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Calcium in PDB 3ssb: Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin

Enzymatic activity of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin

All present enzymatic activity of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin, PDB code: 3ssb was solved by J.L.Arolas, T.O.Botelho, A.Vilcinskas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.640, 78.370, 92.290, 90.00, 90.08, 90.00
R / Rfree (%) 15.9 / 19.3

Other elements in 3ssb:

The structure of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin (pdb code 3ssb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin, PDB code: 3ssb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3ssb

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Calcium binding site 1 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca998

b:31.3
occ:1.00
 O A:GLN61 2.3 26.9 1.0
O A:HOH600 2.3 37.2 1.0
OD1 A:ASP59 2.3 31.9 1.0
OD1 A:ASP57 2.3 28.3 1.0
O A:HOH599 2.5 24.0 1.0
OD2 A:ASP57 2.6 27.8 1.0
CG A:ASP57 2.8 27.1 1.0
CG A:ASP59 3.4 30.8 1.0
C A:GLN61 3.5 25.9 1.0
O A:HOH534 3.8 24.9 1.0
OD2 A:ASP59 3.9 32.1 1.0
N A:GLN61 4.0 26.4 1.0
CA A:GLN61 4.1 27.1 1.0
O A:HOH970 4.2 45.6 1.0
CB A:GLN61 4.2 28.6 1.0
N A:ASP59 4.3 28.2 1.0
CB A:ASP57 4.3 25.9 1.0
O A:HOH576 4.3 29.0 1.0
O A:HOH574 4.5 22.8 1.0
N A:PHE62 4.5 24.2 1.0
N A:ALA58 4.6 27.1 1.0
CB A:ASP59 4.6 30.2 1.0
N A:ASN60 4.6 26.5 1.0
OD2 A:ASP67 4.7 22.5 1.0
CA A:PHE62 4.7 23.1 1.0
CA A:ASP59 4.8 29.1 1.0
C A:ASP59 4.9 28.1 1.0
CA A:ASP57 5.0 26.7 1.0

Calcium binding site 2 out of 6 in 3ssb

Go back to Calcium Binding Sites List in 3ssb
Calcium binding site 2 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:16.9
occ:1.00
 O A:GLU187 2.3 16.6 1.0
OD1 A:ASP138 2.4 17.6 1.0
OE1 A:GLU177 2.4 18.6 1.0
O A:HOH656 2.4 19.0 1.0
OD2 A:ASP185 2.5 20.2 1.0
OE2 A:GLU190 2.5 19.4 1.0
OE2 A:GLU177 2.6 17.8 1.0
OE1 A:GLU190 2.6 21.5 1.0
CD A:GLU177 2.8 18.7 1.0
CD A:GLU190 2.9 19.6 1.0
CG A:ASP138 3.4 15.8 1.0
C A:GLU187 3.4 18.6 1.0
CG A:ASP185 3.5 21.5 1.0
NA A:NA995 3.8 21.2 1.0
OD1 A:ASP185 3.9 20.1 1.0
CB A:ASP138 3.9 15.6 1.0
O A:ASP185 4.0 18.0 1.0
O A:HOH521 4.2 19.0 1.0
N A:GLU187 4.2 19.8 1.0
N A:ILE188 4.3 18.1 1.0
OD2 A:ASP138 4.3 17.1 1.0
CG A:GLU177 4.3 19.6 1.0
CA A:GLU187 4.3 20.0 1.0
CG A:GLU190 4.4 19.6 1.0
CA A:ILE188 4.4 16.8 1.0
O A:HOH525 4.4 19.4 1.0
N A:GLY189 4.4 16.8 1.0
C A:ASP185 4.4 18.8 1.0
CB A:GLU187 4.6 21.0 1.0
N A:ASP185 4.6 19.2 1.0
CB A:ASP185 4.7 19.9 1.0
CA A:ASP185 4.8 19.8 1.0
C A:ILE188 4.8 16.9 1.0
CB A:GLU177 4.9 18.6 1.0

Calcium binding site 3 out of 6 in 3ssb

Go back to Calcium Binding Sites List in 3ssb
Calcium binding site 3 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:26.2
occ:1.00
 O A:HOH695 2.2 33.0 1.0
O A:ILE197 2.2 35.3 1.0
O A:HOH659 2.3 21.0 1.0
O A:TYR193 2.3 26.8 1.0
OD1 A:ASP200 2.4 32.1 1.0
O A:THR194 2.4 34.2 1.0
OG1 A:THR194 2.6 32.2 1.0
C A:THR194 3.2 34.2 1.0
C A:TYR193 3.4 28.5 1.0
C A:ILE197 3.4 38.1 1.0
CG A:ASP200 3.5 32.1 1.0
CB A:THR194 3.6 32.5 1.0
CA A:THR194 3.7 32.5 1.0
OD2 A:ASP200 3.9 37.3 1.0
N A:THR194 3.9 29.4 1.0
N A:ILE197 4.0 40.0 1.0
CA A:ILE197 4.1 39.5 1.0
CB A:ILE197 4.1 39.2 1.0
N A:PRO195 4.3 36.2 1.0
O A:GLU190 4.4 20.3 1.0
O A:ASP200 4.4 24.7 1.0
N A:SER198 4.4 37.5 1.0
CA A:TYR193 4.6 26.4 1.0
CA A:PRO195 4.6 37.6 1.0
CA A:SER198 4.6 36.5 1.0
N A:ASP200 4.7 29.7 1.0
C A:ASP200 4.8 26.1 1.0
CD2 A:TYR193 4.8 30.5 1.0
CB A:ASP200 4.8 29.4 1.0
CG2 A:ILE197 4.8 39.8 1.0
CB A:TYR193 4.8 27.2 1.0
CG2 A:THR194 4.9 32.8 1.0
C A:PRO195 4.9 39.4 1.0
CA A:ASP200 5.0 28.6 1.0
C A:SER198 5.0 34.8 1.0

Calcium binding site 4 out of 6 in 3ssb

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Calcium binding site 4 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca998

b:30.1
occ:1.00
 O B:GLN61 2.3 27.0 1.0
OD1 B:ASP59 2.3 28.3 1.0
OD1 B:ASP57 2.3 26.6 1.0
O B:HOH722 2.4 30.6 1.0
O B:HOH725 2.5 24.1 1.0
OD2 B:ASP57 2.6 26.0 1.0
CG B:ASP57 2.8 25.4 1.0
O B:HOH969 2.8 37.9 1.0
CG B:ASP59 3.3 29.1 1.0
C B:GLN61 3.5 27.1 1.0
OD2 B:ASP59 3.8 31.2 1.0
O B:HOH781 3.8 28.7 1.0
N B:GLN61 3.9 26.4 1.0
O B:HOH833 4.1 41.5 1.0
CA B:GLN61 4.2 27.6 1.0
CB B:ASP57 4.3 24.1 1.0
N B:ASP59 4.3 25.4 1.0
O B:HOH718 4.4 26.1 1.0
CB B:GLN61 4.5 29.1 1.0
N B:PHE62 4.5 26.8 1.0
CB B:ASP59 4.6 27.4 1.0
N B:ASN60 4.6 25.2 1.0
O B:HOH719 4.6 22.5 1.0
OD2 B:ASP67 4.7 23.7 1.0
CA B:PHE62 4.7 25.9 1.0
N B:ALA58 4.8 25.1 1.0
CA B:ASP59 4.8 26.5 1.0
C B:ASP59 4.9 26.1 1.0
CA B:ASP57 5.0 23.7 1.0

Calcium binding site 5 out of 6 in 3ssb

Go back to Calcium Binding Sites List in 3ssb
Calcium binding site 5 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:23.8
occ:1.00
 OE2 B:GLU190 2.3 25.8 1.0
O B:HOH799 2.3 23.8 1.0
O B:GLU187 2.3 25.8 1.0
OD1 B:ASP138 2.4 22.5 1.0
OE1 B:GLU177 2.4 24.6 1.0
OD2 B:ASP185 2.5 26.0 1.0
OE2 B:GLU177 2.6 23.7 1.0
OE1 B:GLU190 2.7 25.5 1.0
CD B:GLU177 2.8 26.0 1.0
CD B:GLU190 2.8 24.8 1.0
CG B:ASP138 3.4 20.8 1.0
C B:GLU187 3.4 25.9 1.0
CG B:ASP185 3.5 27.4 1.0
NA B:NA995 3.7 29.0 1.0
OD1 B:ASP185 3.8 26.9 1.0
CB B:ASP138 4.0 20.5 1.0
O B:ASP185 4.0 25.2 1.0
O B:HOH796 4.2 23.8 1.0
O B:HOH795 4.2 23.6 1.0
N B:GLU187 4.2 26.4 1.0
N B:ILE188 4.3 25.1 1.0
CG B:GLU177 4.3 23.9 1.0
OD2 B:ASP138 4.3 22.3 1.0
CG B:GLU190 4.3 25.5 1.0
CA B:GLU187 4.3 26.9 1.0
CA B:ILE188 4.3 24.0 1.0
N B:GLY189 4.4 23.9 1.0
C B:ASP185 4.5 26.2 1.0
N B:ASP185 4.6 26.8 1.0
CB B:GLU187 4.6 27.6 1.0
CB B:ASP185 4.7 26.7 1.0
C B:ILE188 4.8 24.1 1.0
CA B:ASP185 4.9 27.1 1.0
CB B:GLU177 4.9 24.0 1.0

Calcium binding site 6 out of 6 in 3ssb

Go back to Calcium Binding Sites List in 3ssb
Calcium binding site 6 out of 6 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca996

b:34.5
occ:1.00
 O B:HOH884 2.3 37.9 1.0
O B:ILE197 2.3 41.1 1.0
OD1 B:ASP200 2.4 33.9 1.0
O B:THR194 2.4 39.2 1.0
O B:TYR193 2.4 31.3 1.0
O B:HOH883 2.5 27.6 1.0
OG1 B:THR194 2.6 34.9 1.0
C B:THR194 3.2 38.3 1.0
CG B:ASP200 3.4 34.9 1.0
C B:TYR193 3.4 32.2 1.0
C B:ILE197 3.5 43.3 1.0
CB B:THR194 3.5 36.5 1.0
CA B:THR194 3.7 36.3 1.0
OD2 B:ASP200 3.8 34.1 1.0
N B:THR194 4.0 33.5 1.0
CB B:ILE197 4.1 44.3 1.0
CA B:ILE197 4.2 44.4 1.0
N B:ILE197 4.2 44.8 1.0
N B:PRO195 4.3 40.2 1.0
O B:ASP200 4.5 31.9 1.0
N B:SER198 4.5 43.3 1.0
O B:GLU190 4.6 25.7 1.0
CA B:TYR193 4.6 30.7 1.0
CA B:SER198 4.6 42.6 1.0
CA B:PRO195 4.6 42.0 1.0
N B:ASP200 4.7 35.4 1.0
CB B:TYR193 4.7 31.0 1.0
CB B:ASP200 4.7 34.7 1.0
C B:ASP200 4.8 32.5 1.0
CG2 B:THR194 4.9 36.3 1.0
CG2 B:ILE197 4.9 43.8 1.0
C B:PRO195 4.9 44.1 1.0
C B:SER198 4.9 41.6 1.0
CA B:ASP200 5.0 34.3 1.0
CD2 B:TYR193 5.0 35.6 1.0

Reference:

J.L.Arolas, T.O.Botelho, A.Vilcinskas, F.X.Gomis-Ruth. Structural Evidence For Standard-Mechanism Inhibition in Metallopeptidases From A Complex Poised to Resynthesize A Peptide Bond. Angew.Chem.Int.Ed.Engl. V. 50 10357 2011.
ISSN: ISSN 1433-7851
PubMed: 21915964
DOI: 10.1002/ANIE.201103262
Page generated: Sat Jul 13 19:23:46 2024

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