Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Human Collagen X NC1 Trimer, PDB code: 1gr3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Human Collagen X NC1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca901 b:21.4 occ:0.33 O A:HOH2024 2.6 19.5 1.0 OD1 A:ASP634 2.6 16.8 1.0 OD2 A:ASP634 2.7 15.4 1.0 CG A:ASP634 3.0 16.3 1.0 CA A:CA903 3.7 33.9 1.0 O A:HOH2027 4.2 18.5 1.0 CB A:ASP634 4.5 16.4 1.0 O A:HOH2021 4.6 16.0 1.0 OG1 A:THR629 4.9 19.2 1.0

Calcium binding site 2 out of 2 in the Structure of the Human Collagen X NC1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Human Collagen X NC1 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:33.9 occ:1.00 O A:GLU627 2.3 17.6 1.0 OD1 A:ASP626 2.4 16.9 1.0 OD2 A:ASP634 2.4 15.4 1.0 O A:HOH2024 3.0 19.5 1.0 CG A:ASP634 3.3 16.3 1.0 C A:GLU627 3.4 21.0 1.0 CG A:ASP626 3.5 19.9 1.0 N A:GLU627 3.6 18.8 1.0 CA A:CA901 3.7 21.4 0.3 O A:HOH2021 3.9 16.0 1.0 CB A:ASP634 4.0 16.4 1.0 CA A:GLU627 4.0 19.4 1.0 OD2 A:ASP626 4.0 20.1 1.0 OD1 A:ASP634 4.1 16.8 1.0 O A:HOH2027 4.3 18.5 1.0 C A:ASP626 4.5 19.8 1.0 N A:TYR628 4.6 19.4 1.0 CB A:GLU627 4.6 20.6 1.0 CB A:ASP626 4.7 17.7 1.0 CA A:ASP626 4.8 19.1 1.0 CA A:TYR628 5.0 20.1 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