Calcium in PDB 2gd4: Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

All present enzymatic activity of Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex:
3.4.21.6;

The structure of Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex, PDB code: 2gd4 was solved by D.J.Johnson, W.Li, T.E.Adams, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.90 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.263, 60.588, 156.174, 90.00, 113.14, 90.00
R / Rfree (%)	24.7 / 29.8

The binding sites of Calcium atom in the Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex (pdb code 2gd4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex, PDB code: 2gd4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:20.0 occ:1.00 O H:ASN72 1.9 33.8 1.0 OE1 H:GLU80 2.1 18.1 1.0 OD1 H:ASP70 2.3 30.2 1.0 O H:HOH402 2.4 1.0 1.0 O H:GLN75 2.8 40.6 1.0 OE1 H:GLU77 2.9 58.2 1.0 C H:ASN72 3.0 33.8 1.0 CD H:GLU80 3.1 18.6 1.0 CG H:ASP70 3.3 29.2 1.0 N H:ASN72 3.4 31.6 1.0 CA H:ASN72 3.5 32.8 1.0 CB H:ASN72 3.6 32.6 1.0 C H:GLN75 3.6 41.2 1.0 CD H:GLU77 3.7 57.8 1.0 OE2 H:GLU80 3.7 16.3 1.0 OE2 H:GLU77 3.8 59.2 1.0 CA H:GLU76 3.8 44.5 1.0 OD2 H:ASP70 3.9 31.0 1.0 N H:GLU76 4.1 42.2 1.0 CG H:GLU80 4.1 21.2 1.0 N H:THR73 4.1 35.3 1.0 N H:GLU77 4.4 47.1 1.0 CB H:ASP70 4.4 27.2 1.0 CA H:THR73 4.5 37.3 1.0 C H:GLU76 4.6 46.0 1.0 N H:ARG71 4.6 29.1 1.0 CG H:ASN72 4.6 33.1 1.0 C H:ARG71 4.7 31.2 1.0 OD1 H:ASN72 4.7 33.5 1.0 CA H:GLN75 4.8 41.6 1.0 N H:GLN75 4.8 41.7 1.0 CA H:ASP70 4.8 24.9 1.0 CB H:GLU76 4.8 44.4 1.0 C H:ASP70 4.9 26.9 1.0 C H:THR73 5.0 38.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:12.8 occ:1.00 OE1 B:GLU80 2.1 40.3 1.0 O B:ASN72 2.2 36.0 1.0 O B:GLN75 2.4 53.8 1.0 OD1 B:ASP70 2.4 31.8 1.0 OE2 B:GLU80 2.5 40.5 1.0 CD B:GLU80 2.6 40.9 1.0 OE1 B:GLU77 3.2 65.7 1.0 C B:ASN72 3.3 36.2 1.0 CG B:ASP70 3.4 31.4 1.0 C B:GLN75 3.5 53.4 1.0 CA B:GLU76 3.8 56.3 1.0 N B:ASN72 3.8 32.9 1.0 CA B:ASN72 3.9 34.3 1.0 CB B:ASN72 3.9 35.1 1.0 CG B:GLU80 4.0 40.8 1.0 OD2 B:ASP70 4.0 34.7 1.0 N B:GLU76 4.1 54.7 1.0 CD B:GLU77 4.3 66.1 1.0 CB B:ASP70 4.4 28.4 1.0 N B:THR73 4.4 39.1 1.0 C B:GLU76 4.6 58.0 1.0 N B:GLU77 4.7 59.3 1.0 CA B:GLN75 4.7 52.4 1.0 CB B:GLU76 4.7 55.2 1.0 CA B:THR73 4.7 42.0 1.0 N B:GLN75 4.8 51.5 1.0 N B:ARG71 4.8 30.9 1.0 OE2 B:GLU77 4.8 67.4 1.0 CB B:GLU80 4.9 40.6 1.0 CA B:ASP70 4.9 26.0 1.0 CG B:ASN72 4.9 37.3 1.0 OD1 B:ASN72 5.0 39.0 1.0

D.J.Johnson, W.Li, T.E.Adams, J.A.Huntington. Antithrombin-S195A Factor Xa-Heparin Structure Reveals the Allosteric Mechanism of Antithrombin Activation. Embo J. V. 25 2029 2006.
ISSN: ISSN 0261-4189
PubMed: 16619025
DOI: 10.1038/SJ.EMBOJ.7601089