Sodium in PDB 4d7c: Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin

The structure of Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin, PDB code: 4d7c 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)	43.084 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.550, 141.700, 46.030, 90.00, 110.61, 90.00
R / Rfree (%)	17.34 / 21.24

The binding sites of Sodium atom in the Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin (pdb code 4d7c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin, PDB code: 4d7c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Monoclinic Crystal Form 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 Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1544 b:11.1 occ:1.00 O A:ALA472 2.3 10.3 1.0 O A:LEU517 2.3 10.0 1.0 OD1 A:ASN423 2.3 13.0 1.0 OD1 A:ASN471 2.4 10.9 1.0 O A:HOH2188 2.5 12.4 1.0 O A:HOH2189 2.9 17.8 1.0 H A:ALA472 3.0 11.8 1.0 HB3 A:LEU517 3.1 12.4 1.0 H A:LEU517 3.2 11.6 1.0 CG A:ASN423 3.4 13.6 1.0 C A:LEU517 3.4 10.6 1.0 C A:ALA472 3.5 10.2 1.0 HD22 A:ASN423 3.5 17.7 1.0 CG A:ASN471 3.6 9.5 1.0 N A:ALA472 3.8 9.8 1.0 N A:LEU517 3.9 9.6 1.0 ND2 A:ASN423 3.9 14.7 1.0 CB A:LEU517 3.9 10.3 1.0 HE2 A:PHE415 3.9 12.7 1.0 CA A:LEU517 3.9 9.7 1.0 HD22 A:ASN471 4.0 14.7 1.0 HG A:SER518 4.2 21.0 0.2 HA A:PHE473 4.2 11.8 1.0 CA A:ALA472 4.2 10.6 1.0 ND2 A:ASN471 4.3 12.2 1.0 O A:HOH2103 4.4 18.9 1.0 HB3 A:PHE473 4.4 12.4 1.0 HA A:SER518 4.4 16.4 0.2 HA A:SER518 4.4 15.5 0.8 HB2 A:LEU517 4.5 12.4 1.0 CE2 A:PHE415 4.5 10.6 1.0 N A:PHE473 4.5 10.7 1.0 O A:HOH2180 4.6 15.4 1.0 N A:SER518 4.6 11.6 0.2 N A:SER518 4.6 11.0 0.8 HB1 A:ALA472 4.6 13.5 1.0 HG A:LEU517 4.6 12.9 1.0 HD21 A:LEU517 4.6 14.4 1.0 CB A:ASN423 4.7 12.4 1.0 HB3 A:ASN471 4.7 12.4 1.0 CB A:ASN471 4.7 10.3 1.0 OG A:SER518 4.7 17.5 0.2 HB2 A:ASN423 4.7 14.9 1.0 HD21 A:ASN423 4.7 17.7 1.0 CA A:PHE473 4.8 9.8 1.0 CG A:LEU517 4.8 10.8 1.0 HA A:LEU517 4.9 11.6 1.0 HA A:MET516 4.9 12.4 1.0 HD2 A:PHE415 4.9 13.4 1.0 HB2 A:SER518 4.9 17.6 0.8 C A:ASN471 4.9 9.5 1.0 CA A:SER518 5.0 13.6 0.2 CA A:SER518 5.0 12.9 0.8 HD13 A:ILE434 5.0 15.8 1.0 HA A:ASN471 5.0 11.7 1.0 HB3 A:ASN423 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Monoclinic Crystal Form 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 2 of Monoclinic Crystal Form of the Extracellular Olfactomedin Domain From Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1544 b:13.5 occ:1.00 HD22 B:ASN423 1.6 16.9 0.2 OD1 B:ASN423 1.9 10.4 0.8 ND2 B:ASN423 2.1 14.1 0.2 OD1 B:ASN423 2.3 12.6 0.2 O B:ALA472 2.3 11.1 1.0 CG B:ASN423 2.4 13.2 0.2 O B:LEU517 2.4 12.6 1.0 O B:HOH2152 2.5 13.0 1.0 OD1 B:ASN471 2.6 10.5 1.0 HD21 B:ASN423 2.8 16.9 0.2 O B:HOH2151 2.8 15.6 1.0 HD22 B:ASN423 2.9 17.6 0.8 CG B:ASN423 2.9 13.1 0.8 H B:ALA472 3.2 12.3 1.0 ND2 B:ASN423 3.2 14.6 0.8 HB3 B:LEU517 3.4 11.9 1.0 H B:LEU517 3.4 11.9 1.0 C B:ALA472 3.5 11.0 1.0 C B:LEU517 3.5 11.0 1.0 HE2 B:PHE415 3.8 14.8 1.0 CG B:ASN471 3.8 10.0 1.0 CB B:ASN423 3.9 12.3 0.2 N B:ALA472 4.0 10.2 1.0 HA B:PHE473 4.1 12.7 1.0 N B:LEU517 4.1 9.9 1.0 HB2 B:ASN423 4.1 14.7 0.2 HD21 B:ASN423 4.1 17.6 0.8 CA B:LEU517 4.2 9.9 1.0 CB B:LEU517 4.2 9.9 1.0 CB B:ASN423 4.2 12.5 0.8 HD22 B:ASN471 4.3 16.6 1.0 HA B:SER518 4.3 13.4 0.7 HA B:SER518 4.3 14.5 0.3 HB3 B:ASN423 4.3 14.7 0.2 CA B:ALA472 4.3 10.3 1.0 HB3 B:PHE473 4.4 12.8 1.0 HB2 B:ASN423 4.4 15.0 0.8 CE2 B:PHE415 4.5 12.3 1.0 ND2 B:ASN471 4.5 13.8 1.0 HB1 B:ALA472 4.5 12.9 1.0 N B:PHE473 4.5 11.4 1.0 HB3 B:ASN423 4.6 15.0 0.8 N B:SER518 4.6 10.6 1.0 CA B:PHE473 4.7 10.6 1.0 O B:HOH2085 4.7 20.2 1.0 HG B:LEU517 4.7 13.3 1.0 HB2 B:SER518 4.7 13.8 0.7 OG B:SER518 4.8 14.3 0.3 HD21 B:LEU517 4.8 14.8 1.0 HB2 B:LEU517 4.8 11.9 1.0 HD13 B:ILE434 4.8 17.8 1.0 O B:HOH2148 4.9 15.8 1.0 CA B:SER518 4.9 11.2 0.7 CA B:SER518 4.9 12.1 0.3 HB3 B:ASN471 4.9 13.8 1.0 CB B:ASN471 5.0 11.5 1.0 HA2 B:GLY370 5.0 13.3 1.0 HD2 B:PHE415 5.0 14.8 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