Sodium in PDB 5eiv: Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide

The structure of Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide, PDB code: 5eiv was solved by L.Zhou, M.Blaszczyk, D.Chirgadze, D.Bihan, R.W.Farndale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.58 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.707, 136.585, 70.584, 90.00, 90.05, 90.00
R / Rfree (%)	17.4 / 22

The structure of Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide (pdb code 5eiv). 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 Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide, PDB code: 5eiv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide


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 Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:38.3 occ:1.00 OE1 B:GLU101 2.7 28.5 1.0 NE2 B:GLN183 3.1 32.3 1.0 O B:HOH342 3.5 29.0 1.0 CD B:GLU101 3.7 28.0 1.0 O B:LEU102 3.7 26.8 1.0 CB B:GLN183 4.0 29.3 1.0 CA B:PRO103 4.2 21.7 1.0 C B:LEU102 4.3 24.1 1.0 CD B:GLN183 4.3 32.5 1.0 CG B:GLU101 4.4 28.2 1.0 OE2 B:GLU101 4.5 25.6 1.0 N B:PRO103 4.5 26.7 1.0 O B:GLU101 4.6 27.4 1.0 N B:ARG104 4.6 25.6 1.0 CB B:GLU101 4.6 30.4 1.0 CG B:GLN183 4.7 33.3 1.0 O B:HOH309 4.8 35.0 1.0 C B:GLU101 4.8 26.0 1.0 C B:PRO103 4.9 26.7 1.0 N B:GLN183 5.0 27.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide


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 Complex of Osteoclast-Associated Immunoglobulin- Like Receptor (Oscar) and A Synthetic Collagen Consensus Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:32.6 occ:1.00 O B:HOH332 2.8 36.3 1.0 OG B:SER133 2.9 34.2 1.0 CB B:SER133 3.0 27.1 1.0 O B:HOH324 3.3 36.3 1.0 C B:ARG148 3.7 33.2 1.0 N B:HIS149 3.8 31.6 1.0 O B:ARG148 3.9 29.8 1.0 CA B:SER133 4.0 27.4 1.0 N B:ARG148 4.0 27.8 1.0 CA B:ARG148 4.1 30.6 1.0 CD1 B:TYR147 4.1 32.3 1.0 CA B:HIS149 4.3 27.2 1.0 CB B:TYR147 4.3 30.5 1.0 C B:TYR147 4.4 31.4 1.0 O C:HOH105 4.4 31.8 1.0 CB B:HIS149 4.4 30.1 1.0 ND1 B:HIS149 4.6 31.1 1.0 O B:TYR147 4.7 33.1 1.0 CG B:TYR147 4.7 32.4 1.0 CE1 B:HIS173 4.8 25.2 1.0 C B:SER133 4.9 27.4 1.0 N B:PHE134 4.9 30.1 1.0 CA B:TYR147 5.0 27.1 1.0 NE2 B:HIS173 5.0 25.3 1.0 CG B:HIS149 5.0 29.8 1.0 OD1 C:HYP3 5.0 28.2 1.0

L.Zhou, J.M.Hinerman, M.Blaszczyk, J.L.Miller, D.G.Conrady, A.D.Barrow, D.Y.Chirgadze, D.Bihan, R.W.Farndale, A.B.Herr. Structural Basis For Collagen Recognition By the Immune Receptor Oscar. Blood V. 127 529 2016.
ISSN: ESSN 1528-0020
PubMed: 26552697
DOI: 10.1182/BLOOD-2015-08-667055