Atomistry » Sodium » PDB 5imd-5j28 » 5iu9
Atomistry »
  Sodium »
    PDB 5imd-5j28 »
      5iu9 »

Sodium in PDB 5iu9: Crystal Structure of Zebrafish Protocadherin-19 EC1-4

Protein crystallography data

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9 was solved by S.R.Cooper, J.D.Jontes, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.390, 59.776, 165.925, 90.00, 94.39, 90.00
R / Rfree (%) 24.6 / 30.5

Other elements in 5iu9:

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4 also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4 (pdb code 5iu9). 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 Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5iu9

Go back to Sodium Binding Sites List in 5iu9
Sodium binding site 1 out of 2 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1010

b:47.6
occ:1.00
OD1 A:ASN238 2.5 65.1 1.0
O A:THR272 2.7 63.5 1.0
OG1 A:THR272 3.1 68.6 1.0
OD1 A:ASP236 3.3 59.7 1.0
O A:LEU237 3.5 58.6 1.0
OD2 A:ASP236 3.6 62.7 1.0
CG A:ASN238 3.7 64.4 1.0
C A:THR272 3.8 63.8 1.0
CG A:ASP236 3.9 60.5 1.0
CA A:THR272 4.2 66.4 1.0
CB A:THR272 4.3 68.6 1.0
ND2 A:ASN238 4.4 64.9 1.0
C A:LEU237 4.7 57.9 1.0
CB A:ASN238 4.7 62.8 1.0
N A:GLY273 4.9 62.1 1.0
CA A:ASN238 5.0 60.1 1.0
OH A:TYR252 5.0 52.7 1.0

Sodium binding site 2 out of 2 in 5iu9

Go back to Sodium Binding Sites List in 5iu9
Sodium binding site 2 out of 2 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1010

b:48.9
occ:1.00
O B:THR272 2.5 64.1 1.0
O B:LEU237 2.6 54.5 1.0
OD1 B:ASN238 3.0 59.7 1.0
OD1 B:ASP236 3.2 60.3 1.0
C B:THR272 3.7 64.2 1.0
C B:LEU237 3.8 55.0 1.0
OD2 B:ASP236 3.8 62.6 1.0
CG B:ASP236 3.9 61.0 1.0
CG B:ASN238 4.0 59.5 1.0
CA B:ASN238 4.3 55.4 1.0
CB B:ASN238 4.3 58.3 1.0
N B:ASN238 4.5 55.1 1.0
CA B:THR272 4.5 66.9 1.0
N B:GLY273 4.7 61.9 1.0
N B:LEU237 4.7 56.3 1.0
OH B:TYR252 4.8 59.2 1.0
CA B:GLY273 4.8 60.2 1.0
CA B:LEU237 4.9 55.1 1.0
O B:GLY273 4.9 59.3 1.0
CB B:THR272 4.9 68.8 1.0
C B:GLY273 5.0 60.0 1.0
CE2 B:TYR252 5.0 58.4 1.0

Reference:

S.R.Cooper, J.D.Jontes, M.Sotomayor. Structural Determinants of Adhesion By Protocadherin-19 and Implications For Its Role in Epilepsy. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27787195
DOI: 10.7554/ELIFE.18529
Page generated: Tue Dec 15 11:06:40 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy