Sodium in PDB 2y5f: Factor Xa - Cation Inhibitor Complex

All present enzymatic activity of Factor Xa - Cation Inhibitor Complex:
3.4.21.6;

The structure of Factor Xa - Cation Inhibitor Complex, PDB code: 2y5f was solved by D.W.Banner, L.M.Salonen, M.C.Holland, W.Haap, J.Benz, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.937, 74.300, 77.201, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 17.47

The structure of Factor Xa - Cation Inhibitor Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Factor Xa - Cation Inhibitor Complex (pdb code 2y5f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Factor Xa - Cation Inhibitor Complex, PDB code: 2y5f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Factor Xa - Cation Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Factor Xa - Cation Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1245 b:22.1 occ:1.00 O A:GLN75 2.2 33.9 1.0 OD1 A:ASP70 2.3 27.6 1.0 OE2 A:GLU80 2.3 26.4 1.0 O A:ASN72 2.4 24.3 1.0 O A:HOH2075 2.4 35.7 1.0 O A:HOH2073 2.5 30.7 1.0 HG2 A:GLU80 3.1 26.7 1.0 H A:ASN72 3.3 23.1 1.0 CD A:GLU80 3.3 26.9 1.0 CG A:ASP70 3.3 27.2 1.0 C A:GLN75 3.4 29.3 1.0 H A:GLU77 3.4 32.9 1.0 C A:ASN72 3.5 23.0 1.0 H A:GLN75 3.5 26.2 1.0 HA A:GLU76 3.7 30.6 1.0 CG A:GLU80 3.7 25.2 1.0 HA A:THR73 3.8 25.6 1.0 OD2 A:ASP70 3.8 29.4 1.0 HB3 A:ASN72 3.9 26.2 1.0 HG3 A:GLU80 3.9 24.7 1.0 HA A:ASP70 3.9 24.6 1.0 HB2 A:GLU77 3.9 37.5 1.0 H A:ARG71 4.1 21.6 1.0 N A:ASN72 4.1 23.4 1.0 HB3 A:GLN75 4.2 27.9 1.0 O A:HOH2091 4.2 45.4 1.0 N A:GLU77 4.2 32.7 1.0 N A:GLN75 4.2 25.8 1.0 CA A:ASN72 4.3 24.0 1.0 N A:GLU76 4.3 32.1 1.0 CA A:GLN75 4.3 27.4 1.0 CA A:GLU76 4.4 32.8 1.0 N A:THR73 4.4 22.3 1.0 CA A:THR73 4.4 24.6 1.0 OE1 A:GLU80 4.5 28.7 1.0 O A:HOH2072 4.5 30.2 1.0 CB A:ASP70 4.5 24.5 1.0 CB A:ASN72 4.6 24.1 1.0 CA A:ASP70 4.7 24.0 1.0 N A:ARG71 4.7 23.4 1.0 C A:THR73 4.7 27.4 1.0 CB A:GLN75 4.8 28.2 1.0 CB A:GLU77 4.8 39.9 1.0 C A:GLU76 4.8 31.4 1.0 HB2 A:ASP70 4.9 24.8 1.0 HB3 A:GLU77 4.9 38.9 1.0

Sodium binding site 2 out of 2 in the Factor Xa - Cation Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Factor Xa - Cation Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1246 b:19.9 occ:1.00 O A:HOH2244 2.3 22.7 1.0 O A:LYS224 2.3 19.5 1.0 O A:TYR185 2.3 19.1 1.0 O A:ARG222 2.3 20.7 1.0 O A:ASP185A 2.5 21.2 1.0 O A:HOH2278 2.9 21.2 1.0 H A:LYS224 3.1 19.4 1.0 C A:ASP185A 3.2 19.5 1.0 C A:ARG222 3.4 22.0 1.0 C A:TYR185 3.4 18.1 1.0 HA A:ASP185A 3.5 21.4 1.0 C A:LYS224 3.5 19.0 1.0 HA A:LYS223 3.5 22.3 1.0 H A:GLY223A 3.7 21.8 1.0 CA A:ASP185A 3.8 19.1 1.0 N A:LYS224 3.8 19.9 1.0 HA A:ALA221 3.9 20.9 1.0 N A:ASP185A 4.0 19.5 1.0 HA A:THR185B 4.1 21.2 1.0 N A:GLY223A 4.1 21.4 1.0 C A:ALA221 4.1 21.0 1.0 N A:THR185B 4.2 19.9 1.0 N A:ARG222 4.2 21.4 1.0 N A:LYS223 4.2 23.5 1.0 HA A:TYR225 4.2 17.5 1.0 CA A:LYS223 4.2 23.2 1.0 CA A:LYS224 4.2 18.9 1.0 HB2 A:LYS224 4.2 20.4 1.0 O A:ALA221 4.3 23.6 1.0 O A:HOH2249 4.3 18.9 1.0 H A:TYR185 4.3 16.4 1.0 CA A:ARG222 4.4 21.3 1.0 H A:ARG222 4.4 21.6 1.0 C A:LYS223 4.4 22.4 1.0 HB2 A:TYR185 4.5 17.7 1.0 CA A:THR185B 4.6 20.8 1.0 CA A:ALA221 4.6 20.4 1.0 N A:TYR225 4.6 18.6 1.0 O A:LYS186 4.6 20.3 1.0 CA A:TYR185 4.6 17.1 1.0 CB A:LYS224 4.8 20.2 1.0 C A:GLY223A 4.8 21.6 1.0 H A:THR185B 4.8 19.8 1.0 CA A:TYR225 4.9 18.4 1.0 N A:TYR185 4.9 16.8 1.0 H A:ASP185A 4.9 19.4 1.0 C A:THR185B 4.9 20.4 1.0 CA A:GLY223A 4.9 22.1 1.0 HD1 A:TYR225 5.0 19.4 1.0 H A:LYS223 5.0 23.3 1.0 CB A:TYR185 5.0 18.1 1.0

L.M.Salonen, M.C.Holland, P.S.Kaib, W.Haap, J.Benz, J.L.Mary, O.Kuster, W.B.Schweizer, D.W.Banner, F.Diederich. Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water. Chemistry V. 18 213 2012.
ISSN: ISSN 0947-6539
PubMed: 22162109
DOI: 10.1002/CHEM.201102571