Calcium in PDB 3tk5: Factor Xa in Complex with D102-4380

All present enzymatic activity of Factor Xa in Complex with D102-4380:
3.4.21.6;

The structure of Factor Xa in Complex with D102-4380, PDB code: 3tk5 was solved by M.Suzuki, A.Mochizuki, T.Nagata, H.Takano, H.Kanno, M.Kishida, T.Ohta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.278, 71.928, 78.775, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.3

The structure of Factor Xa in Complex with D102-4380 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Factor Xa in Complex with D102-4380 (pdb code 3tk5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Factor Xa in Complex with D102-4380, PDB code: 3tk5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Factor Xa in Complex with D102-4380


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Xa in Complex with D102-4380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca261 b:61.5 occ:1.00 O A:LYS224 2.3 35.4 1.0 O A:TYR185 2.4 34.5 1.0 O A:HOH326 2.5 46.3 1.0 O A:ARG222 2.6 37.8 1.0 O A:ASP185A 2.6 37.2 1.0 O A:HOH342 2.7 29.2 1.0 C A:ASP185A 3.3 36.9 1.0 C A:LYS224 3.4 35.3 1.0 C A:TYR185 3.5 34.6 1.0 C A:ARG222 3.6 37.4 1.0 N A:LYS224 3.6 36.7 1.0 CA A:ASP185A 3.8 36.8 1.0 CA A:LYS224 4.1 35.8 1.0 N A:ASP185A 4.1 35.7 1.0 N A:GLY223A 4.1 37.1 1.0 O A:HOH323 4.1 29.4 1.0 C A:ALA221 4.1 36.0 1.0 O A:ALA221 4.2 36.6 1.0 N A:THR185B 4.2 36.9 1.0 CA A:LYS223 4.3 37.6 1.0 N A:LYS223 4.3 37.4 1.0 C A:LYS223 4.4 37.3 1.0 N A:ARG222 4.4 36.2 1.0 CA A:ALA221 4.5 35.5 1.0 N A:TYR225 4.5 34.2 1.0 CA A:ARG222 4.6 37.0 1.0 CB A:LYS224 4.6 36.0 1.0 C A:GLY223A 4.6 37.1 1.0 CA A:THR185B 4.6 37.0 1.0 CA A:TYR185 4.7 33.8 1.0 O A:LYS186 4.8 40.3 1.0 N A:TYR185 4.8 33.0 1.0 CA A:TYR225 4.8 33.6 1.0 CA A:GLY223A 4.8 36.9 1.0

Calcium binding site 2 out of 2 in the Factor Xa in Complex with D102-4380


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Factor Xa in Complex with D102-4380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca262 b:40.6 occ:1.00 O A:GLN75 2.2 51.6 1.0 OD1 A:ASP70 2.3 33.1 1.0 OE2 A:GLU80 2.3 36.3 1.0 O A:ASN72 2.3 38.8 1.0 O A:HOH9 2.5 31.1 1.0 O A:HOH324 2.5 51.9 1.0 CD A:GLU80 3.4 36.1 1.0 C A:GLN75 3.4 51.9 1.0 CG A:ASP70 3.4 33.1 1.0 C A:ASN72 3.4 38.5 1.0 CG A:GLU80 3.8 36.2 1.0 OD2 A:ASP70 4.0 33.9 1.0 N A:GLU77 4.1 51.0 1.0 N A:ASN72 4.1 35.3 1.0 CA A:GLU76 4.2 51.6 1.0 N A:GLU76 4.2 51.7 1.0 N A:GLN75 4.3 51.1 1.0 CA A:ASN72 4.3 36.7 1.0 N A:THR73 4.3 40.2 1.0 CA A:THR73 4.4 42.6 1.0 CA A:GLN75 4.4 52.3 1.0 OE1 A:GLU80 4.5 35.8 1.0 CB A:ASP70 4.6 32.3 1.0 CB A:ASN72 4.6 36.6 1.0 C A:THR73 4.6 44.3 1.0 C A:GLU76 4.7 51.4 1.0 N A:ARG71 4.7 31.9 1.0 CA A:ASP70 4.7 31.9 1.0 CB A:GLU77 4.7 50.6 1.0 O A:THR73 5.0 44.8 1.0

A.Mochizuki, T.Nagata, H.Takano, H.Kanno, M.Kishida, M.Suzuki, T.Ohta. Zwitter Ionic Potent Durable Orally Active Factor Xa Inhibitor. To Be Published.