Sodium in PDB 2fir: Crystal Structure of Dfpr-Viia/Stf

All present enzymatic activity of Crystal Structure of Dfpr-Viia/Stf:
3.4.21.21;

The structure of Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, D.Prevost, H.Schreuder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.020, 80.980, 126.330, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 28.1

The structure of Crystal Structure of Dfpr-Viia/Stf also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Zinc	(Zn)	2 atoms
Calcium	(Ca)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir:

Sodium binding site 1 out of 1 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1010 b:27.8 occ:1.00 O H:HOH1290 2.5 72.0 1.0 O H:THR221 2.5 19.1 1.0 O H:TYR184 2.7 16.7 1.0 N H:GLY187 3.0 20.3 1.0 O H:HOH1198 3.1 24.5 1.0 O H:HIS224 3.1 17.2 1.0 C H:SER185 3.2 16.3 1.0 C H:THR221 3.3 17.9 1.0 CA H:SER185 3.3 15.7 1.0 O H:SER185 3.4 17.3 1.0 CA H:GLY187 3.4 17.0 1.0 N H:THR221 3.6 15.2 1.0 C H:ALA221A 3.6 13.7 1.0 C H:TYR184 3.6 16.5 1.0 N H:ASP186 3.7 16.7 1.0 N H:VAL222 3.9 18.3 1.0 N H:SER185 3.9 14.9 1.0 CA H:ALA221A 3.9 14.8 1.0 O H:ALA221A 4.0 14.1 1.0 CA H:VAL222 4.0 15.4 1.0 CA H:THR221 4.1 17.2 1.0 C H:ASP186 4.1 20.3 1.0 C H:HIS224 4.2 15.0 1.0 N H:HIS224 4.3 13.9 1.0 CA H:ASP186 4.4 18.6 1.0 C H:GLY187 4.5 18.8 1.0 N H:GLY223 4.5 14.6 1.0 C H:VAL222 4.6 16.4 1.0 CB H:SER185 4.6 16.5 1.0 N H:SER188A 4.6 15.2 1.0 O H:HOH1216 4.7 19.0 1.0 CB H:ALA221A 4.8 11.8 1.0 CA H:HIS224 4.8 15.8 1.0 O H:HOH1067 4.8 16.9 1.0 N H:ALA221A 4.9 17.8 1.0 OD1 H:ASP186 4.9 22.6 1.0 CA H:TYR184 5.0 15.5 1.0

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+ and ZN2+ Sites in Factor Viia J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200