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Calcium in PDB 3t87: Thermolysin in Complex with UBTLN28

Enzymatic activity of Thermolysin in Complex with UBTLN28

All present enzymatic activity of Thermolysin in Complex with UBTLN28:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN28, PDB code: 3t87 was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.23 / 1.28
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.700, 92.700, 131.100, 90.00, 90.00, 120.00
R / Rfree (%) 10.5 / 12.7

Other elements in 3t87:

The structure of Thermolysin in Complex with UBTLN28 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with UBTLN28 (pdb code 3t87). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin in Complex with UBTLN28, PDB code: 3t87:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t87

Go back to Calcium Binding Sites List in 3t87
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN28


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with UBTLN28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:7.4
occ:1.00
O A:GLU187 2.3 7.9 1.0
OD2 A:ASP138 2.4 7.5 1.0
O A:HOH785 2.4 7.8 1.0
OE1 A:GLU177 2.5 7.8 1.0
OE1 A:GLU190 2.5 8.0 1.0
OD1 A:ASP185 2.5 8.1 1.0
OE2 A:GLU190 2.5 8.7 1.0
OE2 A:GLU177 2.7 8.4 1.0
CD A:GLU190 2.8 8.0 1.0
CD A:GLU177 2.9 7.7 1.0
CG A:ASP138 3.4 7.5 1.0
C A:GLU187 3.4 8.5 1.0
CG A:ASP185 3.5 8.9 1.0
CA A:CA328 3.8 10.0 1.0
OD2 A:ASP185 3.8 10.2 1.0
CB A:ASP138 4.0 6.6 1.0
O A:ASP185 4.1 8.0 1.0
N A:GLU187 4.2 8.7 1.0
N A:ILE188 4.2 7.9 1.0
OD1 A:ASP138 4.3 8.9 1.0
CA A:GLU187 4.3 8.9 1.0
CA A:ILE188 4.3 7.5 1.0
O A:HOH743 4.3 21.7 1.0
CG A:GLU190 4.4 8.9 1.0
CG A:GLU177 4.4 7.7 1.0
N A:GLY189 4.4 8.0 1.0
O A:HOH522 4.4 13.8 1.0
CB A:GLU187 4.5 10.2 1.0
C A:ASP185 4.6 7.8 1.0
C A:ILE188 4.8 7.9 1.0
CB A:ASP185 4.8 8.9 1.0
N A:ASP185 4.8 9.2 1.0
CB A:GLU177 4.9 7.3 1.0
O A:HOH790 4.9 12.0 1.0
N A:GLU190 5.0 8.8 1.0
CA A:ASP185 5.0 8.7 1.0

Calcium binding site 2 out of 4 in 3t87

Go back to Calcium Binding Sites List in 3t87
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN28


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with UBTLN28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:10.0
occ:1.00
O A:ASN183 2.3 11.0 1.0
OE2 A:GLU190 2.3 8.7 1.0
O A:HOH791 2.3 12.3 1.0
OD2 A:ASP185 2.3 10.2 1.0
O A:HOH790 2.4 12.0 1.0
OE2 A:GLU177 2.4 8.4 1.0
CG A:ASP185 3.2 8.9 1.0
CD A:GLU177 3.2 7.7 1.0
CD A:GLU190 3.3 8.0 1.0
C A:ASN183 3.5 11.6 1.0
OD1 A:ASP185 3.6 8.1 1.0
OE1 A:GLU177 3.7 7.8 1.0
CA A:CA327 3.8 7.4 1.0
CG A:GLU190 3.8 8.9 1.0
CA A:PRO184 4.1 9.9 1.0
O A:HOH333 4.1 36.5 1.0
CB A:ASN183 4.1 15.4 1.0
N A:ASP185 4.2 9.2 1.0
OD2 A:ASP191 4.2 12.7 1.0
OD1 A:ASP191 4.2 12.3 1.0
C A:PRO184 4.3 10.2 1.0
CG A:GLU177 4.3 7.7 1.0
OE1 A:GLU190 4.3 8.0 1.0
N A:PRO184 4.3 10.5 1.0
CB A:ASP185 4.4 8.9 1.0
O A:LYS182 4.4 14.3 1.0
O A:HOH743 4.5 21.7 1.0
CA A:ASN183 4.5 13.4 1.0
CG A:ASP191 4.6 11.0 1.0
O A:HOH331 4.6 33.7 1.0
CA A:ASP185 4.9 8.7 1.0
O A:PRO184 5.0 11.6 1.0

Calcium binding site 3 out of 4 in 3t87

Go back to Calcium Binding Sites List in 3t87
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN28


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with UBTLN28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca329

b:11.2
occ:1.00
O A:ILE197 2.3 14.2 1.0
OG1 A:THR194 2.4 10.9 1.0
O A:TYR193 2.4 10.4 1.0
O A:THR194 2.4 11.8 1.0
OD1 A:ASP200 2.4 11.3 1.0
O A:HOH792 2.4 15.3 1.0
O A:HOH788 2.4 12.6 1.0
C A:THR194 3.2 11.4 1.0
C A:TYR193 3.4 9.7 1.0
CB A:THR194 3.4 11.2 1.0
CG A:ASP200 3.5 11.4 1.0
C A:ILE197 3.5 15.8 1.0
CA A:THR194 3.6 10.4 1.0
OD2 A:ASP200 3.8 12.2 1.0
N A:THR194 3.9 9.7 1.0
CA A:ILE197 4.2 16.1 1.0
CB A:ILE197 4.2 17.0 1.0
N A:PRO195 4.3 12.3 1.0
N A:ILE197 4.3 15.9 1.0
O A:HOH751 4.5 31.2 1.0
N A:SER198 4.5 17.6 1.0
O A:ASP200 4.5 11.9 1.0
CA A:TYR193 4.6 9.2 1.0
CD2 A:TYR193 4.6 11.0 1.0
O A:GLU190 4.6 9.7 1.0
CA A:PRO195 4.6 13.8 1.0
N A:ASP200 4.6 13.3 1.0
CA A:SER198 4.7 19.4 1.0
CB A:TYR193 4.7 9.7 1.0
O A:HOH779 4.7 35.7 1.0
O A:HOH653 4.7 25.3 1.0
CG2 A:THR194 4.7 11.5 1.0
CB A:ASP200 4.7 12.1 1.0
C A:ASP200 4.8 11.7 1.0
CG2 A:ILE197 4.8 17.3 1.0
CA A:ASP200 5.0 12.3 1.0
C A:PRO195 5.0 15.8 1.0
C A:SER198 5.0 18.5 1.0
N A:GLY199 5.0 16.9 1.0

Calcium binding site 4 out of 4 in 3t87

Go back to Calcium Binding Sites List in 3t87
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN28


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with UBTLN28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca330

b:7.9
occ:1.00
O A:GLN61 2.3 8.2 1.0
O A:HOH787 2.3 10.3 1.0
OD1 A:ASP57 2.4 8.2 1.0
OD1 A:ASP59 2.4 8.4 1.0
O A:HOH786 2.4 9.4 1.0
O A:HOH789 2.4 9.8 1.0
OD2 A:ASP57 2.6 7.9 1.0
CG A:ASP57 2.8 7.3 1.0
CG A:ASP59 3.4 9.1 1.0
C A:GLN61 3.5 7.7 1.0
OD2 A:ASP59 3.8 11.7 1.0
N A:GLN61 4.0 8.1 1.0
O A:HOH551 4.0 15.1 1.0
CA A:GLN61 4.1 8.8 0.5
CA A:GLN61 4.1 8.8 0.5
CB A:GLN61 4.3 11.0 0.5
CB A:GLN61 4.3 11.1 0.5
N A:ASP59 4.3 8.5 1.0
CB A:ASP57 4.3 7.0 1.0
O A:HOH512 4.5 10.7 1.0
N A:PHE62 4.5 7.3 1.0
O A:HOH661 4.5 16.8 1.0
CB A:ASP59 4.6 8.7 1.0
OD2 A:ASP67 4.6 7.9 1.0
N A:ASN60 4.6 7.8 1.0
O A:HOH411 4.6 7.7 1.0
O A:HOH424 4.7 28.0 1.0
O A:HOH656 4.7 25.2 1.0
N A:ALA58 4.7 7.8 1.0
CA A:PHE62 4.8 7.5 1.0
CA A:ASP59 4.8 8.7 1.0
C A:ASP59 4.9 8.1 1.0

Reference:

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.
Page generated: Sat Dec 12 04:31:12 2020

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