Sodium in PDB 1sfq: Fast Form of Thrombin Mutant R(77A)A Bound to Ppack

All present enzymatic activity of Fast Form of Thrombin Mutant R(77A)A Bound to Ppack:
3.4.21.5;

The structure of Fast Form of Thrombin Mutant R(77A)A Bound to Ppack, PDB code: 1sfq was solved by A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.51 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.340, 68.200, 162.930, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.1

The binding sites of Sodium atom in the Fast Form of Thrombin Mutant R(77A)A Bound to Ppack (pdb code 1sfq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Fast Form of Thrombin Mutant R(77A)A Bound to Ppack, PDB code: 1sfq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Fast Form of Thrombin Mutant R(77A)A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fast Form of Thrombin Mutant R(77A)A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:27.5 occ:1.00 O B:ARG221A 2.4 26.7 1.0 O B:HOH701 2.4 31.6 1.0 O B:HOH722 2.5 24.0 1.0 O B:LYS224 2.5 21.4 1.0 O B:HOH723 2.5 22.3 1.0 O B:HOH718 2.8 27.1 1.0 C B:ARG221A 3.4 29.3 1.0 C B:LYS224 3.6 23.6 1.0 N B:ARG221A 3.8 25.1 1.0 O B:HOH738 3.9 26.2 1.0 N B:LYS224 3.9 25.5 1.0 C B:ASP221 4.0 25.7 1.0 O B:HOH759 4.0 30.5 1.0 O B:TYR184A 4.1 23.9 1.0 N B:ASP222 4.2 29.0 1.0 O B:HOH706 4.2 19.1 1.0 N B:GLY223 4.2 26.4 1.0 CA B:ASP222 4.3 29.8 1.0 CA B:ARG221A 4.3 28.2 1.0 CA B:LYS224 4.3 22.8 1.0 CA B:ASP221 4.3 23.9 1.0 O B:HOH724 4.5 30.1 1.0 O B:ASP221 4.5 24.2 1.0 C B:ASP222 4.5 29.1 1.0 OD1 B:ASP221 4.5 25.1 1.0 CB B:LYS224 4.6 23.5 1.0 N B:TYR225 4.6 20.8 1.0 CA B:TYR225 4.8 20.8 1.0 C B:GLY223 4.9 25.8 1.0

Sodium binding site 2 out of 2 in the Fast Form of Thrombin Mutant R(77A)A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fast Form of Thrombin Mutant R(77A)A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ E:Na402 b:31.1 occ:1.00 O E:ARG221A 2.4 26.9 1.0 O E:HOH733 2.5 26.4 1.0 O E:HOH706 2.5 23.1 1.0 O E:LYS224 2.6 26.8 1.0 O E:HOH783 2.6 36.2 1.0 O E:HOH762 2.7 30.1 1.0 C E:ARG221A 3.4 31.0 1.0 C E:LYS224 3.6 24.2 1.0 O E:HOH790 3.8 30.3 1.0 N E:LYS224 3.8 28.3 1.0 N E:ARG221A 3.9 27.2 1.0 C E:ASP221 4.0 28.7 1.0 O E:HOH765 4.0 34.0 1.0 O E:TYR184A 4.0 27.2 1.0 O E:HOH718 4.2 23.5 1.0 N E:GLY223 4.2 31.1 1.0 CA E:LYS224 4.2 25.7 1.0 N E:ASP222 4.3 32.2 1.0 CA E:ASP221 4.3 27.8 1.0 CA E:ASP222 4.3 33.1 1.0 CA E:ARG221A 4.3 29.9 1.0 O E:ASP221 4.4 29.3 1.0 OD1 E:ASP221 4.5 29.5 1.0 C E:ASP222 4.5 31.0 1.0 O E:HOH785 4.6 33.2 1.0 CB E:LYS224 4.6 25.7 1.0 N E:TYR225 4.7 21.2 1.0 C E:GLY223 4.9 27.6 1.0 CA E:TYR225 4.9 20.6 1.0

A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, E.Di Cera. Molecular Dissection of Na+ Binding to Thrombin. J.Biol.Chem. V. 279 31842 2004.
ISSN: ISSN 0021-9258
PubMed: 15152000
DOI: 10.1074/JBC.M401756200