Sodium in PDB 6mv4: Crystal Structure of Human Coagulation Factor Ixa

All present enzymatic activity of Crystal Structure of Human Coagulation Factor Ixa:
3.4.21.22;

The structure of Crystal Structure of Human Coagulation Factor Ixa, PDB code: 6mv4 was solved by K.Vadivel, H.A.Schreuder, A.Liesum, S.P.Bajaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.64 / 1.37
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.758, 109.758, 112.458, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21

The structure of Crystal Structure of Human Coagulation Factor Ixa also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Coagulation Factor Ixa (pdb code 6mv4). 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 Human Coagulation Factor Ixa, PDB code: 6mv4:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Coagulation Factor Ixa


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 Human Coagulation Factor Ixa within 5.0Å range: probe atom residue distance (Å) B Occ H:Na312 b:38.2 occ:1.00 O H:MET221A 2.4 26.8 0.5 O H:MET221A 2.4 26.7 0.5 O H:PHE184A 2.4 26.2 1.0 O H:HOH593 2.5 30.7 1.0 O H:LYS224 2.8 20.9 1.0 N H:GLY187 3.1 28.5 1.0 O H:HOH543 3.1 40.0 1.0 CA H:GLY187 3.1 27.2 1.0 O H:HIS185 3.3 26.4 0.6 C H:MET221A 3.3 27.5 0.5 C H:MET221A 3.3 27.7 0.5 C H:PHE184A 3.6 23.8 1.0 C H:HIS185 3.7 26.2 0.6 C H:HIS185 3.8 26.4 0.4 CA H:HIS185 3.9 25.8 0.4 N H:MET221A 3.9 26.1 0.5 C H:LYS224 4.0 19.5 1.0 C H:ALA221 4.0 25.1 1.0 N H:MET221A 4.0 26.0 0.5 N H:LYS222 4.1 28.3 1.0 CA H:LYS222 4.1 28.9 1.0 N H:LYS224 4.1 20.9 1.0 O H:HOH565 4.1 22.0 1.0 O H:HIS185 4.1 27.0 0.4 N H:GLU186 4.2 27.3 0.5 C H:GLU186 4.2 28.7 0.5 O H:ALA221 4.2 26.4 1.0 N H:HIS185 4.2 25.1 0.4 C H:GLY187 4.2 27.1 1.0 CA H:HIS185 4.2 25.4 0.6 C H:GLU186 4.3 28.6 0.5 CA H:MET221A 4.3 27.6 0.5 N H:HIS185 4.3 24.5 0.6 CA H:MET221A 4.3 28.0 0.5 CA H:ALA221 4.4 24.5 1.0 N H:GLY223 4.4 26.2 1.0 N H:GLU186 4.4 27.5 0.5 C H:LYS222 4.5 27.8 1.0 CA H:LYS224 4.6 20.0 1.0 CA H:PHE184A 4.6 22.0 1.0 N H:GLY188 4.7 24.7 1.0 CB H:PHE184A 4.8 21.8 1.0 N H:PHE184A 4.8 20.2 1.0 CA H:GLU186 4.9 27.8 0.5 CA H:GLU186 4.9 28.1 0.5 O H:ARG188A 4.9 17.0 1.0 O H:GLY187 5.0 30.1 1.0

K.Vadivel, H.A.Schreuder, A.Liesum, A.E.Schmidt, G.Goldsmith, S.P.Bajaj. Sodium-Site in Serine Protease Domain of Human Coagulation Factor Ixa: Evidence From the Crystal Structure and Molecular Dynamics Simulations Study. J. Thromb. Haemost. V. 17 574 2019.
ISSN: ESSN 1538-7836
PubMed: 30725510
DOI: 10.1111/JTH.14401