Sodium in PDB 8a1f: Human Ptprk N-Terminal Domains Mam-Ig-FN1

All present enzymatic activity of Human Ptprk N-Terminal Domains Mam-Ig-FN1:
3.1.3.48;

The structure of Human Ptprk N-Terminal Domains Mam-Ig-FN1, PDB code: 8a1f was solved by I.M.Hay, S.C.Graham, H.J.Sharpe, J.E.Deane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.46 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.79, 93.862, 181.737, 90, 90, 90
R / Rfree (%)	22.8 / 27.4

The binding sites of Sodium atom in the Human Ptprk N-Terminal Domains Mam-Ig-FN1 (pdb code 8a1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Ptprk N-Terminal Domains Mam-Ig-FN1, PDB code: 8a1f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Ptprk N-Terminal Domains Mam-Ig-FN1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Ptprk N-Terminal Domains Mam-Ig-FN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:109.6 occ:1.00 O A:THR37 2.3 108.7 1.0 O A:SER76 2.3 108.6 1.0 OD1 A:ASP183 2.3 114.9 1.0 O A:HOH501 2.3 125.2 1.0 OD2 A:ASP183 2.6 107.9 1.0 CG A:ASP183 2.8 96.8 1.0 C A:THR37 3.5 106.7 1.0 C A:SER76 3.5 109.7 1.0 CA A:THR37 4.1 100.1 1.0 N A:SER76 4.2 98.9 1.0 CB A:THR37 4.3 103.9 1.0 CB A:ASP183 4.3 86.2 1.0 CA A:SER76 4.3 110.2 1.0 OD1 A:ASP39 4.4 136.5 1.0 N A:TYR77 4.5 102.1 1.0 CB A:TYR77 4.5 97.2 1.0 N A:PHE38 4.5 103.9 1.0 N A:ASP184 4.6 90.4 1.0 CA A:TYR77 4.6 98.6 1.0 CB A:PHE38 4.7 91.4 1.0 CB A:SER76 4.7 124.4 1.0 CD2 A:PHE38 4.8 97.8 1.0 CA A:PHE38 5.0 113.2 1.0 CG A:ASP39 5.0 127.7 1.0

Sodium binding site 2 out of 2 in the Human Ptprk N-Terminal Domains Mam-Ig-FN1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Ptprk N-Terminal Domains Mam-Ig-FN1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:110.7 occ:1.00 O B:THR37 2.2 152.4 1.0 O B:HOH501 2.3 137.2 1.0 OD1 B:ASP183 2.5 115.5 1.0 O B:SER76 2.5 118.4 1.0 CG B:ASP183 3.3 105.8 1.0 OD2 B:ASP183 3.3 104.8 1.0 C B:THR37 3.4 120.4 1.0 C B:SER76 3.8 117.1 1.0 CA B:THR37 4.0 122.6 1.0 CB B:THR37 4.2 120.1 1.0 OD1 B:ASP39 4.2 134.0 1.0 N B:PHE38 4.4 114.6 1.0 N B:SER76 4.5 119.8 1.0 CB B:PHE38 4.6 107.3 1.0 CA B:SER76 4.6 115.4 1.0 N B:ASP184 4.6 94.7 1.0 N B:TYR77 4.7 106.0 1.0 CB B:ASP183 4.8 87.4 1.0 CB B:SER76 4.8 122.3 1.0 N B:ASP39 4.8 123.3 1.0 CA B:PHE38 4.8 117.6 1.0 C B:PHE38 4.8 120.8 1.0 CG B:ASP39 4.8 135.2 1.0 CA B:TYR77 4.9 97.2 1.0 CD2 B:PHE38 4.9 102.1 1.0 OG1 B:THR37 4.9 117.0 1.0 CB B:TYR77 4.9 96.8 1.0

I.M.Hay, M.Shamin, E.R.Caroe, A.S.A.Mohammed, D.I.Svergun, C.M.Jeffries, S.C.Graham, H.J.Sharpe, J.E.Deane. Determinants of Receptor Tyrosine Phosphatase Homophilic Adhesion: Structural Comparison of Ptprk and Ptprm Extracellular Domains. J.Biol.Chem. V. 299 02750 2023.
ISSN: ESSN 1083-351X
PubMed: 36436563
DOI: 10.1016/J.JBC.2022.102750