Sodium in PDB 4d77: High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin

The structure of High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin, PDB code: 4d77 was solved by H.Han, P.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.683 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.840, 62.480, 88.290, 90.00, 90.00, 90.00
R / Rfree (%)	13.73 / 16.28

The binding sites of Sodium atom in the High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin (pdb code 4d77). 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 High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin, PDB code: 4d77:

Sodium binding site 1 out of 1 in the High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of the Extracellular Olfactomedin Domain From Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1543 b:17.8 occ:1.00 OD1 A:ASN423 2.3 21.2 1.0 O A:LEU517 2.3 18.4 1.0 OD1 A:ASN471 2.3 18.4 1.0 O A:ALA472 2.3 15.9 1.0 O A:HOH2063 2.4 21.0 1.0 H A:ALA472 3.0 18.5 1.0 HB3 A:LEU517 3.2 22.3 1.0 H A:LEU517 3.2 19.5 1.0 CG A:ASN423 3.3 23.7 1.0 O A:HOH2102 3.3 24.2 1.0 HD22 A:ASN423 3.4 32.8 1.0 C A:LEU517 3.4 16.6 1.0 CG A:ASN471 3.5 18.1 1.0 C A:ALA472 3.5 16.5 1.0 ND2 A:ASN423 3.8 27.3 1.0 N A:ALA472 3.8 15.4 1.0 N A:LEU517 3.9 16.3 1.0 HE2 A:PHE415 3.9 25.2 1.0 O A:HOH2103 3.9 36.2 1.0 HD22 A:ASN471 3.9 27.5 1.0 CB A:LEU517 4.0 18.6 1.0 CA A:LEU517 4.0 16.6 1.0 ND2 A:ASN471 4.2 22.9 1.0 HA A:PHE473 4.2 20.1 1.0 CA A:ALA472 4.2 15.8 1.0 HA A:SER518 4.3 22.9 0.4 HB3 A:PHE473 4.4 20.1 1.0 HA A:SER518 4.4 22.1 0.6 O A:HOH2064 4.5 23.8 1.0 CE2 A:PHE415 4.6 21.0 1.0 N A:PHE473 4.6 16.1 1.0 N A:SER518 4.6 17.9 0.4 N A:SER518 4.6 17.2 0.6 HG A:LEU517 4.6 23.8 1.0 HB1 A:ALA472 4.6 20.3 1.0 CB A:ASN423 4.6 20.1 1.0 HD21 A:ASN423 4.6 32.8 1.0 HB2 A:LEU517 4.6 22.3 1.0 HD21 A:LEU517 4.6 26.2 1.0 HB2 A:ASN423 4.7 24.1 1.0 CB A:ASN471 4.7 18.5 1.0 HB3 A:ASN471 4.7 22.1 1.0 HG A:SER518 4.7 31.3 0.4 CA A:PHE473 4.8 16.8 1.0 HA A:MET516 4.8 24.0 1.0 CG A:LEU517 4.8 19.8 1.0 HD2 A:PHE415 4.8 24.4 1.0 HB3 A:ASN423 4.9 24.1 1.0 C A:ASN471 4.9 17.0 1.0 HA A:LEU517 4.9 20.0 1.0 CA A:SER518 4.9 19.1 0.4 OG A:SER518 5.0 26.1 0.4 CA A:SER518 5.0 18.4 0.6 HA A:ASN471 5.0 20.4 1.0

H.Han, P.Kursula. The Olfactomedin Domain From Gliomedin Is A Beta-Propeller with Unique Structural Properties J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.627547