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Silicon in PDB 4mqa: Human Beta-Tryptase Co-Crystal Structure with {(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Bis[5-(Methylsulfanyl)Benzene-3,1- 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)Bis[5-(Methylsulfanyl)Benzene-3,1- 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)Bis[5-(Methylsulfanyl)Benzene-3,1- 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)Bis[5-(Methylsulfanyl)Benzene-3,1- Diyl]}Bis({4-[3-(Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone), PDB code: 4mqa was solved by A.White, D.Lakshminarasimhan, R.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.36 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.168, 78.168, 165.458, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 25.1

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)Bis[5-(Methylsulfanyl)Benzene-3,1- Diyl]}Bis({4-[3-(Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) (pdb code 4mqa). 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)Bis[5-(Methylsulfanyl)Benzene-3,1- Diyl]}Bis({4-[3-(Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone), PDB code: 4mqa:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in 4mqa

Go back to Silicon Binding Sites List in 4mqa
Silicon binding site 1 out of 2 in the Human Beta-Tryptase Co-Crystal Structure with {(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Bis[5-(Methylsulfanyl)Benzene-3,1- 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)Bis[5-(Methylsulfanyl)Benzene-3,1- Diyl]}Bis({4-[3-(Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Si301

b:77.9
occ:1.00
SI1 B:X00301 0.0 77.9 1.0
O B:X00301 1.7 73.1 1.0
C8 B:X00301 1.8 79.6 1.0
C9 B:X00301 1.8 77.4 1.0
C5 B:X00301 1.9 61.8 1.0
C6 B:X00301 2.8 53.8 1.0
C4 B:X00301 2.8 53.7 1.0
SI2 B:X00301 3.2 79.8 1.0
C12 B:X00301 3.6 79.8 1.0
C1 B:X00301 4.1 54.2 1.0
C3 B:X00301 4.2 46.8 1.0
C11 B:X00301 4.3 77.1 1.0
C2 B:X00301 4.6 50.5 1.0
C13 B:X00301 4.7 62.9 1.0

Silicon binding site 2 out of 2 in 4mqa

Go back to Silicon Binding Sites List in 4mqa
Silicon binding site 2 out of 2 in the Human Beta-Tryptase Co-Crystal Structure with {(1,1,3,3- Tetramethyldisiloxane-1,3-Diyl)Bis[5-(Methylsulfanyl)Benzene-3,1- 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)Bis[5-(Methylsulfanyl)Benzene-3,1- Diyl]}Bis({4-[3-(Aminomethyl)Phenyl]Piperidin-1-Yl}Methanone) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Si301

b:79.8
occ:1.00
SI2 B:X00301 0.0 79.8 1.0
O B:X00301 1.7 73.1 1.0
C12 B:X00301 1.9 79.8 1.0
C11 B:X00301 1.9 77.1 1.0
C13 B:X00301 1.9 62.9 1.0
C14 B:X00301 2.8 57.0 1.0
C19 B:X00301 2.9 56.2 1.0
SI1 B:X00301 3.2 77.9 1.0
C9 B:X00301 3.7 77.4 1.0
C15 B:X00301 4.1 54.7 1.0
C18 B:X00301 4.2 47.8 1.0
C8 B:X00301 4.2 79.6 1.0
C5 B:X00301 4.6 61.8 1.0
C17 B:X00301 4.6 49.4 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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