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Calcium 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:

Silicon (Si) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin, PDB code: 1y3g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1y3g

Go back to Calcium Binding Sites List in 1y3g
Calcium binding site 1 out of 4 in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca317

b:15.9
occ:1.00
O E:GLU187 2.3 10.8 1.0
OE1 E:GLU177 2.4 19.3 1.0
OD2 E:ASP138 2.4 12.2 1.0
OD1 E:ASP185 2.4 16.1 1.0
OE2 E:GLU190 2.5 13.4 1.0
O E:HOH346 2.6 10.4 1.0
OE1 E:GLU190 2.6 14.3 1.0
OE2 E:GLU177 2.7 19.7 1.0
CD E:GLU177 2.8 16.1 1.0
CD E:GLU190 2.9 19.0 1.0
CG E:ASP185 3.3 18.1 1.0
C E:GLU187 3.4 14.8 1.0
CG E:ASP138 3.5 14.0 1.0
OD2 E:ASP185 3.6 17.1 1.0
CA E:CA318 3.7 19.6 1.0
CB E:ASP138 4.0 9.8 1.0
O E:ASP185 4.1 21.7 1.0
N E:GLU187 4.2 20.2 1.0
CA E:GLU187 4.2 18.9 1.0
N E:ILE188 4.2 14.9 1.0
OD1 E:ASP138 4.3 19.7 1.0
CG E:GLU177 4.3 14.4 1.0
CG E:GLU190 4.3 16.7 1.0
CA E:ILE188 4.3 19.6 1.0
N E:GLY189 4.4 18.9 1.0
C E:ASP185 4.6 24.2 1.0
CB E:GLU187 4.6 21.4 1.0
O E:HOH350 4.7 22.6 1.0
CB E:ASP185 4.7 17.3 1.0
N E:ASP185 4.7 21.2 1.0
C E:ILE188 4.8 25.0 1.0
CB E:GLU177 4.9 14.8 1.0
O E:HOH353 4.9 21.5 1.0
CA E:ASP185 4.9 14.5 1.0
N E:GLU190 5.0 14.5 1.0

Calcium binding site 2 out of 4 in 1y3g

Go back to Calcium Binding Sites List in 1y3g
Calcium binding site 2 out of 4 in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:19.6
occ:1.00
OE2 E:GLU190 2.2 13.4 1.0
OD2 E:ASP185 2.3 17.1 1.0
O E:HOH475 2.4 22.2 1.0
OE2 E:GLU177 2.4 19.7 1.0
O E:HOH353 2.4 21.5 1.0
O E:ASN183 2.4 21.6 1.0
CG E:ASP185 3.3 18.1 1.0
CD E:GLU177 3.3 16.1 1.0
CD E:GLU190 3.4 19.0 1.0
C E:ASN183 3.6 16.6 1.0
CA E:CA317 3.7 15.9 1.0
OD1 E:ASP185 3.7 16.1 1.0
OE1 E:GLU177 3.8 19.3 1.0
CG E:GLU190 3.8 16.7 1.0
O E:LYS182 3.8 37.4 1.0
N E:ASP185 4.1 21.2 1.0
CG E:GLU177 4.2 14.4 1.0
C E:PRO184 4.2 27.6 1.0
CA E:PRO184 4.3 21.7 1.0
OD1 E:ASP191 4.3 25.1 1.0
CB E:ASN183 4.3 26.2 1.0
CB E:ASP185 4.3 17.3 1.0
OD2 E:ASP191 4.3 19.6 1.0
OE1 E:GLU190 4.3 14.3 1.0
N E:PRO184 4.3 22.3 1.0
CA E:ASN183 4.5 16.5 1.0
CG E:ASP191 4.6 21.0 1.0
CA E:ASP185 4.8 14.5 1.0
O E:PRO184 4.9 22.5 1.0
C E:LYS182 4.9 41.5 1.0

Calcium binding site 3 out of 4 in 1y3g

Go back to Calcium Binding Sites List in 1y3g
Calcium binding site 3 out of 4 in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:17.0
occ:1.00
O E:GLN61 2.1 18.5 1.0
O E:HOH503 2.2 16.1 1.0
OD1 E:ASP59 2.4 19.8 1.0
O E:HOH419 2.4 13.6 1.0
O E:HOH482 2.4 25.1 1.0
OD1 E:ASP57 2.4 19.7 1.0
OD2 E:ASP57 2.6 14.1 1.0
CG E:ASP57 2.8 18.6 1.0
C E:GLN61 3.3 25.9 1.0
CG E:ASP59 3.3 20.2 1.0
OD2 E:ASP59 3.8 24.5 1.0
O E:HOH484 3.8 33.3 1.0
N E:GLN61 3.9 24.5 1.0
CA E:GLN61 4.0 22.2 1.0
CB E:ASP57 4.3 20.1 1.0
CB E:GLN61 4.3 18.7 1.0
N E:ASP59 4.4 15.8 1.0
N E:PHE62 4.4 17.0 1.0
O E:HOH508 4.5 24.9 1.0
OD2 E:ASP67 4.6 19.7 1.0
CA E:PHE62 4.6 16.9 1.0
CB E:ASP59 4.6 17.6 1.0
N E:ASN60 4.7 23.4 1.0
O E:HOH356 4.7 22.8 1.0
N E:ALA58 4.8 14.1 1.0
CA E:ASP59 4.8 17.9 1.0
C E:ASP59 5.0 12.6 1.0

Calcium binding site 4 out of 4 in 1y3g

Go back to Calcium Binding Sites List in 1y3g
Calcium binding site 4 out of 4 in the Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:22.5
occ:1.00
OG1 E:THR194 2.1 20.9 1.0
O E:HOH480 2.1 27.4 1.0
OD1 E:ASP200 2.2 18.3 1.0
O E:ILE197 2.2 44.9 1.0
O E:TYR193 2.3 19.5 1.0
O E:THR194 2.3 19.8 1.0
O E:HOH354 2.5 17.1 1.0
C E:THR194 3.1 24.9 1.0
CG E:ASP200 3.2 20.4 1.0
C E:TYR193 3.2 16.3 1.0
CB E:THR194 3.2 19.3 1.0
C E:ILE197 3.3 40.5 1.0
CA E:THR194 3.5 15.2 1.0
OD2 E:ASP200 3.5 16.1 1.0
N E:ILE197 3.6 53.0 1.0
N E:THR194 3.7 18.1 1.0
CA E:ILE197 3.9 31.9 1.0
N E:PRO195 4.2 23.0 1.0
CB E:ILE197 4.2 31.6 1.0
N E:SER198 4.4 38.4 1.0
O E:ASP200 4.4 24.6 1.0
CA E:TYR193 4.5 15.1 1.0
CG2 E:THR194 4.5 16.6 1.0
CB E:ASP200 4.5 17.2 1.0
O E:HOH476 4.5 34.7 1.0
O E:GLU190 4.6 24.8 1.0
CA E:SER198 4.6 42.2 1.0
CB E:TYR193 4.6 16.6 1.0
CD2 E:TYR193 4.7 23.6 1.0
N E:ASP200 4.7 25.3 1.0
C E:ASP200 4.7 28.1 1.0
C E:GLY196 4.8 59.2 1.0
CG2 E:ILE197 4.8 23.2 1.0
CA E:ASP200 4.8 16.5 1.0
CA E:PRO195 4.9 33.9 1.0
CG E:TYR193 5.0 22.2 1.0
CA E:GLY196 5.0 43.0 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: Sat Dec 12 03:28:07 2020

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