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Chlorine in PDB 5pb3: Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea

Enzymatic activity of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea

All present enzymatic activity of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea, PDB code: 5pb3 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) 47.62 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.192, 95.192, 116.080, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.1

Other elements in 5pb3:

The structure of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea (pdb code 5pb3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea, PDB code: 5pb3:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5pb3

Go back to Chlorine Binding Sites List in 5pb3
Chlorine binding site 1 out of 3 in the Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:74.9
occ:1.00
 O C:HOH671 3.1 46.9 1.0
N C:GLU454 3.7 30.6 1.0
O C:HOH767 3.9 50.0 1.0
CA C:SER453 4.0 30.6 1.0
CB C:SER453 4.1 30.7 1.0
CB C:GLU454 4.4 30.7 1.0
C C:SER453 4.4 30.6 1.0
CG C:GLU454 4.6 30.0 1.0
CA C:GLU454 4.6 30.9 1.0
O C:GLU454 4.8 31.6 1.0

Chlorine binding site 2 out of 3 in 5pb3

Go back to Chlorine Binding Sites List in 5pb3
Chlorine binding site 2 out of 3 in the Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:77.2
occ:1.00
 O C:HOH783 3.5 44.8 1.0
N C:VAL459 3.5 33.1 1.0
CA C:GLY458 3.8 34.1 0.5
CA C:GLY458 3.8 34.0 0.5
CG2 C:VAL459 3.9 33.0 1.0
C C:GLY458 4.2 33.6 0.5
C C:GLY458 4.2 33.5 0.5
CB C:VAL459 4.4 32.7 1.0
O C:HOH720 4.5 48.6 1.0
CA C:VAL459 4.6 32.6 1.0
CB C:TRP261 4.7 43.5 1.0
NE C:ARG262 4.9 53.5 1.0
N C:GLY458 4.9 34.4 0.5
N C:GLY458 4.9 34.4 0.5

Chlorine binding site 3 out of 3 in 5pb3

Go back to Chlorine Binding Sites List in 5pb3
Chlorine binding site 3 out of 3 in the Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Factor Viia in Complex with 1-[[3-[4-(5-Amino-1H- Pyrrolo[3,2-B]Pyridin-2-Yl)-5-Hydroxypyrazol-1-Yl]Phenyl]Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl505

b:50.4
occ:0.50
 CE1 C:HIS309 0.8 28.4 0.5
NE2 C:HIS309 1.6 28.6 0.5
ND1 C:HIS309 1.9 27.8 0.5
CD2 C:HIS309 2.6 28.3 0.5
CG C:HIS309 2.8 27.0 0.5
N C:ARG284 3.5 24.5 1.0
CD2 C:HIS309 3.6 27.0 0.5
NH1 C:ARG284 3.6 45.7 1.0
CA C:ARG283 3.9 22.9 1.0
CZ C:ARG284 3.9 43.8 1.0
CD C:ARG283 4.0 23.3 1.0
CG C:ARG284 4.0 29.9 1.0
CB C:HIS309 4.1 25.9 0.5
O C:HOH834 4.1 58.5 1.0
CB C:ARG284 4.1 26.3 1.0
CG C:HIS309 4.2 26.3 0.5
CB C:HIS309 4.2 26.1 0.5
C C:ARG283 4.3 23.6 1.0
O C:HOH822 4.3 56.0 1.0
CB C:GLN310 4.3 26.5 1.0
NH2 C:ARG284 4.3 46.1 1.0
CA C:ARG284 4.4 25.6 1.0
CB C:ARG283 4.5 22.7 1.0
NE C:ARG284 4.5 40.2 1.0
NE2 C:GLN310 4.6 35.5 1.0
O C:SER282 4.6 21.5 1.0
N C:GLN310 4.7 25.7 1.0
NE2 C:HIS309 4.8 26.9 0.5
CD C:ARG284 4.9 35.5 1.0
CG C:ARG283 4.9 23.4 1.0
O C:ARG284 4.9 24.8 1.0

Reference:

A.Mayweg, S.Roever, M.G.Rudolph. Crystal Structure of A Factor Viia Complex To Be Published.
Page generated: Sat Jul 12 07:13:59 2025

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