Sodium in PDB 2y5g: 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: 2y5g 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)	40.88 / 1.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.946, 74.353, 77.029, 90.00, 90.00, 90.00
R / Rfree (%)	14.549 / 18.555

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 2y5g). 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: 2y5g:
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:25.1 occ:1.00 O A:GLN75 2.1 35.1 1.0 OD1 A:ASP70 2.3 31.0 1.0 OE2 A:GLU80 2.3 29.4 1.0 O A:HOH2064 2.3 37.2 1.0 O A:ASN72 2.4 26.4 1.0 O A:HOH2065 2.5 32.8 1.0 HG2 A:GLU80 3.1 28.5 1.0 CG A:ASP70 3.3 29.2 1.0 CD A:GLU80 3.3 29.4 1.0 H A:ASN72 3.4 25.2 1.0 C A:GLN75 3.4 31.2 1.0 C A:ASN72 3.5 26.2 1.0 H A:GLU77 3.6 34.0 1.0 H A:GLN75 3.6 26.8 1.0 HA A:GLU76 3.6 31.8 1.0 CG A:GLU80 3.7 26.4 1.0 HA A:THR73 3.7 28.5 1.0 OD2 A:ASP70 3.8 33.2 1.0 HG3 A:GLU80 3.9 26.0 1.0 HB3 A:ASN72 3.9 28.9 1.0 HA A:ASP70 4.0 26.4 1.0 O A:HOH2078 4.1 47.4 1.0 H A:ARG71 4.1 22.9 1.0 N A:ASN72 4.1 25.9 1.0 N A:GLN75 4.2 27.4 1.0 HB3 A:GLN75 4.3 30.3 1.0 CA A:ASN72 4.3 25.7 1.0 N A:GLU76 4.3 34.7 1.0 N A:GLU77 4.3 35.0 1.0 CA A:GLU76 4.3 33.8 1.0 CA A:GLN75 4.4 28.1 1.0 N A:THR73 4.4 24.8 1.0 CA A:THR73 4.4 27.2 1.0 OE1 A:GLU80 4.4 30.4 1.0 CB A:ASP70 4.5 26.8 1.0 O A:HOH2062 4.6 31.8 1.0 CB A:ASN72 4.6 26.6 1.0 HB3 A:GLU77 4.6 38.5 1.0 CA A:ASP70 4.7 25.8 1.0 HB2 A:GLU77 4.7 36.9 1.0 N A:ARG71 4.7 26.4 1.0 C A:THR73 4.7 29.2 1.0 HB2 A:ASP70 4.8 26.6 1.0 CB A:GLN75 4.9 28.6 1.0 OE1 A:GLU76 4.9 54.8 1.0 C A:GLU76 4.9 32.5 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:21.4 occ:1.00 O A:LYS224 2.3 21.4 1.0 O A:TYR185 2.3 20.4 1.0 O A:ARG222 2.3 21.6 1.0 O A:HOH2225 2.3 24.3 1.0 O A:ASP185A 2.5 22.7 1.0 O A:HOH2257 2.9 23.2 1.0 H A:LYS224 3.1 21.2 1.0 C A:ASP185A 3.2 21.0 1.0 C A:ARG222 3.4 23.7 1.0 C A:TYR185 3.4 20.0 1.0 C A:LYS224 3.5 19.4 1.0 HA A:ASP185A 3.5 22.5 1.0 HA A:LYS223 3.6 23.7 1.0 H A:GLY223A 3.7 22.2 1.0 N A:LYS224 3.8 21.8 1.0 CA A:ASP185A 3.8 20.6 1.0 HA A:ALA221 3.9 22.0 1.0 N A:ASP185A 4.0 21.2 1.0 N A:GLY223A 4.1 22.8 1.0 HA A:THR185B 4.1 22.8 1.0 C A:ALA221 4.1 23.8 1.0 CA A:LYS224 4.2 20.8 1.0 N A:THR185B 4.2 21.5 1.0 HA A:TYR225 4.2 18.2 1.0 N A:ARG222 4.2 23.1 1.0 HB2 A:LYS224 4.2 22.4 1.0 CA A:LYS223 4.2 24.8 1.0 N A:LYS223 4.2 24.5 1.0 H A:TYR185 4.3 17.7 1.0 O A:ALA221 4.3 25.6 1.0 O A:HOH2230 4.3 20.5 1.0 H A:ARG222 4.4 23.9 1.0 CA A:ARG222 4.4 24.0 1.0 C A:LYS223 4.4 22.4 1.0 HB2 A:TYR185 4.5 18.4 1.0 N A:TYR225 4.5 19.3 1.0 CA A:ALA221 4.6 22.2 1.0 CA A:THR185B 4.6 22.4 1.0 O A:LYS186 4.6 21.7 1.0 CA A:TYR185 4.6 18.4 1.0 C A:GLY223A 4.7 23.7 1.0 CB A:LYS224 4.7 22.2 1.0 H A:THR185B 4.8 21.3 1.0 CA A:TYR225 4.9 18.4 1.0 N A:TYR185 4.9 17.7 1.0 CA A:GLY223A 4.9 23.1 1.0 H A:ASP185A 4.9 20.6 1.0 HD1 A:TYR225 5.0 20.9 1.0 C A:THR185B 5.0 21.6 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