Sodium in PDB 3pmb: 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup

All present enzymatic activity of 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup:
3.4.21.5;

The structure of 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup, PDB code: 3pmb was solved by H.T.Wright, J.N.Scarsdale, B.J.Desai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.644, 87.644, 194.514, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 30.1

The binding sites of Sodium atom in the 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup (pdb code 3pmb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup, PDB code: 3pmb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:34.0 occ:1.00 O B:LYS224 2.6 22.8 1.0 O B:ARG221A 2.9 22.8 1.0 O B:HOH263 3.6 18.4 1.0 O B:TYR184A 3.8 27.0 1.0 C B:LYS224 3.8 23.0 1.0 C B:ARG221A 4.0 23.3 1.0 N B:ARG221A 4.1 22.5 1.0 OD1 B:ASP221 4.3 23.4 1.0 C B:ASP221 4.3 22.8 1.0 CA B:ASP221 4.3 22.2 1.0 O B:GLY188 4.6 22.9 1.0 N B:TYR225 4.6 22.8 1.0 N B:LYS224 4.6 24.6 1.0 CA B:TYR225 4.6 22.3 1.0 CA B:ARG221A 4.7 23.1 1.0 CA B:LYS224 4.7 23.8 1.0 N B:TYR184A 4.8 25.6 1.0 CD2 B:TYR225 4.8 23.1 1.0 N B:ASP222 4.9 24.1 1.0 C B:TYR184A 4.9 27.4 1.0 O B:ASP221 4.9 23.4 1.0

Sodium binding site 2 out of 2 in the 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.9 Angstrom Crystal Structure of Bovine Thrombin in Tetragonal Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1 b:25.1 occ:1.00 O D:ARG221A 2.7 19.5 1.0 O D:HOH10 2.7 8.6 1.0 O D:HOH261 2.9 5.4 1.0 O D:LYS224 3.0 18.7 1.0 C D:ARG221A 3.6 20.3 1.0 O D:TYR184A 3.8 22.6 1.0 N D:ARG221A 4.0 20.1 1.0 C D:ASP221 4.1 20.8 1.0 OD1 D:ASP221 4.1 21.5 1.0 C D:LYS224 4.1 18.4 1.0 CA D:ASP221 4.3 20.3 1.0 O D:HOH77 4.3 13.1 1.0 N D:ASP222 4.5 21.1 1.0 CA D:ARG221A 4.5 20.5 1.0 O D:ASP221 4.6 21.9 1.0 CA D:ASP222 4.6 21.4 1.0 N D:LYS224 4.6 19.8 1.0 N D:GLY223 4.8 21.0 1.0 CA D:LYS224 4.9 19.1 1.0 CG D:ASP221 4.9 21.5 1.0 C D:TYR184A 4.9 22.8 1.0 NH2 D:ARG187 4.9 23.5 1.0 O D:GLY188 5.0 20.6 1.0 N D:TYR184A 5.0 21.4 1.0

B.J.Desai, R.S.Boothello, A.Y.Mehta, J.N.Scarsdale, H.T.Wright, U.R.Desai. Interaction of Thrombin with Sucrose Octasulfate. Biochemistry V. 50 6973 2011.
ISSN: ISSN 0006-2960
PubMed: 21736375
DOI: 10.1021/BI2004526