Atomistry » Sodium » PDB 5ppq-5pqt » 5pqa
Atomistry »
  Sodium »
    PDB 5ppq-5pqt »
      5pqa »

Sodium in PDB 5pqa: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 47)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 47), PDB code: 5pqa 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) 29.08 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.594, 56.321, 101.857, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.6

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 47) (pdb code 5pqa). 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 47), PDB code: 5pqa:

Sodium binding site 1 out of 1 in 5pqa

Go back to Sodium Binding Sites List in 5pqa
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 47)


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

b:16.5
occ:1.00
O B:MET107 2.3 13.2 1.0
O B:ASN110 2.3 16.7 1.0
O A:LYS108 2.4 14.2 1.0
O A:HOH336 2.4 15.7 1.0
O A:HOH366 2.5 16.9 1.0
C A:LYS108 3.4 14.3 1.0
C B:ASN110 3.5 18.4 1.0
C B:MET107 3.5 14.4 1.0
CE2 B:TYR117 3.6 11.9 1.0
CD2 B:TYR117 3.7 12.1 1.0
CA A:LYS108 3.9 14.9 0.6
O B:LYS108 3.9 14.2 1.0
CA A:LYS108 3.9 14.9 0.4
CA B:ALA111 4.0 17.1 1.0
O A:MET107 4.0 17.5 1.0
O B:HOH414 4.0 27.3 1.0
N B:ARG112 4.2 16.6 1.0
N B:ALA111 4.2 17.3 1.0
C B:LYS108 4.2 12.8 1.0
C B:ALA111 4.2 15.9 1.0
O A:ASN110 4.2 16.7 1.0
CA B:LYS108 4.3 13.3 0.7
CA B:LYS108 4.3 13.2 0.3
N B:LYS108 4.4 12.0 1.0
CA B:MET107 4.5 15.3 1.0
N B:ASN110 4.5 16.8 1.0
N A:TYR109 4.6 15.3 1.0
CA B:ASN110 4.6 17.1 1.0
C A:ASN110 4.7 17.1 1.0
C A:TYR109 4.8 17.2 1.0
C A:MET107 4.8 14.8 1.0
CZ B:TYR117 4.8 13.3 1.0
N A:LYS108 4.8 14.7 1.0
O A:TYR109 4.8 16.7 1.0
CB A:LYS108 4.9 15.4 0.6
CA B:ARG112 4.9 18.1 1.0
O B:ALA111 4.9 15.7 1.0
CB A:LYS108 5.0 15.5 0.4

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 23:27:52 2024

Last articles

Cl in 5F4Q
Cl in 5F60
Cl in 5F5P
Cl in 5F53
Cl in 5F4U
Cl in 5F4S
Cl in 5F4R
Cl in 5F4P
Cl in 5F4L
Cl in 5F4B
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy