Calcium in PDB 3q3k: Factor Xa in Complex with A Phenylenediamine Derivative

All present enzymatic activity of Factor Xa in Complex with A Phenylenediamine Derivative:
3.4.21.6;

The structure of Factor Xa in Complex with A Phenylenediamine Derivative, PDB code: 3q3k was solved by M.Suzuki, E.Imai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.073, 73.202, 79.520, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 21.6

The structure of Factor Xa in Complex with A Phenylenediamine Derivative also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Factor Xa in Complex with A Phenylenediamine Derivative (pdb code 3q3k). 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 A Phenylenediamine Derivative, PDB code: 3q3k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Factor Xa in Complex with A Phenylenediamine Derivative


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 A Phenylenediamine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca261 b:59.6 occ:1.00 O A:TYR185 2.2 33.6 1.0 O A:LYS224 2.3 34.2 1.0 O A:ARG222 2.4 40.1 1.0 O A:HOH357 2.6 42.9 1.0 O A:ASP185A 2.8 40.5 1.0 C A:LYS224 3.4 34.7 1.0 C A:TYR185 3.4 33.9 1.0 C A:ASP185A 3.5 39.9 1.0 C A:ARG222 3.6 39.5 1.0 N A:LYS224 3.6 36.1 1.0 CA A:LYS224 4.0 35.6 1.0 CA A:ASP185A 4.0 39.0 1.0 N A:ASP185A 4.2 36.7 1.0 C A:ALA221 4.2 37.5 1.0 O A:HOH316 4.2 32.3 1.0 N A:GLY223A 4.2 37.7 1.0 N A:ARG222 4.2 38.5 1.0 CA A:LYS223 4.3 39.3 1.0 O A:ALA221 4.4 37.4 1.0 N A:THR185B 4.4 40.7 1.0 N A:LYS223 4.4 39.5 1.0 N A:TYR225 4.4 33.7 1.0 C A:LYS223 4.5 38.7 1.0 CB A:LYS224 4.5 36.3 1.0 CA A:TYR185 4.5 33.0 1.0 CA A:ARG222 4.5 39.0 1.0 CA A:ALA221 4.6 36.6 1.0 N A:TYR185 4.6 31.7 1.0 O A:LYS186 4.6 41.0 1.0 C A:GLY223A 4.7 37.1 1.0 CA A:TYR225 4.7 32.5 1.0 CA A:THR185B 4.8 41.6 1.0 CA A:GLY223A 4.9 36.9 1.0

Calcium binding site 2 out of 2 in the Factor Xa in Complex with A Phenylenediamine Derivative


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 A Phenylenediamine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca262 b:41.4 occ:1.00 O A:HOH399 2.2 48.8 1.0 OD1 A:ASP70 2.3 31.5 1.0 O A:GLN75 2.3 54.6 1.0 O A:ASN72 2.4 38.9 1.0 OE2 A:GLU80 2.4 42.3 1.0 O A:HOH387 2.9 45.0 1.0 CG A:ASP70 3.2 30.9 1.0 CD A:GLU80 3.3 41.0 1.0 C A:GLN75 3.3 54.2 1.0 C A:ASN72 3.4 38.7 1.0 OD2 A:ASP70 3.6 34.1 1.0 CG A:GLU80 3.7 37.8 1.0 CA A:GLU76 3.9 55.1 1.0 N A:ASN72 4.0 35.4 1.0 N A:GLU76 4.0 54.7 1.0 N A:GLU77 4.1 54.3 1.0 CA A:ASN72 4.1 37.4 1.0 N A:THR73 4.3 40.6 1.0 CA A:THR73 4.4 42.5 1.0 N A:GLN75 4.4 52.3 1.0 OE1 A:GLU80 4.4 41.5 1.0 CB A:ASP70 4.4 30.9 1.0 CA A:GLN75 4.4 53.5 1.0 CB A:ASN72 4.5 37.7 1.0 C A:GLU76 4.5 54.8 1.0 N A:ARG71 4.6 30.9 1.0 CA A:ASP70 4.6 30.3 1.0 C A:THR73 4.8 44.6 1.0 CB A:GLU77 5.0 53.8 1.0

K.Yoshikawa, T.Yoshino, Y.Yokomizo, K.Uoto, H.Naito, K.Kawakami, A.Mochizuki, T.Nagata, M.Suzuki, H.Kanno, M.Takemura, T.Ohta. Design, Synthesis and Sar of Novel Ethylenediamine and Phenylenediamine Derivatives As Factor Xa Inhibitors. Bioorg.Med.Chem.Lett. V. 21 2133 2011.
ISSN: ISSN 0960-894X
PubMed: 21345673
DOI: 10.1016/J.BMCL.2011.01.132