Atomistry » Sodium » PDB 3p2y-3pkh » 3peb
Atomistry »
  Sodium »
    PDB 3p2y-3pkh »
      3peb »

Sodium in PDB 3peb: The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus.

Protein crystallography data

The structure of The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus., PDB code: 3peb was solved by M.E.Cuff, J.C.Mack, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.43 / 1.86
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.503, 70.503, 160.388, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus. (pdb code 3peb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus., PDB code: 3peb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3peb

Go back to Sodium Binding Sites List in 3peb
Sodium binding site 1 out of 2 in the The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na146

b:50.1
occ:1.00
O A:PHE116 2.3 34.5 1.0
O A:HOH203 2.3 49.5 1.0
O A:HOH267 2.4 43.6 1.0
O A:HOH262 2.5 47.5 1.0
O A:GLN113 2.6 31.8 1.0
O A:HOH234 3.3 56.2 1.0
C A:PHE116 3.4 34.8 1.0
C A:GLN113 3.5 30.6 1.0
CA A:GLN113 3.7 29.4 1.0
CA A:GLU117 4.0 41.2 1.0
CB A:GLN113 4.0 31.4 1.0
N A:GLU117 4.1 37.6 1.0
OE1 A:GLU117 4.2 58.7 1.0
N A:GLY118 4.5 39.4 1.0
CG A:GLN113 4.5 34.4 1.0
CA A:PHE116 4.6 31.2 1.0
N A:PHE116 4.7 29.5 1.0
N A:THR114 4.7 29.7 1.0
C A:GLU117 4.8 40.4 1.0
O A:GLY118 4.8 39.0 1.0

Sodium binding site 2 out of 2 in 3peb

Go back to Sodium Binding Sites List in 3peb
Sodium binding site 2 out of 2 in the The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na147

b:37.2
occ:1.00
O A:HOH304 2.3 48.6 1.0
O A:LEU68 2.3 37.3 1.0
O A:SER65 2.4 34.7 1.0
O A:HOH278 2.4 36.0 1.0
O A:HOH305 2.5 47.3 1.0
O A:HOH279 2.5 54.3 1.0
C A:SER65 3.4 34.1 1.0
C A:LEU68 3.6 36.3 1.0
O A:HOH151 3.8 57.6 0.5
CA A:SER65 3.9 32.0 1.0
CA A:ASP69 4.3 40.1 1.0
CB A:SER65 4.3 33.2 1.0
N A:ASP69 4.4 37.1 1.0
N A:LEU68 4.5 34.9 1.0
O A:PHE70 4.5 32.3 1.0
CA A:LEU68 4.6 34.1 1.0
N A:SER66 4.6 35.1 1.0
OD2 A:ASP69 4.8 57.8 1.0
C A:ASP69 4.8 38.2 1.0
O A:HOH306 4.9 54.1 1.0
N A:PHE70 4.9 34.9 1.0
O A:HOH277 5.0 44.0 1.0

Reference:

M.E.Cuff, J.C.Mack, S.Clancy, A.Joachimiak. The Structure of A CREATINE_N Superfamily Domain of A Dipeptidase From Streptococcus Thermophilus. To Be Published.
Page generated: Tue Dec 15 06:21:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy