Atomistry » Sodium » PDB 5pom-5ppp » 5ppm
Atomistry »
  Sodium »
    PDB 5pom-5ppp »
      5ppm »

Sodium in PDB 5ppm: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 23)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 23), PDB code: 5ppm 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) 29.03 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.612, 56.179, 101.724, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 23) (pdb code 5ppm). 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 23), PDB code: 5ppm:

Sodium binding site 1 out of 1 in 5ppm

Go back to Sodium Binding Sites List in 5ppm
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 23)


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 23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:23.7
occ:1.00
O A:HOH317 2.3 16.9 1.0
O B:MET107 2.3 20.5 1.0
O A:HOH359 2.4 22.5 1.0
O A:LYS108 2.4 19.8 1.0
O B:ASN110 2.4 20.3 1.0
C A:LYS108 3.4 19.5 1.0
C B:MET107 3.5 18.5 1.0
C B:ASN110 3.6 22.2 1.0
CE2 B:TYR117 3.8 15.5 1.0
O B:LYS108 3.8 18.9 1.0
CD2 B:TYR117 3.9 15.8 1.0
O A:MET107 3.9 21.3 1.0
O A:ASN110 3.9 22.9 1.0
CA A:LYS108 3.9 19.7 0.6
CA A:LYS108 4.0 19.0 0.4
O B:HOH392 4.0 27.6 1.0
CA B:ALA111 4.1 20.7 1.0
C B:LYS108 4.2 20.8 1.0
N B:ARG112 4.2 20.4 1.0
CA B:LYS108 4.3 19.1 0.3
CA B:LYS108 4.3 20.6 0.7
C B:ALA111 4.3 18.2 1.0
N B:ALA111 4.3 21.2 1.0
N B:LYS108 4.3 18.5 1.0
C A:ASN110 4.5 21.5 1.0
CA B:MET107 4.5 17.9 1.0
N B:ASN110 4.6 19.8 1.0
N A:TYR109 4.6 19.9 1.0
CA B:ASN110 4.7 18.8 1.0
C A:TYR109 4.7 20.3 1.0
C A:MET107 4.7 19.5 1.0
O A:TYR109 4.8 21.9 1.0
N A:LYS108 4.8 20.7 1.0
N A:ASN110 4.9 18.6 1.0
CA A:ALA111 5.0 24.1 1.0
CA B:ARG112 5.0 22.0 1.0
N B:TYR109 5.0 17.9 1.0
C B:TYR109 5.0 20.5 1.0
CA A:TYR109 5.0 17.8 1.0
CZ B:TYR117 5.0 16.2 1.0
N A:ALA111 5.0 23.1 1.0

Reference:

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
Page generated: Mon Oct 7 23:25:15 2024

Last articles

Cl in 5I1T
Cl in 5I3W
Cl in 5I21
Cl in 5HZ9
Cl in 5I1F
Cl in 5I0D
Cl in 5I13
Cl in 5I1C
Cl in 5I0W
Cl in 5I0V
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy