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Silicon in PDB 4mpw: Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone)

Enzymatic activity of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone)

All present enzymatic activity of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone):
3.4.21.59;

Protein crystallography data

The structure of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone), PDB code: 4mpw was solved by A.White, A.J.Stein, R.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.67 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.087, 78.087, 164.980, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 20.6

Other elements in 4mpw:

The structure of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Silicon Binding Sites:

The binding sites of Silicon atom in the Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) (pdb code 4mpw). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 2 binding sites of Silicon where determined in the Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone), PDB code: 4mpw:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in 4mpw

Go back to Silicon Binding Sites List in 4mpw
Silicon binding site 1 out of 2 in the Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone)


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Si301

b:26.7
occ:1.00
SI1 B:2AJ301 0.0 26.7 1.0
O B:2AJ301 1.6 23.4 1.0
C1 B:2AJ301 1.9 25.5 1.0
C2 B:2AJ301 1.9 31.6 1.0
C27 B:2AJ301 1.9 22.6 1.0
C28 B:2AJ301 2.9 21.3 1.0
SI3 B:2AJ301 3.0 26.5 1.0
C34 B:2AJ301 3.0 22.0 1.0
O B:HOH438 3.4 30.3 1.0
C4 B:2AJ301 3.5 30.1 1.0
C33 B:2AJ301 3.7 20.7 1.0
C5 B:2AJ301 4.0 24.4 1.0
O3 B:2AJ301 4.0 21.2 1.0
C29 B:2AJ301 4.1 20.0 1.0
C6 B:2AJ301 4.3 22.8 1.0

Silicon binding site 2 out of 2 in 4mpw

Go back to Silicon Binding Sites List in 4mpw
Silicon binding site 2 out of 2 in the Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone)


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Human Beta-Tryptase Co-Crystal Structure with [(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Di-1-Benzofuran-3,5-Diyl]Bis({4-[3- (Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Si301

b:26.5
occ:1.00
SI3 B:2AJ301 0.0 26.5 1.0
O B:2AJ301 1.6 23.4 1.0
C5 B:2AJ301 1.8 24.4 1.0
C4 B:2AJ301 1.9 30.1 1.0
C6 B:2AJ301 1.9 22.8 1.0
C7 B:2AJ301 2.8 22.0 1.0
SI1 B:2AJ301 3.0 26.7 1.0
C13 B:2AJ301 3.0 21.7 1.0
C12 B:2AJ301 3.7 20.2 1.0
C1 B:2AJ301 3.8 25.5 1.0
C27 B:2AJ301 3.9 22.6 1.0
O1 B:2AJ301 4.1 22.0 1.0
C8 B:2AJ301 4.1 22.0 1.0
O B:HOH438 4.1 30.3 1.0
C2 B:2AJ301 4.5 31.6 1.0
C28 B:2AJ301 4.5 21.3 1.0
O A:HOH517 4.6 33.3 1.0
O A:HOH472 4.8 30.5 1.0
C34 B:2AJ301 4.9 22.0 1.0

Reference:

S.F.Giardina, M.Pingle, K.W.Foreman, D.S.Werner, D.E.Bergstrom, F.Barany, L.D.Arnold. Target-Directed Self-Assembly of Homodimeric Drugs To Be Published.
Page generated: Wed Dec 16 02:09:33 2020

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