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Calcium in PDB 5pb4: Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A

Enzymatic activity of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A

All present enzymatic activity of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A, PDB code: 5pb4 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) 47.67 / 2.43
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.345, 95.345, 117.608, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23

Other elements in 5pb4:

The structure of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A (pdb code 5pb4). 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 Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A, PDB code: 5pb4:

Calcium binding site 1 out of 1 in 5pb4

Go back to Calcium Binding Sites List in 5pb4
Calcium binding site 1 out of 1 in the Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-3-Methyl-4-(1H- Pyrrolo[3,2-C]Pyridin-2-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 2.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:66.0
occ:1.00
 O C:GLU275 2.4 50.7 1.0
OE1 C:GLU270 2.4 45.2 1.0
OE2 C:GLU280 2.6 41.7 1.0
O C:HOH696 2.7 49.2 1.0
O C:ASP272 2.7 45.1 1.0
O C:HOH629 3.1 48.6 1.0
CD C:GLU270 3.4 44.0 1.0
C C:GLU275 3.5 49.7 1.0
CD C:GLU280 3.5 42.2 1.0
OE2 C:GLU270 3.6 44.4 1.0
C C:ASP272 3.6 45.3 1.0
O C:HOH656 3.7 39.5 1.0
CG C:GLU280 3.8 41.1 1.0
N C:ASP272 4.0 44.6 1.0
CA C:HIS276 4.3 48.9 1.0
N C:HIS276 4.3 49.0 1.0
N C:HIS271 4.3 43.6 1.0
CA C:ASP272 4.3 44.9 1.0
O C:HOH602 4.4 52.7 1.0
CG C:GLU275 4.5 52.6 1.0
N C:ASP277 4.5 47.6 1.0
CA C:GLU275 4.6 50.2 1.0
N C:LEU273 4.6 45.8 1.0
N C:GLU275 4.7 49.7 1.0
OD1 C:ASP277 4.7 47.3 1.0
O C:HOH664 4.7 56.9 1.0
OE1 C:GLU280 4.7 41.1 1.0
CG C:GLU270 4.7 43.0 1.0
CG C:ASP277 4.8 47.3 1.0
CA C:LEU273 4.8 46.3 1.0
CB C:ASP272 4.9 44.9 1.0
OD2 C:ASP277 4.9 46.4 1.0
C C:HIS276 4.9 48.4 1.0
C C:HIS271 4.9 44.3 1.0
CA C:GLU270 5.0 42.5 1.0

Reference:

A.Mayweg, S.Roever, M.G.Rudolph. Crystal Structure of A Factor Viia Complex To Be Published.
Page generated: Wed Jul 9 09:28:46 2025

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