Calcium in PDB 2w26: Factor Xa in Complex with BAY59-7939

The structure of Factor Xa in Complex with BAY59-7939, PDB code: 2w26 was solved by S.Roehrig, A.Straub, J.Pohlmann, T.Lampe, J.Pernerstorfer, K.Schlemmer, P.Reinemer, E.Perzborn, M.Schaefer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.042, 72.028, 78.446, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.9

The structure of Factor Xa in Complex with BAY59-7939 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Factor Xa in Complex with BAY59-7939 (pdb code 2w26). 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 BAY59-7939, PDB code: 2w26:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Factor Xa in Complex with BAY59-7939


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 BAY59-7939 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1244 b:46.8 occ:1.00 OE2 A:GLU80 2.0 52.8 1.0 OD1 A:ASP70 2.2 47.6 1.0 O A:GLN75 2.3 69.5 1.0 O A:ASN72 2.4 40.7 1.0 O A:HOH2019 2.4 57.3 1.0 O A:HOH2020 2.5 45.2 1.0 CD A:GLU80 3.1 51.8 1.0 CG A:ASP70 3.2 44.4 1.0 C A:ASN72 3.4 42.6 1.0 C A:GLN75 3.4 69.5 1.0 OD2 A:ASP70 3.6 45.4 1.0 CG A:GLU80 3.7 48.6 1.0 N A:GLU77 4.1 70.9 1.0 N A:ASN72 4.1 38.7 1.0 OE1 A:GLU80 4.1 54.4 1.0 CA A:ASN72 4.3 41.3 1.0 N A:THR73 4.3 45.6 1.0 CA A:GLU76 4.3 70.4 1.0 N A:GLU76 4.3 69.9 1.0 N A:GLN75 4.3 66.2 1.0 CA A:THR73 4.3 50.3 1.0 CA A:GLN75 4.4 68.8 1.0 OE2 A:GLU76 4.5 76.8 1.0 CB A:ASP70 4.5 42.2 1.0 CB A:ASN72 4.6 41.6 1.0 C A:THR73 4.6 53.6 1.0 C A:GLU76 4.7 70.6 1.0 N A:ARG71 4.7 38.0 1.0 CB A:GLU77 4.8 73.3 1.0 CA A:ASP70 4.8 38.7 1.0 O A:THR73 4.8 54.0 1.0

Calcium binding site 2 out of 2 in the Factor Xa in Complex with BAY59-7939


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 BAY59-7939 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1245 b:46.7 occ:0.50 O A:TYR185 2.2 38.6 1.0 O A:LYS224 2.3 43.1 1.0 O A:ARG222 2.3 46.3 1.0 O A:ASP185A 2.6 46.2 1.0 O A:HOH2066 3.0 40.2 1.0 C A:ASP185A 3.2 46.3 1.0 C A:TYR185 3.3 40.7 1.0 C A:ARG222 3.4 46.4 1.0 C A:LYS224 3.4 44.2 1.0 CA A:ASP185A 3.6 45.6 1.0 N A:LYS224 3.6 46.5 1.0 N A:ASP185A 3.9 43.7 1.0 CA A:LYS224 4.0 45.1 1.0 N A:GLY223A 4.1 46.5 1.0 C A:ALA221 4.1 45.4 1.0 CA A:LYS223 4.1 46.9 1.0 N A:LYS223 4.2 45.7 1.0 N A:ARG222 4.2 45.1 1.0 O A:ALA221 4.2 44.7 1.0 N A:THR185B 4.2 47.2 1.0 C A:LYS223 4.3 46.6 1.0 O A:HOH2063 4.4 40.3 1.0 CA A:ARG222 4.4 45.8 1.0 O A:LYS186 4.5 50.1 1.0 N A:TYR225 4.5 41.7 1.0 CB A:LYS224 4.5 46.5 1.0 CA A:TYR185 4.5 39.4 1.0 CA A:ALA221 4.6 44.6 1.0 C A:GLY223A 4.7 47.9 1.0 CA A:THR185B 4.7 47.9 1.0 N A:TYR185 4.8 38.1 1.0 CA A:TYR225 4.8 39.3 1.0 CA A:GLY223A 4.9 47.3 1.0 C A:THR185B 5.0 47.7 1.0 CD1 A:TYR225 5.0 44.7 1.0 CB A:TYR185 5.0 39.6 1.0

S.Roehrig, A.Straub, J.Pohlmann, T.Lampe, J.Pernerstorfer, K.Schlemmer, P.Reinemer, E.Perzborn. Discovery of the Novel Antithrombotic Agent 5-Chloro-N-({(5S)-2-Oxo-3- [4-(3-Oxomorpholin-4-Yl)Phenyl]-1,3-Oxazolidin-5-Yl}Methyl) Thiophene-2- Carboxamide (Bay 59-7939): An Oral, Direct Factor Xa Inhibitor. J.Med.Chem. V. 48 5900 2005.
ISSN: ISSN 0022-2623
PubMed: 16161994
DOI: 10.1021/JM050101D