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Sodium in PDB 5n8e: Crystal Structure of Streptavidin with Peptide Rdpapawahggg

Protein crystallography data

The structure of Crystal Structure of Streptavidin with Peptide Rdpapawahggg, PDB code: 5n8e was solved by V.Lyamichev, L.Goodrich, E.Sullivan, R.Bannen, J.Benz, T.Albert, J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.78 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.810, 84.733, 58.497, 90.00, 99.40, 90.00
R / Rfree (%) 13.5 / 15.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Streptavidin with Peptide Rdpapawahggg (pdb code 5n8e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Streptavidin with Peptide Rdpapawahggg, PDB code: 5n8e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5n8e

Go back to Sodium Binding Sites List in 5n8e
Sodium binding site 1 out of 2 in the Crystal Structure of Streptavidin with Peptide Rdpapawahggg


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 Streptavidin with Peptide Rdpapawahggg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:15.8
occ:1.00
O B:VAL55 2.7 11.4 1.0
NE C:ARG59 2.9 11.8 1.0
O B:ALA78 2.9 11.1 1.0
N B:ALA78 2.9 9.2 1.0
O B:HOH402 3.0 17.8 1.0
NH2 C:ARG59 3.5 13.8 1.0
CA B:ALA78 3.6 9.8 1.0
CB B:ALA78 3.6 10.2 1.0
CZ C:ARG59 3.6 12.5 1.0
C B:ALA78 3.6 10.1 1.0
C B:VAL55 3.6 11.2 1.0
CG C:ARG59 3.8 11.3 1.0
CD C:ARG59 3.8 11.8 1.0
C B:VAL77 3.9 9.1 1.0
CB C:ARG59 4.0 10.5 1.0
CB B:VAL55 4.0 12.6 1.0
CA B:VAL77 4.0 9.0 1.0
N B:VAL55 4.0 11.8 1.0
CA B:VAL55 4.1 11.8 1.0
O B:HOH382 4.2 16.5 1.0
CG1 B:VAL77 4.3 10.3 1.0
CG1 B:VAL55 4.6 13.0 1.0
N B:LEU56 4.8 10.5 1.0
CB B:VAL77 4.8 9.3 1.0
CB B:TYR54 4.8 11.2 1.0
C B:TYR54 4.8 12.0 1.0
NH1 C:ARG59 4.9 13.6 1.0
O B:LYS80 4.9 12.3 1.0
N B:TRP79 4.9 10.0 1.0

Sodium binding site 2 out of 2 in 5n8e

Go back to Sodium Binding Sites List in 5n8e
Sodium binding site 2 out of 2 in the Crystal Structure of Streptavidin with Peptide Rdpapawahggg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Streptavidin with Peptide Rdpapawahggg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:19.8
occ:1.00
O A:HOH248 2.8 12.1 1.0
O D:HOH309 2.9 15.3 1.0
O D:GLY113 3.5 14.2 1.0
CB D:HIS87 3.6 11.2 1.0
CB A:ALA65 3.6 15.5 1.0
C D:GLY113 3.9 11.9 1.0
CG D:HIS87 4.1 12.4 1.0
CA D:GLY113 4.1 10.8 1.0
CB A:SER69 4.2 16.1 1.0
OG A:SER69 4.5 18.3 1.0
N A:ALA65 4.5 12.9 1.0
O A:GLY70 4.5 10.8 1.0
O A:HOH293 4.5 35.5 1.0
CD2 D:HIS87 4.6 14.1 1.0
O D:HIS87 4.6 10.2 1.0
O D:HOH355 4.6 31.3 1.0
O A:HOH216 4.6 10.7 1.0
CA A:ALA65 4.7 14.4 1.0
N D:GLY113 4.7 10.1 1.0
ND1 D:HIS87 4.8 12.8 1.0
N D:THR114 4.8 11.3 1.0
CA D:HIS87 5.0 10.2 1.0

Reference:

V.I.Lyamichev, L.E.Goodrich, E.H.Sullivan, R.M.Bannen, J.Benz, T.J.Albert, J.J.Patel. Stepwise Evolution Improves Identification of Diverse Peptides Binding to A Protein Target. Sci Rep V. 7 12116 2017.
ISSN: ESSN 2045-2322
PubMed: 28935886
DOI: 10.1038/S41598-017-12440-1
Page generated: Tue Dec 15 11:20:12 2020

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