Sodium in PDB 1gr3: Structure of the Human Collagen X NC1 Trimer

The structure of Structure of the Human Collagen X NC1 Trimer, PDB code: 1gr3 was solved by O.Bogin, M.Kvansakul, E.Rom, J.Singer, A.Yayon, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	78.360, 78.360, 141.036, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 19.9

The structure of Structure of the Human Collagen X NC1 Trimer also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of the Human Collagen X NC1 Trimer (pdb code 1gr3). 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 Structure of the Human Collagen X NC1 Trimer, PDB code: 1gr3:

Sodium binding site 1 out of 1 in the Structure of the Human Collagen X NC1 Trimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Human Collagen X NC1 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:14.5 occ:0.33 O A:GLN635 2.4 16.4 1.0 O A:HOH2021 2.6 16.0 1.0 O A:HOH2029 2.9 10.5 0.3 C A:GLN635 3.6 16.6 1.0 N A:GLN635 4.1 15.1 1.0 CA A:GLN635 4.3 15.2 1.0 OD2 A:ASP626 4.4 20.1 1.0 N A:ALA636 4.6 17.4 1.0 CB A:GLN635 4.6 16.1 1.0 OE1 A:GLN635 4.7 18.8 1.0 OD1 A:ASP634 4.8 16.8 1.0 CA A:ALA636 4.8 17.2 1.0

O.Bogin, M.Kvansakul, E.Rom, J.Singer, A.Yayon, E.Hohenester. Insight Into Schmid Metaphyseal Chondrodysplasia From the Crystal Structure of the Collagen X NC1 Domain Trimer. Structure V. 10 165 2002.
ISSN: ISSN 0969-2126
PubMed: 11839302
DOI: 10.1016/S0969-2126(02)00697-4