Atomistry » Sodium » PDB 2xzj-2yeq » 2yd3
Atomistry »
  Sodium »
    PDB 2xzj-2yeq »
      2yd3 »

Sodium in PDB 2yd3: Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

Enzymatic activity of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

All present enzymatic activity of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd3 was solved by C.H.Coles, Y.Shen, A.P.Tenney, C.Siebold, G.C.Sutton, W.Lu, J.T.Gallagher, E.Y.Jones, J.G.Flanagan, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.957 / 2.30
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.218, 104.218, 94.850, 90.00, 90.00, 90.00
R / Rfree (%) 20.07 / 23.5

Other elements in 2yd3:

The structure of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma (pdb code 2yd3). 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 N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd3:

Sodium binding site 1 out of 1 in 2yd3

Go back to Sodium Binding Sites List in 2yd3
Sodium binding site 1 out of 1 in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma


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 N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1229

b:26.6
occ:1.00
 N A:VAL53 3.4 30.4 1.0
N A:LYS40 3.4 41.5 1.0
CA A:PRO39 3.6 32.1 1.0
NZ A:LYS37 3.7 50.5 1.0
NE2 A:GLN42 3.8 57.9 1.0
CA A:PHE52 3.8 34.0 1.0
O A:SER51 3.9 35.4 1.0
C A:PRO39 4.0 35.5 1.0
C A:PHE52 4.1 33.4 1.0
O A:VAL53 4.2 35.2 1.0
CB A:PRO39 4.2 29.1 1.0
CA A:VAL53 4.3 27.4 1.0
O A:LYS40 4.3 40.1 1.0
CB A:VAL53 4.3 26.6 1.0
CG2 A:VAL53 4.4 23.0 1.0
CD1 A:PHE52 4.4 38.7 1.0
CA A:LYS40 4.4 44.8 1.0
CB A:LYS40 4.4 52.0 1.0
CB A:PHE52 4.5 31.5 1.0
CG A:LYS40 4.6 59.4 1.0
C A:VAL53 4.7 34.4 1.0
O A:GLU38 4.8 34.2 1.0
C A:SER51 4.8 34.7 1.0
N A:PHE52 4.8 33.9 1.0
N A:PRO39 4.8 29.3 1.0
C A:LYS40 4.9 41.0 1.0
CG A:PHE52 4.9 37.7 1.0
CE A:LYS37 4.9 51.8 1.0
CD A:GLN42 5.0 55.2 1.0

Reference:

C.H.Coles, Y.Shen, A.P.Tenney, C.Siebold, G.C.Sutton, W.Lu, J.T.Gallagher, E.Y.Jones, J.G.Flanagan, A.R.Aricescu. Proteoglycan-Specific Molecular Switch For Rptp Sigma Clustering and Neuronal Extension. Science V. 332 484 2011.
ISSN: ISSN 0036-8075
PubMed: 21454754
DOI: 10.1126/SCIENCE.1200840
Page generated: Mon Oct 7 05:24:06 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy