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Silicon in PDB 1y3g: Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin

Enzymatic activity of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin

All present enzymatic activity of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin, PDB code: 1y3g was solved by D.H.Juers, J.Kim, B.W.Matthews, S.M.Sieburth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.520, 93.520, 131.770, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 22.5

Other elements in 1y3g:

The structure of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 1 atom

Silicon Binding Sites:

The binding sites of Silicon atom in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin (pdb code 1y3g). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total only one binding site of Silicon was determined in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin, PDB code: 1y3g:

Silicon binding site 1 out of 1 in 1y3g

Go back to Silicon Binding Sites List in 1y3g
Silicon binding site 1 out of 1 in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Si804

b:14.3
occ:1.00
SI E:AMM804 0.0 14.3 1.0
O2 E:AMM804 1.6 17.2 1.0
O1 E:AMM804 1.6 11.0 1.0
CA E:AMM804 1.8 15.0 1.0
CH2 E:AMM804 1.9 6.2 1.0
N E:AMM804 2.8 22.4 1.0
CE E:AMM804 2.9 12.6 1.0
ZN E:ZN321 3.1 17.6 1.0
C E:AMM804 3.5 22.5 1.0
O E:ALA113 3.6 21.1 1.0
N E:LEU805 3.8 16.1 1.0
NE2 E:HIS231 3.8 14.3 1.0
OE2 E:GLU143 3.8 34.7 1.0
O E:DMS802 3.8 21.8 1.0
C E:3PL803 4.0 28.4 1.0
OE1 E:GLU143 4.1 27.1 1.0
NE2 E:HIS146 4.2 16.4 1.0
CB E:AMM804 4.2 8.0 1.0
NE2 E:HIS142 4.3 16.5 1.0
OH E:TYR157 4.3 21.9 1.0
C1 E:DMS802 4.3 41.7 1.0
O E:AMM804 4.3 15.6 1.0
CE1 E:HIS231 4.3 11.4 1.0
OD1 E:ASN112 4.4 17.5 1.0
CD E:GLU143 4.4 10.8 1.0
OE2 E:GLU166 4.5 13.9 1.0
C E:ALA113 4.6 19.8 1.0
CD2 E:HIS146 4.6 13.7 1.0
O E:3PL803 4.6 36.0 1.0
O E:LEU805 4.6 21.0 1.0
CD2 E:HIS142 4.7 14.9 1.0
CA E:PHE114 4.7 12.8 1.0
S E:DMS802 4.8 34.1 1.0
CA E:LEU805 4.9 17.1 1.0
CD2 E:HIS231 4.9 16.7 1.0

Reference:

D.H.Juers, J.Kim, B.W.Matthews, S.M.Sieburth. Structural Analysis of Silanediols As Transition-State-Analogue Inhibitors of the Benchmark Metalloprotease Thermolysin(,). Biochemistry V. 44 16524 2005.
ISSN: ISSN 0006-2960
PubMed: 16342943
DOI: 10.1021/BI051346V
Page generated: Wed Dec 16 02:09:28 2020

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