Calcium in PDB 1z6j: Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor

All present enzymatic activity of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor:
3.4.21.21;

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor, PDB code: 1z6j was solved by B.A.Schweitzer, W.L.Neumann, H.K.Rahman, C.L.Kusturin, K.R.Sample, G.I.Poda, R.G.Kurumbail, A.M.Stevens, R.A.Stegeman, W.C.Stallings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.652, 81.137, 125.577, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.8

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor (pdb code 1z6j). 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 A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor, PDB code: 1z6j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor


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 A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca401 b:92.0 occ:1.00 OD1 L:ASP46 2.2 57.3 1.0 O L:GLN64 2.3 35.7 1.0 OD2 L:ASP63 2.5 38.1 1.0 O L:GLY47 2.8 46.3 1.0 OE1 L:GLN49 2.9 43.0 1.0 CG L:ASP46 3.2 56.0 1.0 C L:GLN64 3.5 34.7 1.0 CG L:ASP63 3.7 35.0 1.0 CB L:ASP46 3.7 54.6 1.0 CD L:GLN49 3.8 42.8 1.0 C L:GLY47 4.0 47.0 1.0 NE2 L:GLN49 4.0 41.9 1.0 N L:GLN66 4.1 40.1 1.0 N L:GLN64 4.2 31.6 1.0 CA L:LEU65 4.2 39.9 1.0 OD2 L:ASP46 4.3 56.6 1.0 N L:LEU65 4.3 37.7 1.0 CB L:ASP63 4.4 33.0 1.0 C L:ASP46 4.4 52.4 1.0 N L:GLY47 4.5 50.8 1.0 CA L:GLN64 4.5 32.0 1.0 O L:SER67 4.6 30.8 1.0 C L:LEU65 4.6 40.3 1.0 CD2 L:LEU65 4.6 40.2 1.0 OD1 L:ASP63 4.7 37.2 1.0 O L:ASP46 4.7 52.5 1.0 CA L:ASP46 4.8 53.4 1.0 CA L:GLY47 4.8 48.8 1.0 N L:ASP48 4.9 46.2 1.0 CA L:ASP48 4.9 44.5 1.0 N L:GLN49 5.0 41.2 1.0 C L:ASP63 5.0 31.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor


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 A Ternary Complex of Factor Viia/Tissue Factor/Pyrazinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca400 b:46.1 occ:1.00 O H:GLU75 2.1 30.3 1.0 OE1 H:GLU70 2.3 10.4 1.0 O H:ASP72 2.4 14.3 1.0 O H:HOH508 2.5 28.4 1.0 O H:HOH446 2.6 17.6 1.0 OE1 H:GLU80 2.6 25.5 1.0 CD H:GLU80 3.1 27.1 1.0 CD H:GLU70 3.2 10.3 1.0 C H:GLU75 3.3 30.8 1.0 C H:ASP72 3.4 14.1 1.0 OE2 H:GLU70 3.4 12.2 1.0 OE2 H:GLU80 3.5 29.9 1.0 CA H:HIS76 3.9 34.1 1.0 N H:ASP72 3.9 13.1 1.0 N H:HIS76 4.0 31.4 1.0 O H:HOH465 4.1 21.1 1.0 CG H:GLU80 4.2 23.2 1.0 CA H:ASP72 4.2 14.3 1.0 OE2 H:GLU75 4.2 50.3 1.0 N H:GLU75 4.2 26.5 1.0 CD H:GLU75 4.2 47.4 1.0 CA H:GLU75 4.3 29.9 1.0 N H:LEU73 4.4 14.4 1.0 N H:HIS71 4.4 13.6 1.0 CB H:ASP72 4.5 13.1 1.0 CA H:LEU73 4.5 14.3 1.0 OE1 H:GLU75 4.6 47.5 1.0 CG H:GLU70 4.6 10.7 1.0 N H:ASP77 4.6 32.4 1.0 C H:HIS76 4.6 33.8 1.0 CG H:GLU75 4.6 42.0 1.0 ND1 H:HIS76 4.7 41.9 1.0 C H:LEU73 4.7 16.8 1.0 C H:HIS71 4.9 13.2 1.0 O H:LEU73 5.0 16.4 1.0

B.A.Schweitzer, W.L.Neumann, H.K.Rahman, C.L.Kusturin, K.R.Sample, G.I.Poda, R.G.Kurumbail, A.M.Stevens, R.A.Stegeman, W.C.Stallings, M.S.South. Structure-Based Design and Synthesis of Pyrazinones Containing Novel P1 'Side Pocket' Moieties As Inhibitors of Tf/Viia. Bioorg.Med.Chem.Lett. V. 15 3006 2005.
ISSN: ISSN 0960-894X
PubMed: 15913999
DOI: 10.1016/J.BMCL.2005.04.037