.1 51.2 1.0 HA A:ARG416 3.4 46.6 1.0 HB3 A:ARG416 3.4 51.9 1.0 H A:ASP420 3.5 54.3 1.0 HG2 A:ARG419 3.6 56.2 1.0 O A:HOH803 3.7 64.8 1.0 C A:ARG416 3.7 45.7 1.0 HD3 A:ARG419 3.7 58.0 1.0 N A:ASP420 3.9 45.2 1.0 CA A:ARG416 3.9 38.8 1.0 CB A:ARG419 4.0 42.6 1.0 CB A:ASP420 4.0 48.4 1.0 CB A:ARG416 4.1 43.2 1.0 CG A:ARG419 4.1 46.7 1.0 HE A:ARG419 4.2 68.6 1.0 HA A:ASP420 4.2 50.1 1.0 HB2 A:ASP420 4.3 58.2 1.0 CD A:ARG419 4.3 48.3 1.0 CA A:ASP420 4.3 41.7 1.0 HG2 A:ARG416 4.3 65.3 1.0 O A:HOH879 4.5 46.2 1.0 C A:ARG419 4.5 46.8 1.0 HB2 A:ARG419 4.7 51.2 1.0 NE A:ARG419 4.7 57.1 1.0 CA A:ARG419 4.8 40.4 1.0 CG A:ARG416 4.8 54.4 1.0 HB3 A:ASP420 4.8 58.2 1.0 N A:LYS417 4.9 40.7 1.0 HB2 A:ARG416 4.9 51.9 1.0 H A:ARG419 4.9 46.6 1.0 HA A:LYS417 4.9 44.1 1.0 HD3 A:ARG416 5.0 63.1 1.0

N.H.Murray, C.R.M.Asquith, Z.Fang, M.P.East, N.Ptak, R.W.Smith, J.D.Vasta, C.A.Zimprich, C.R.Corona, M.B.Robers, G.L.Johnson, C.A.Bingman, D.J.Pagliarini. Small-Molecule Inhibition of the Archetypal Ubib Protein COQ8. Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469
PubMed: 36302899
DOI: 10.1038/S41589-022-01168-3