Sodium in PDB 5ppx: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34), PDB code: 5ppx was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, J.Ng, P.E.Brennan, O.Cox, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.02 / 1.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.046, 56.178, 101.698, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.2

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34) (pdb code 5ppx). 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 Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34), PDB code: 5ppx:

Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 34) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:14.9 occ:1.00 O B:MET107 2.3 12.6 1.0 O B:ASN110 2.3 13.7 1.0 O A:HOH336 2.4 14.0 1.0 O A:LYS108 2.4 13.6 1.0 O A:HOH360 2.5 16.0 1.0 C A:LYS108 3.4 13.1 1.0 C B:ASN110 3.5 15.5 1.0 C B:MET107 3.5 11.4 1.0 CE2 B:TYR117 3.7 11.0 1.0 CD2 B:TYR117 3.8 10.4 1.0 O B:LYS108 3.9 14.4 1.0 CA A:LYS108 3.9 13.2 0.6 CA A:LYS108 3.9 13.6 0.4 CA B:ALA111 3.9 13.8 1.0 O A:MET107 4.0 15.0 1.0 O B:HOH416 4.1 29.1 1.0 N B:ARG112 4.1 13.6 1.0 C B:LYS108 4.1 12.6 1.0 N B:ALA111 4.2 15.2 1.0 C B:ALA111 4.2 13.8 1.0 O A:ASN110 4.2 14.0 1.0 CA B:LYS108 4.2 13.0 0.3 CA B:LYS108 4.2 12.6 0.7 N B:LYS108 4.3 11.3 1.0 N B:ASN110 4.5 13.2 1.0 CA B:MET107 4.5 12.1 1.0 N A:TYR109 4.6 13.2 1.0 CA B:ASN110 4.6 13.2 1.0 C A:ASN110 4.8 13.1 1.0 C A:MET107 4.8 12.1 1.0 C A:TYR109 4.8 14.6 1.0 CA B:ARG112 4.8 15.0 1.0 N A:LYS108 4.8 12.9 1.0 CZ B:TYR117 4.8 11.9 1.0 O B:ALA111 4.9 13.8 1.0 O A:TYR109 4.9 15.0 1.0 CB A:LYS108 4.9 12.8 0.6 N B:TYR109 4.9 12.5 1.0 N A:ASN110 4.9 13.5 1.0 CA A:TYR109 5.0 12.8 1.0

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123