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Sodium in PDB 5pvi: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 233)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 After Initial Refinement with No Ligand Modelled (Structure 233), PDB code: 5pvi 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) 28.93 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.988, 56.155, 101.254, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 25.6

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 233) (pdb code 5pvi). 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 233), PDB code: 5pvi:

Sodium binding site 1 out of 1 in 5pvi

Go back to Sodium Binding Sites List in 5pvi
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 233)


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

b:17.4
occ:1.00
O B:MET107 2.3 14.6 1.0
O A:LYS108 2.4 14.2 1.0
O B:ASN110 2.4 12.8 1.0
O A:HOH312 2.4 6.1 1.0
O A:HOH365 2.5 16.5 1.0
C A:LYS108 3.4 14.0 1.0
C B:ASN110 3.5 14.3 1.0
C B:MET107 3.6 14.1 1.0
CE2 B:TYR117 3.8 10.4 1.0
CA A:LYS108 3.8 15.2 0.6
O B:LYS108 3.8 16.5 1.0
O A:MET107 3.9 17.2 1.0
CA A:LYS108 3.9 14.2 0.4
CD2 B:TYR117 3.9 10.7 1.0
O A:ASN110 4.0 17.6 1.0
CA B:ALA111 4.1 13.4 1.0
C B:LYS108 4.1 14.9 1.0
N B:ALA111 4.2 13.8 1.0
O B:HOH412 4.2 18.4 1.0
CA B:LYS108 4.2 14.0 0.3
CA B:LYS108 4.2 14.7 0.7
C B:ALA111 4.3 14.4 1.0
N B:LYS108 4.4 14.3 1.0
N B:ARG112 4.4 16.1 1.0
N B:ASN110 4.5 14.6 1.0
C A:ASN110 4.5 16.4 1.0
N A:TYR109 4.5 14.1 1.0
CA B:MET107 4.6 13.8 1.0
CA B:ASN110 4.6 14.0 1.0
C A:MET107 4.7 15.5 1.0
C A:TYR109 4.7 15.2 1.0
N A:LYS108 4.8 14.5 1.0
O A:TYR109 4.8 16.5 1.0
N A:ASN110 4.8 15.4 1.0
CB A:LYS108 4.9 15.6 0.6
N A:ALA111 4.9 16.5 1.0
O B:ALA111 4.9 15.2 1.0
CA A:ALA111 4.9 17.6 1.0
N B:TYR109 5.0 15.3 1.0
C B:TYR109 5.0 15.0 1.0
CA A:TYR109 5.0 15.2 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: Tue Dec 15 11:30:05 2020

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