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Calcium in PDB 4jzd: Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid

Enzymatic activity of Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid

All present enzymatic activity of Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid:
3.4.21.21;

Protein crystallography data

The structure of Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid, PDB code: 4jzd was solved by B.L.Jacobson, R.Anumula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.68 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.830, 94.830, 118.490, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid (pdb code 4jzd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid, PDB code: 4jzd:

Calcium binding site 1 out of 1 in 4jzd

Go back to Calcium Binding Sites List in 4jzd
Calcium binding site 1 out of 1 in the Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Factor Viia in Complex with the Inhibitor 2-{2-[(4- Carbamimidoylphenyl)Carbamoyl]-6-Methoxypyridin-3-Yl}-5-{[(2S)-1- Hydroxy-3,3-Dimethylbutan-2-Yl]Carbamoyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca303

b:59.6
occ:1.00
 N H:ARG84 3.4 16.6 1.0
ND1 H:HIS109 3.6 36.0 1.0
CB H:HIS109 3.6 25.5 1.0
CB H:ARG84 3.9 21.0 1.0
CD H:ARG83 3.9 12.5 1.0
CB H:GLN110 3.9 20.6 1.0
CA H:ARG83 4.0 14.3 1.0
N H:GLN110 4.0 18.6 1.0
CG H:HIS109 4.0 32.4 1.0
CZ H:ARG84 4.2 94.0 1.0
CG H:ARG84 4.2 34.8 1.0
NE H:ARG84 4.2 68.4 1.0
NH2 H:ARG84 4.2 84.2 1.0
C H:ARG83 4.2 17.1 1.0
CA H:ARG84 4.2 16.4 1.0
CB H:ARG83 4.4 13.4 1.0
C H:HIS109 4.4 22.1 1.0
CA H:HIS109 4.5 22.3 1.0
O H:ARG84 4.5 19.5 1.0
CA H:GLN110 4.6 19.0 1.0
NH1 H:ARG84 4.7 88.3 1.0
CG H:ARG83 4.8 15.4 1.0
CE1 H:HIS109 4.8 35.9 1.0
N H:HIS109 4.8 20.9 1.0
CD H:ARG84 4.8 49.0 1.0
C H:ARG84 4.9 21.0 1.0
O H:SER82 5.0 15.8 1.0
NE H:ARG83 5.0 13.6 1.0

Reference:

S.A.Bolton, J.C.Sutton, R.Anumula, G.S.Bisacchi, B.Jacobson, W.A.Slusarchyk, U.D.Treuner, S.C.Wu, G.Zhao, Z.Pi, S.Sheriff, R.A.Smirk, S.Bisaha, D.L.Cheney, A.Wei, W.A.Schumacher, K.S.Hartl, E.Liu, R.Zahler, S.M.Seiler. Discovery of Nonbenzamidine Factor Viia Inhibitors Using A Biaryl Acid Scaffold. Bioorg.Med.Chem.Lett. V. 23 5239 2013.
ISSN: ISSN 0960-894X
PubMed: 23927973
DOI: 10.1016/J.BMCL.2013.06.028
Page generated: Sun Jul 14 08:42:57 2024

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