Calcium in PDB 3tk6: Factor Xa in Complex with D46-5241

All present enzymatic activity of Factor Xa in Complex with D46-5241:
3.4.21.6;

The structure of Factor Xa in Complex with D46-5241, PDB code: 3tk6 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.466, 72.412, 79.074, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.1

The structure of Factor Xa in Complex with D46-5241 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Factor Xa in Complex with D46-5241 (pdb code 3tk6). 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 D46-5241, PDB code: 3tk6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Factor Xa in Complex with D46-5241


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 D46-5241 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca261 b:51.1 occ:1.00 O A:LYS224 2.2 29.3 1.0 O A:TYR185 2.3 32.2 1.0 O A:HOH312 2.4 41.4 1.0 O A:ARG222 2.5 34.8 1.0 O A:ASP185A 2.5 35.9 1.0 O A:HOH329 2.9 33.0 1.0 C A:ASP185A 3.3 36.1 1.0 C A:TYR185 3.4 31.6 1.0 C A:LYS224 3.4 32.0 1.0 C A:ARG222 3.5 35.7 1.0 N A:LYS224 3.7 34.1 1.0 CA A:ASP185A 3.8 35.9 1.0 N A:ASP185A 4.0 33.8 1.0 CA A:LYS224 4.1 33.0 1.0 N A:THR185B 4.1 37.1 1.0 C A:ALA221 4.2 34.0 1.0 N A:ARG222 4.2 34.7 1.0 N A:GLY223A 4.2 35.4 1.0 CA A:LYS223 4.3 36.8 1.0 N A:LYS223 4.3 36.1 1.0 O A:HOH264 4.3 29.3 1.0 O A:ALA221 4.3 34.8 1.0 C A:LYS223 4.5 36.2 1.0 CA A:ARG222 4.5 35.1 1.0 N A:TYR225 4.5 30.6 1.0 CA A:TYR185 4.5 31.7 1.0 CA A:THR185B 4.6 37.7 1.0 CA A:ALA221 4.6 32.9 1.0 O A:LYS186 4.6 36.0 1.0 CB A:LYS224 4.7 33.2 1.0 C A:GLY223A 4.7 35.3 1.0 N A:TYR185 4.7 30.7 1.0 CA A:TYR225 4.8 30.0 1.0 CB A:TYR185 4.9 31.7 1.0 C A:THR185B 5.0 37.2 1.0 CA A:GLY223A 5.0 35.1 1.0

Calcium binding site 2 out of 2 in the Factor Xa in Complex with D46-5241


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 D46-5241 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca262 b:38.3 occ:1.00 O A:GLN75 2.2 55.4 1.0 OD1 A:ASP70 2.3 31.7 1.0 O A:ASN72 2.3 33.0 1.0 OE2 A:GLU80 2.3 43.1 1.0 O A:HOH305 2.3 46.4 1.0 O A:HOH258 2.7 37.1 1.0 CD A:GLU80 3.3 42.8 1.0 CG A:ASP70 3.3 31.6 1.0 C A:ASN72 3.4 32.6 1.0 C A:GLN75 3.4 55.8 1.0 CG A:GLU80 3.7 41.2 1.0 OD2 A:ASP70 3.8 34.0 1.0 N A:ASN72 4.0 28.8 1.0 CA A:GLU76 4.2 58.2 1.0 CA A:ASN72 4.2 30.8 1.0 N A:GLU76 4.3 57.1 1.0 N A:GLU77 4.3 58.6 1.0 N A:GLN75 4.3 52.5 1.0 N A:THR73 4.3 34.2 1.0 CA A:GLN75 4.4 54.6 1.0 CA A:THR73 4.4 37.8 1.0 OE1 A:GLU80 4.4 44.7 1.0 CB A:ASP70 4.5 28.2 1.0 CB A:ASN72 4.6 31.5 1.0 N A:ARG71 4.6 26.2 1.0 CA A:ASP70 4.7 27.1 1.0 C A:THR73 4.8 41.0 1.0 C A:GLU76 4.8 58.6 1.0 CB A:GLN75 5.0 54.8 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.