Calcium in PDB 1ygc: Short Factor Viia with A Small Molecule Inhibitor

All present enzymatic activity of Short Factor Viia with A Small Molecule Inhibitor:
3.4.21.21;

The structure of Short Factor Viia with A Small Molecule Inhibitor, PDB code: 1ygc was solved by A.G.Olivero, C.Eigenbrot, R.Goldsmith, K.Robarge, D.R.Artis, J.Flygare, T.Rawson, C.Refino, S.Bunting, D.Kirchhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.15 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.220, 95.220, 116.320, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Short Factor Viia with A Small Molecule Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Calcium atom in the Short Factor Viia with A Small Molecule Inhibitor (pdb code 1ygc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Short Factor Viia with A Small Molecule Inhibitor, PDB code: 1ygc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Short Factor Viia with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Short Factor Viia with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca300 b:19.2 occ:1.00 O H:GLU75 2.3 21.7 1.0 OE1 H:GLU70 2.4 12.7 1.0 OE2 H:GLU80 2.4 14.2 1.0 O H:HOH454 2.5 15.1 1.0 O H:ASP72 2.5 13.7 1.0 O H:HOH541 2.5 16.9 1.0 CD H:GLU70 3.4 16.8 1.0 CD H:GLU80 3.5 15.8 1.0 C H:ASP72 3.5 11.5 1.0 C H:GLU75 3.5 21.4 1.0 OE2 H:GLU70 3.7 17.4 1.0 CG H:GLU80 3.8 12.5 1.0 N H:ASP72 4.0 11.9 1.0 O H:HOH432 4.2 12.5 1.0 CA H:HIS76 4.2 18.8 1.0 CA H:ASP72 4.2 13.2 1.0 N H:HIS76 4.3 17.5 1.0 N H:LEU73 4.5 14.1 1.0 N H:HIS71 4.5 11.7 1.0 N H:GLU75 4.5 19.2 1.0 CA H:GLU75 4.6 18.3 1.0 CB H:ASP72 4.6 14.3 1.0 N H:ASP77 4.6 17.9 1.0 OE1 H:GLU80 4.6 13.8 1.0 O H:HOH564 4.6 22.1 1.0 CA H:LEU73 4.6 14.7 1.0 O H:HOH863 4.6 21.9 1.0 CG H:GLU70 4.8 13.3 1.0 CG H:GLU75 4.9 25.5 1.0 C H:HIS76 4.9 19.3 1.0 C H:HIS71 4.9 12.8 1.0 OD1 H:ASP77 5.0 16.2 1.0 C H:LEU73 5.0 14.8 1.0

Calcium binding site 2 out of 2 in the Short Factor Viia with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Short Factor Viia with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca538 b:22.5 occ:0.50 O H:HOH553 2.7 15.2 1.0 O H:HOH438 2.9 10.2 1.0 CG2 H:VAL113 3.9 12.0 1.0 CG H:PRO111 4.1 21.8 1.0 O H:PRO111 4.4 11.0 1.0 O H:VAL112 4.4 12.4 1.0 O H:HOH476 4.5 12.4 1.0 CB H:PRO111 4.6 14.7 1.0 CA H:VAL113 4.8 11.3 1.0 C H:VAL112 4.8 13.4 1.0 C H:PRO111 4.8 14.1 1.0 CB H:VAL113 4.9 12.6 1.0 N H:VAL113 5.0 12.5 1.0 O H:HOH462 5.0 12.0 1.0 O H:HOH613 5.0 33.2 1.0

A.G.Olivero, C.Eigenbrot, R.Goldsmith, K.Robarge, D.R.Artis, J.Flygare, T.Rawson, D.P.Sutherlin, S.Kadkhodayan, M.Beresini, L.O.Elliott, G.G.Deguzman, D.W.Banner, M.Ultsch, U.Marzec, S.R.Hanson, C.Refino, S.Bunting, D.Kirchhofer. A Selective, Slow Binding Inhibitor of Factor Viia Binds to A Nonstandard Active Site Conformation and Attenuates Thrombus Formation in Vivo. J.Biol.Chem. V. 280 9160 2005.
ISSN: ISSN 0021-9258
PubMed: 15632123
DOI: 10.1074/JBC.M409068200