Sodium in PDB 4yi9: Crystal Structure of Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3

The structure of Crystal Structure of Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3, PDB code: 4yi9 was solved by R.Prem Kumar, M.J.Ranaghan, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 1.35
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	85.340, 85.340, 58.750, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.4

The structure of Crystal Structure of Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3 (pdb code 4yi9). 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 Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3, PDB code: 4yi9:

Sodium binding site 1 out of 1 in the Crystal Structure of Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3


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 Non-Myristoylated E153A Recoverin at 1.35 A Resolution with A Sodium Ion Bound to Ef-Hand 2 and Calcium Ion Bound to Ef-Hand 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:23.2 occ:1.00 OD1 A:ASP74 2.3 24.5 1.0 OD1 A:ASN76 2.4 28.8 1.0 OD1 A:ASP78 2.4 23.5 1.0 O A:THR80 2.4 20.4 1.0 O A:HOH460 2.5 35.1 1.0 O A:HOH433 3.0 31.7 1.0 CG A:ASP78 3.2 23.7 1.0 CG A:ASP74 3.4 23.6 1.0 CG A:ASN76 3.4 30.2 1.0 C A:THR80 3.5 19.3 1.0 OD2 A:ASP78 3.7 23.9 1.0 N A:ASP78 3.8 28.8 1.0 OG1 A:THR80 3.9 23.2 1.0 ND2 A:ASN76 3.9 33.7 1.0 N A:THR80 4.0 21.3 1.0 CA A:ASP74 4.0 23.9 1.0 OE1 A:GLU85 4.1 23.5 1.0 CB A:ASP74 4.2 23.3 1.0 OD2 A:ASP74 4.2 25.5 1.0 CB A:ASP78 4.2 25.6 1.0 CA A:THR80 4.3 19.9 1.0 C A:ASP74 4.3 26.5 1.0 N A:ASN76 4.3 28.8 1.0 CA A:ASP78 4.4 27.5 1.0 N A:ALA75 4.4 27.1 1.0 N A:SER77 4.5 28.6 1.0 N A:GLY79 4.5 26.5 1.0 N A:LEU81 4.5 18.0 1.0 C A:ASP78 4.7 27.4 1.0 CB A:ASN76 4.7 29.3 1.0 CA A:LEU81 4.7 16.8 1.0 CB A:THR80 4.7 21.8 1.0 C A:ASN76 4.8 29.4 1.0 CA A:ASN76 4.8 29.3 1.0 OE2 A:GLU85 4.8 25.6 1.0 O A:ASP74 4.8 26.8 1.0 CD A:GLU85 4.9 22.8 1.0 C A:SER77 4.9 32.6 1.0

R.P.Kumar, M.J.Ranaghan, A.Y.Ganjei, D.D.Oprian. Crystal Structure of Recoverin with Calcium Ions Bound to Both Functional Ef Hands. Biochemistry V. 54 7222 2015.
ISSN: ISSN 0006-2960
PubMed: 26584024
DOI: 10.1021/ACS.BIOCHEM.5B01160