Calcium in PDB 3iit: Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane Derivative

All present enzymatic activity of Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane Derivative:
3.4.21.6;

The structure of Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane Derivative, PDB code: 3iit was solved by M.Suzuki, 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 (°)	56.055, 72.179, 79.238, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.3

The structure of Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane 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 Cis-1,2-Diaminocyclohexane Derivative (pdb code 3iit). 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 Cis-1,2-Diaminocyclohexane Derivative, PDB code: 3iit:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane 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 Cis-1,2-Diaminocyclohexane Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca261 b:40.3 occ:1.00 OD1 A:ASP70 2.2 28.4 1.0 O A:GLN75 2.2 53.7 1.0 OE2 A:GLU80 2.4 39.3 1.0 O A:ASN72 2.5 32.1 1.0 O A:HOH15 2.5 32.1 1.0 O A:HOH321 2.6 49.1 1.0 CD A:GLU80 3.4 42.5 1.0 CG A:ASP70 3.4 30.8 1.0 C A:GLN75 3.5 53.4 1.0 C A:ASN72 3.5 31.5 1.0 CG A:GLU80 3.7 38.6 1.0 OD2 A:ASP70 4.0 32.2 1.0 N A:ASN72 4.0 29.2 1.0 CA A:ASN72 4.2 29.9 1.0 N A:GLN75 4.2 50.6 1.0 N A:GLU77 4.3 54.6 1.0 CA A:GLU76 4.3 54.5 1.0 N A:GLU76 4.3 53.9 1.0 N A:THR73 4.4 34.9 1.0 CA A:THR73 4.4 38.1 1.0 CA A:GLN75 4.4 52.5 1.0 CB A:ASN72 4.5 29.9 1.0 N A:ARG71 4.5 26.2 1.0 OE1 A:GLU80 4.5 44.5 1.0 CB A:ASP70 4.5 26.4 1.0 CA A:ASP70 4.6 26.7 1.0 C A:THR73 4.8 41.4 1.0 C A:GLU76 4.8 54.7 1.0

Calcium binding site 2 out of 2 in the Factor Xa in Complex with A Cis-1,2-Diaminocyclohexane 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 Cis-1,2-Diaminocyclohexane Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca262 b:51.5 occ:1.00 O A:TYR185 2.2 31.1 1.0 O A:LYS224 2.3 32.7 1.0 O A:ARG222 2.4 34.3 1.0 O A:HOH283 2.4 39.2 1.0 O A:ASP185A 2.6 33.8 1.0 O A:HOH267 3.0 32.6 1.0 C A:ASP185A 3.3 34.4 1.0 C A:TYR185 3.4 31.5 1.0 C A:LYS224 3.4 32.9 1.0 C A:ARG222 3.5 34.8 1.0 N A:LYS224 3.6 33.7 1.0 CA A:ASP185A 3.8 34.6 1.0 N A:ASP185A 4.0 33.6 1.0 CA A:LYS224 4.1 32.8 1.0 C A:ALA221 4.1 34.4 1.0 N A:THR185B 4.2 34.9 1.0 O A:ALA221 4.2 34.5 1.0 N A:ARG222 4.2 34.6 1.0 N A:GLY223A 4.2 34.1 1.0 CA A:LYS223 4.3 34.5 1.0 N A:LYS223 4.3 34.2 1.0 O A:HOH279 4.4 27.9 1.0 C A:LYS223 4.4 34.6 1.0 CA A:ARG222 4.5 35.0 1.0 CA A:ALA221 4.5 33.8 1.0 CA A:THR185B 4.5 35.0 1.0 CA A:TYR185 4.6 30.8 1.0 N A:TYR225 4.6 31.5 1.0 O A:LYS186 4.6 36.0 1.0 CB A:LYS224 4.7 32.7 1.0 C A:GLY223A 4.7 34.6 1.0 N A:TYR185 4.7 29.6 1.0 CA A:TYR225 4.9 29.9 1.0 C A:THR185B 4.9 35.0 1.0

K.Yoshikawa, S.Kobayashi, Y.Nakamoto, N.Haginoya, S.Komoriya, T.Yoshino, T.Nagata, A.Mochizuki, K.Watanabe, M.Suzuki, H.Kanno, T.Ohta. Design, Synthesis, and Sar of Cis-1,2-Diaminocyclohexane Derivatives As Potent Factor Xa Inhibitors. Part II: Exploration of 6-6 Fused Rings As Alternative S1 Moieties. Bioorg.Med.Chem. V. 17 8221 2009.
ISSN: ISSN 0968-0896
PubMed: 19900814
DOI: 10.1016/J.BMC.2009.10.024