Sodium in PDB 6rk1: Crystal Structure of TSP1 Domain From CCN3

The structure of Crystal Structure of TSP1 Domain From CCN3, PDB code: 6rk1 was solved by E.-R.Xu, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.13 / 1.63
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.860, 52.860, 102.390, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.4

The structure of Crystal Structure of TSP1 Domain From CCN3 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of TSP1 Domain From CCN3 (pdb code 6rk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of TSP1 Domain From CCN3, PDB code: 6rk1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of TSP1 Domain From CCN3


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 TSP1 Domain From CCN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:17.9 occ:1.00 O B:THR235 2.4 17.3 1.0 O A:THR235 2.4 16.4 1.0 OG1 B:THR235 2.4 18.0 1.0 O B:HOH427 2.4 17.0 1.0 OG1 A:THR235 2.4 19.0 1.0 O A:HOH424 2.5 17.6 1.0 C B:THR235 3.2 17.9 1.0 C A:THR235 3.2 15.9 1.0 CB B:THR235 3.5 18.0 1.0 CB A:THR235 3.6 18.9 1.0 N B:THR235 3.6 18.7 1.0 CA B:THR235 3.6 16.9 1.0 N A:THR235 3.6 14.6 1.0 CA A:THR235 3.6 15.7 1.0 NH1 B:ARG236 3.9 18.3 1.0 NH1 A:ARG236 4.0 17.5 1.0 O B:HOH426 4.3 25.3 1.0 O A:HOH419 4.3 26.5 1.0 N B:ARG236 4.3 16.4 1.0 N A:ARG236 4.4 16.3 1.0 O B:HOH431 4.5 29.1 1.0 O A:HOH427 4.5 30.3 1.0 CG2 B:THR235 4.6 21.4 1.0 CG2 A:THR235 4.7 19.9 1.0 CA B:ARG236 4.8 16.8 1.0 C B:GLN234 4.9 19.1 1.0 CA A:ARG236 4.9 15.2 1.0 C A:GLN234 4.9 13.9 1.0 CL A:CL306 5.0 17.5 1.0 CL B:CL301 5.0 18.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of TSP1 Domain From CCN3


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 TSP1 Domain From CCN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:22.5 occ:1.00 O A:HOH417 2.4 18.4 1.0 OE1 A:GLU202 2.4 19.9 1.0 O A:HOH454 2.6 26.8 1.0 CD A:GLU202 3.5 19.6 1.0 CB A:GLU202 3.8 17.1 1.0 O A:HOH422 3.9 17.7 1.0 O A:GLU202 4.0 16.6 1.0 CG A:GLU202 4.2 17.9 1.0 O A:HOH426 4.3 26.8 1.0 OE2 A:GLU202 4.4 19.1 1.0 C A:GLU202 4.5 17.5 1.0 CA A:GLU202 4.7 16.0 1.0 CL A:CL308 4.8 27.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:37.9 occ:1.00 O A:HOH426 2.4 26.8 1.0 O A:HOH422 2.4 17.7 1.0 O A:THR204 2.5 17.4 1.0 O A:HOH450 2.5 40.5 1.0 C A:THR204 3.6 14.5 1.0 N A:THR204 4.0 14.0 1.0 CA A:THR204 4.2 13.1 1.0 CB A:THR204 4.3 14.4 1.0 O A:HOH461 4.3 41.8 0.5 OE1 A:GLU202 4.4 19.9 1.0 OE2 A:GLU202 4.6 19.1 1.0 O A:HOH454 4.7 26.8 1.0 N A:THR205 4.7 15.0 1.0 CD A:GLU202 5.0 19.6 1.0

E.-R.Xu, M.Hyvonen. Thrombospondin Module 1 Domain (TSP1) of the Matricellular Protein CCN3 Shows An Atypical Disulfide Pattern and Incomplete Cwr Layers To Be Published.