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Fluorine in PDB 5paf: Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid

Enzymatic activity of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid

All present enzymatic activity of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid, PDB code: 5paf was solved by M.Stihle, A.Mayweg, S.Roever, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.57 / 1.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.050, 95.050, 116.660, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.5

Other elements in 5paf:

The structure of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid (pdb code 5paf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid, PDB code: 5paf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5paf

Go back to Fluorine Binding Sites List in 5paf
Fluorine binding site 1 out of 3 in the Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F509

b:80.0
occ:1.00
 F1 B:TFA509 0.0 80.0 1.0
C2 B:TFA509 1.4 69.0 1.0
F2 B:TFA509 2.3 49.8 1.0
F3 B:TFA509 2.4 63.1 1.0
C1 B:TFA509 2.4 62.7 1.0
OXT B:TFA509 2.6 70.0 1.0
O B:TFA509 3.7 29.0 1.0
O B:HOH733 3.8 33.9 1.0
ND2 B:ASN300 4.7 24.4 1.0

Fluorine binding site 2 out of 3 in 5paf

Go back to Fluorine Binding Sites List in 5paf
Fluorine binding site 2 out of 3 in the Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F509

b:49.8
occ:1.00
 F2 B:TFA509 0.0 49.8 1.0
C2 B:TFA509 1.4 69.0 1.0
F3 B:TFA509 2.3 63.1 1.0
F1 B:TFA509 2.3 80.0 1.0
C1 B:TFA509 2.5 62.7 1.0
NE2 B:HIS301 2.9 22.5 1.0
O B:TFA509 3.2 29.0 1.0
OXT B:TFA509 3.5 70.0 1.0
ND2 B:ASN300 3.7 24.4 1.0
O B:HOH733 3.7 33.9 1.0
CE1 B:HIS301 3.8 21.2 1.0
CE2 B:TYR386 3.8 23.7 1.0
CD2 B:HIS301 3.9 21.2 1.0
CD2 B:TYR386 4.4 22.6 1.0
CZ B:TYR386 4.6 24.1 1.0
O B:HOH690 4.8 39.4 1.0
OH B:TYR386 4.8 26.1 1.0
CG B:ASN300 4.9 22.2 1.0
ND1 B:HIS301 5.0 19.6 1.0

Fluorine binding site 3 out of 3 in 5paf

Go back to Fluorine Binding Sites List in 5paf
Fluorine binding site 3 out of 3 in the Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Factor Viia in Complex with N-(2-Amino-1H- Benzimidazol-5-Yl)-2-[3-[(2-Amino-2-Oxoethyl)-Methylsulfonylamino]-5- Chlorophenyl]Acetamide;2,2,2-Trifluoroacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F509

b:63.1
occ:1.00
 F3 B:TFA509 0.0 63.1 1.0
C2 B:TFA509 1.4 69.0 1.0
F2 B:TFA509 2.3 49.8 1.0
F1 B:TFA509 2.4 80.0 1.0
C1 B:TFA509 2.4 62.7 1.0
O B:TFA509 2.8 29.0 1.0
OXT B:TFA509 3.3 70.0 1.0
CE2 B:TYR386 4.0 23.7 1.0
OE2 B:GLU385 4.0 51.5 1.0
O B:HOH724 4.5 34.2 1.0
OH B:TYR386 4.6 26.1 1.0
CZ B:TYR386 4.8 24.1 1.0
CD2 B:TYR386 4.8 22.6 1.0
NE2 B:HIS301 4.9 22.5 1.0
ND2 B:ASN300 5.0 24.4 1.0

Reference:

A.Mayweg, S.Roever, M.G.Rudolph. Crystal Structure of A Factor Viia Complex To Be Published.
Page generated: Tue Jul 15 06:01:50 2025

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