Atomistry » Sodium » PDB 5puc-5pvf » 5puc
Atomistry »
  Sodium »
    PDB 5puc-5pvf »
      5puc »

Sodium in PDB 5puc: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 190)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 190), PDB code: 5puc 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) 49.40 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.700, 56.480, 101.930, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.2

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 190) (pdb code 5puc). 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 190), PDB code: 5puc:

Sodium binding site 1 out of 1 in 5puc

Go back to Sodium Binding Sites List in 5puc
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 190)


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

b:15.4
occ:1.00
O B:MET107 2.3 13.6 1.0
O A:LYS108 2.3 14.4 1.0
O A:HOH325 2.3 16.7 1.0
O B:ASN110 2.3 16.7 1.0
O A:HOH362 2.4 14.8 1.0
C A:LYS108 3.4 13.5 1.0
C B:ASN110 3.5 17.4 1.0
C B:MET107 3.5 13.9 1.0
CE2 B:TYR117 3.6 12.5 1.0
CD2 B:TYR117 3.8 12.3 1.0
CA A:LYS108 3.8 14.0 0.6
CA A:LYS108 3.9 14.4 0.4
O B:LYS108 3.9 15.1 1.0
CA B:ALA111 4.0 16.6 1.0
O A:MET107 4.1 15.2 1.0
O B:HOH412 4.1 24.7 1.0
O A:ASN110 4.1 14.7 1.0
N B:ALA111 4.2 17.4 1.0
N B:ARG112 4.2 16.2 1.0
C B:LYS108 4.2 13.6 1.0
C B:ALA111 4.2 15.5 1.0
CA B:LYS108 4.3 13.2 0.7
CA B:LYS108 4.3 13.8 0.3
N B:LYS108 4.4 12.9 1.0
CA B:MET107 4.5 14.7 1.0
N A:TYR109 4.5 13.4 1.0
N B:ASN110 4.5 15.8 1.0
CA B:ASN110 4.6 17.2 1.0
C A:ASN110 4.7 14.9 1.0
C A:TYR109 4.8 16.4 1.0
O A:TYR109 4.8 16.0 1.0
C A:MET107 4.8 13.0 1.0
N A:LYS108 4.8 13.3 1.0
CB A:LYS108 4.8 13.9 0.6
CZ B:TYR117 4.8 12.4 1.0
N A:ASN110 4.9 13.8 1.0
CB A:LYS108 4.9 15.4 0.4
CA A:TYR109 5.0 14.3 1.0
O B:ALA111 5.0 16.9 1.0
CA B:ARG112 5.0 17.2 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 23:43:16 2024

Last articles

Cl in 5IUY
Cl in 5ISO
Cl in 5IS8
Cl in 5IRP
Cl in 5IUS
Cl in 5IS0
Cl in 5ISJ
Cl in 5IRC
Cl in 5IQV
Cl in 5IRA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy