Atomistry » Sodium » PDB 5vb8-5vwn » 5vf5
Atomistry »
  Sodium »
    PDB 5vb8-5vwn »
      5vf5 »

Sodium in PDB 5vf5: Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement

Protein crystallography data

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5 was solved by P.J.Porebski, A.Wlodawer, Z.Dauter, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.71 / 1.49
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 119.330, 119.330, 158.190, 90.00, 90.00, 120.00
R / Rfree (%) 13.1 / 16.3

Other elements in 5vf5:

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement also contains other interesting chemical elements:

Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement (pdb code 5vf5). 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 Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5:

Sodium binding site 1 out of 1 in 5vf5

Go back to Sodium Binding Sites List in 5vf5
Sodium binding site 1 out of 1 in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:12.6
occ:1.00
O A:HOH910 2.3 16.9 1.0
O A:ALA25 2.3 11.4 1.0
O A:GLY28 2.4 12.0 1.0
O A:HOH847 2.4 13.4 1.0
O A:HOH827 2.5 13.2 1.0
C A:GLY28 3.5 11.8 1.0
C A:ALA25 3.5 11.3 1.0
N A:ALA25 4.0 11.4 1.0
CA A:ALA25 4.2 11.8 1.0
N A:GLY28 4.2 11.1 1.0
CB A:ASP29 4.3 14.3 1.0
O A:HOH691 4.3 33.3 1.0
CA A:GLY28 4.4 12.6 1.0
O A:HOH612 4.4 29.5 1.0
N A:ASP29 4.4 13.0 1.0
O A:HOH887 4.5 38.8 1.0
CB A:ALA25 4.5 12.1 1.0
CA A:ASP29 4.5 13.7 1.0
N A:SER26 4.6 10.7 1.0
O A:SER26 4.6 13.1 1.0
C A:SER26 4.6 11.4 1.0
CG A:ASP29 4.6 18.2 1.0
OD1 A:ASP29 4.7 20.2 1.0
CA A:SER26 4.8 11.6 1.0

Reference:

A.Wlodawer, Z.Dauter, P.J.Porebski, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp. Detect, Correct, Retract: How to Manage Incorrect Structural Models. Febs J. V. 285 444 2018.
ISSN: ISSN 1742-4658
PubMed: 29113027
DOI: 10.1111/FEBS.14320
Page generated: Tue Dec 15 11:45:05 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy