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Calcium in PDB 5pb5: Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A

Enzymatic activity of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A

All present enzymatic activity of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A, PDB code: 5pb5 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) 47.51 / 1.84
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.037, 95.037, 116.512, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20

Other elements in 5pb5:

The structure of Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A (pdb code 5pb5). 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-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A, PDB code: 5pb5:

Calcium binding site 1 out of 1 in 5pb5

Go back to Calcium Binding Sites List in 5pb5
Calcium binding site 1 out of 1 in the Human Factor Viia in Complex with 1-[[3-[5-Hydroxy-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A


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-4-(7H-Pyrrolo[2,3- D]Pyrimidin-6-Yl)Pyrazol-1-Yl]Phenyl]Methyl]-3-Phenylurea at 1.84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:31.8
occ:1.00
 O B:GLU275 2.3 30.6 1.0
OE1 B:GLU270 2.3 21.8 1.0
OE2 B:GLU280 2.4 25.4 1.0
O B:ASP272 2.5 23.8 1.0
O B:HOH774 2.5 28.3 1.0
O B:HOH656 2.7 30.9 1.0
CD B:GLU270 3.3 23.5 1.0
C B:GLU275 3.5 30.1 1.0
C B:ASP272 3.5 23.6 1.0
CD B:GLU280 3.5 24.0 1.0
OE2 B:GLU270 3.6 25.4 1.0
CG B:GLU280 3.9 22.4 1.0
O B:HOH655 3.9 22.8 1.0
N B:ASP272 4.0 22.8 1.0
CA B:ASP272 4.2 23.7 1.0
CA B:HIS276 4.2 29.1 1.0
N B:HIS276 4.3 29.1 1.0
N B:HIS271 4.4 21.5 1.0
O B:HOH602 4.4 43.5 1.0
N B:LEU273 4.4 24.7 1.0
N B:GLU275 4.5 29.6 1.0
CA B:GLU275 4.5 30.4 1.0
CG B:GLU275 4.6 34.1 1.0
CA B:LEU273 4.6 25.9 1.0
N B:ASP277 4.6 27.3 1.0
O B:HOH780 4.6 39.9 1.0
OE1 B:GLU280 4.6 24.9 1.0
CG B:GLU270 4.7 22.5 1.0
O B:HOH619 4.7 32.6 1.0
CB B:ASP272 4.7 23.6 1.0
C B:LEU273 4.9 26.8 1.0
C B:HIS276 4.9 28.4 1.0
C B:HIS271 4.9 22.2 1.0
OD1 B:ASP277 4.9 24.6 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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