Sodium in PDB 2a1d: Staphylocoagulase Bound to Bovine Thrombin

All present enzymatic activity of Staphylocoagulase Bound to Bovine Thrombin:
3.4.21.5;

The structure of Staphylocoagulase Bound to Bovine Thrombin, PDB code: 2a1d was solved by R.Friedrich, P.Panizzi, S.Kawabata, W.Bode, P.E.Bock, P.Fuentes-Prior, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.69 / 3.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.780, 102.540, 134.040, 90.00, 129.14, 90.00
R / Rfree (%)	23.3 / 30.6

The binding sites of Sodium atom in the Staphylocoagulase Bound to Bovine Thrombin (pdb code 2a1d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Staphylocoagulase Bound to Bovine Thrombin, PDB code: 2a1d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Staphylocoagulase Bound to Bovine Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Staphylocoagulase Bound to Bovine Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:55.0 occ:1.00 O B:ARG221A 3.1 52.2 1.0 OD1 B:ASP221 3.7 38.9 1.0 O B:LYS224 3.8 65.8 1.0 O B:TYR184 3.9 0.5 1.0 CA B:ASP221 4.0 54.0 1.0 C B:ASP221 4.0 54.0 1.0 O B:GLY188 4.0 79.1 1.0 O B:ASP221 4.2 54.0 1.0 C B:ARG221A 4.3 52.2 1.0 N B:ARG221A 4.5 52.2 1.0 CG B:ASP221 4.5 38.9 1.0 N B:TYR184 4.7 0.5 1.0 OD2 B:ASP222 4.8 91.1 1.0 CB B:ASP221 4.9 38.9 1.0 CD1 B:TYR225 4.9 0.2 1.0 C B:TYR184 4.9 0.5 1.0 N B:ASP221 5.0 54.0 1.0

Sodium binding site 2 out of 2 in the Staphylocoagulase Bound to Bovine Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Staphylocoagulase Bound to Bovine Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ F:Na902 b:55.0 occ:1.00 O F:GLY188 3.2 64.2 1.0 O F:TYR184 3.6 76.0 1.0 OD1 F:ASP221 3.7 46.6 1.0 N F:TYR184 3.8 76.0 1.0 O F:ARG221A 4.2 58.0 1.0 C F:GLY188 4.4 64.2 1.0 CA F:ASP221 4.4 51.6 1.0 N F:GLY188 4.4 64.2 1.0 O F:LYS224 4.4 56.9 1.0 CB F:TYR184 4.4 76.2 1.0 CA F:TYR184 4.4 76.0 1.0 C F:TYR184 4.5 76.0 1.0 CA F:GLY184A 4.6 61.2 1.0 CG F:ASP221 4.7 46.6 1.0 C F:GLY184A 4.7 61.2 1.0 C F:ASP221 4.7 51.6 1.0 CD1 F:TYR225 4.8 90.5 1.0 CB F:ASP189 4.8 48.1 1.0 O F:ASP221 4.9 51.6 1.0 OD1 F:ASP189 5.0 48.1 1.0

R.Friedrich, P.Panizzi, S.Kawabata, W.Bode, P.E.Bock, P.Fuentes-Prior. Structural Basis For Reduced Staphylocoagulase-Mediated Bovine Prothrombin Activation J.Biol.Chem. V. 281 1188 2006.
ISSN: ISSN 0021-9258
PubMed: 16230338
DOI: 10.1074/JBC.M507957200