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Calcium in PDB 3t8h: Thermolysin in Complex with UBTLN29

Enzymatic activity of Thermolysin in Complex with UBTLN29

All present enzymatic activity of Thermolysin in Complex with UBTLN29:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN29, PDB code: 3t8h 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) 40.18 / 1.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.800, 92.800, 130.100, 90.00, 90.00, 120.00
R / Rfree (%) 12.3 / 15.3

Other elements in 3t8h:

The structure of Thermolysin in Complex with UBTLN29 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 UBTLN29 (pdb code 3t8h). 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 UBTLN29, PDB code: 3t8h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t8h

Go back to Calcium Binding Sites List in 3t8h
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN29


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 UBTLN29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:9.3
occ:1.00
O A:GLU187 2.4 9.6 1.0
OD2 A:ASP138 2.4 9.0 1.0
O A:HOH720 2.5 9.3 1.0
OE2 A:GLU190 2.5 10.7 1.0
OE1 A:GLU177 2.5 9.7 1.0
OD1 A:ASP185 2.5 9.4 1.0
OE1 A:GLU190 2.5 10.4 1.0
OE2 A:GLU177 2.7 10.4 1.0
CD A:GLU190 2.8 9.9 1.0
CD A:GLU177 2.9 9.2 1.0
CG A:ASP138 3.4 9.6 1.0
C A:GLU187 3.4 9.8 1.0
CG A:ASP185 3.5 9.5 1.0
CA A:CA328 3.8 11.2 1.0
OD2 A:ASP185 3.8 11.3 1.0
CB A:ASP138 4.0 7.9 1.0
O A:ASP185 4.1 9.5 1.0
N A:GLU187 4.2 10.3 1.0
OD1 A:ASP138 4.3 11.4 1.0
N A:ILE188 4.3 8.8 1.0
CA A:GLU187 4.3 10.3 1.0
O A:HOH734 4.3 29.1 1.0
CG A:GLU190 4.3 10.2 1.0
CA A:ILE188 4.3 8.5 1.0
CG A:GLU177 4.4 9.1 1.0
N A:GLY189 4.4 8.6 1.0
O A:HOH498 4.4 16.3 1.0
C A:ASP185 4.6 9.7 1.0
CB A:GLU187 4.6 12.3 1.0
CB A:ASP185 4.8 9.6 1.0
N A:ASP185 4.8 9.8 1.0
C A:ILE188 4.8 8.3 1.0
CB A:GLU177 4.9 8.7 1.0
O A:HOH727 4.9 13.8 1.0
N A:GLU190 5.0 10.2 1.0

Calcium binding site 2 out of 4 in 3t8h

Go back to Calcium Binding Sites List in 3t8h
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN29


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 UBTLN29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:11.2
occ:1.00
O A:ASN183 2.3 12.6 1.0
OE2 A:GLU190 2.3 10.7 1.0
O A:HOH726 2.4 14.1 1.0
O A:HOH727 2.4 13.8 1.0
OD2 A:ASP185 2.4 11.3 1.0
OE2 A:GLU177 2.4 10.4 1.0
CD A:GLU177 3.2 9.2 1.0
CG A:ASP185 3.2 9.5 1.0
CD A:GLU190 3.3 9.9 1.0
C A:ASN183 3.5 12.6 1.0
OD1 A:ASP185 3.6 9.4 1.0
OE1 A:GLU177 3.7 9.7 1.0
CA A:CA327 3.8 9.3 1.0
CG A:GLU190 3.8 10.2 1.0
O A:HOH750 4.1 31.9 1.0
CA A:PRO184 4.1 10.9 1.0
CB A:ASN183 4.1 16.0 1.0
N A:ASP185 4.2 9.8 1.0
OD2 A:ASP191 4.2 15.0 1.0
CG A:GLU177 4.2 9.1 1.0
OD1 A:ASP191 4.2 14.5 1.0
C A:PRO184 4.2 11.4 1.0
OE1 A:GLU190 4.3 10.4 1.0
N A:PRO184 4.3 11.0 1.0
CB A:ASP185 4.4 9.6 1.0
O A:LYS182 4.4 14.4 1.0
CA A:ASN183 4.5 13.7 1.0
O A:HOH734 4.5 29.1 1.0
CG A:ASP191 4.5 13.3 1.0
O A:HOH694 4.7 39.1 1.0
CA A:ASP185 4.9 9.2 1.0
O A:PRO184 4.9 12.9 1.0

Calcium binding site 3 out of 4 in 3t8h

Go back to Calcium Binding Sites List in 3t8h
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN29


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 UBTLN29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca329

b:12.6
occ:1.00
O A:ILE197 2.3 15.1 1.0
O A:TYR193 2.3 12.3 1.0
O A:THR194 2.4 13.5 1.0
OD1 A:ASP200 2.4 13.0 1.0
OG1 A:THR194 2.4 12.3 1.0
O A:HOH721 2.4 13.3 1.0
O A:HOH728 2.4 17.6 1.0
C A:THR194 3.2 12.8 1.0
C A:TYR193 3.4 11.7 1.0
CG A:ASP200 3.4 13.0 1.0
CB A:THR194 3.5 12.8 1.0
C A:ILE197 3.5 16.9 1.0
CA A:THR194 3.7 12.2 1.0
OD2 A:ASP200 3.8 13.3 1.0
N A:THR194 3.9 11.7 1.0
CA A:ILE197 4.2 17.7 1.0
CB A:ILE197 4.3 18.6 1.0
N A:PRO195 4.3 14.3 1.0
N A:ILE197 4.3 18.3 1.0
O A:HOH349 4.4 32.6 1.0
N A:SER198 4.5 18.1 1.0
O A:ASP200 4.5 12.5 1.0
CA A:TYR193 4.6 11.0 1.0
O A:HOH394 4.6 24.4 1.0
O A:GLU190 4.6 11.7 1.0
N A:ASP200 4.6 13.7 1.0
O A:HOH421 4.7 34.5 1.0
CD2 A:TYR193 4.7 13.5 1.0
CA A:SER198 4.7 19.3 0.7
CA A:SER198 4.7 18.7 0.3
CA A:PRO195 4.7 15.8 1.0
CB A:TYR193 4.7 11.6 1.0
CG2 A:THR194 4.7 12.8 1.0
CB A:ASP200 4.8 12.6 1.0
C A:ASP200 4.8 12.2 1.0
CG2 A:ILE197 4.9 18.1 1.0
CA A:ASP200 5.0 12.7 1.0
C A:PRO195 5.0 17.9 1.0
C A:SER198 5.0 18.4 1.0

Calcium binding site 4 out of 4 in 3t8h

Go back to Calcium Binding Sites List in 3t8h
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN29


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 UBTLN29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca330

b:10.0
occ:1.00
O A:GLN61 2.3 9.7 1.0
OD1 A:ASP57 2.4 10.2 1.0
O A:HOH723 2.4 12.3 1.0
O A:HOH724 2.4 12.1 1.0
OD1 A:ASP59 2.4 10.3 1.0
O A:HOH722 2.4 11.3 1.0
OD2 A:ASP57 2.5 9.5 1.0
CG A:ASP57 2.8 9.8 1.0
CG A:ASP59 3.4 10.9 1.0
C A:GLN61 3.4 8.5 1.0
OD2 A:ASP59 3.8 13.7 1.0
N A:GLN61 3.9 9.6 1.0
O A:HOH529 4.0 15.9 1.0
CA A:GLN61 4.1 9.8 0.4
CA A:GLN61 4.1 9.7 0.6
CB A:GLN61 4.3 11.5 0.4
CB A:ASP57 4.3 9.3 1.0
N A:ASP59 4.3 9.2 1.0
CB A:GLN61 4.4 11.1 0.6
O A:HOH475 4.5 13.2 1.0
N A:PHE62 4.5 8.1 1.0
O A:HOH615 4.5 24.7 1.0
CB A:ASP59 4.6 9.9 1.0
O A:HOH342 4.6 9.6 1.0
N A:ASN60 4.7 8.8 1.0
OD2 A:ASP67 4.7 9.7 1.0
O A:HOH631 4.7 32.9 1.0
N A:ALA58 4.8 9.1 1.0
CA A:PHE62 4.8 9.0 1.0
CA A:ASP59 4.8 9.3 1.0
C A:ASP59 4.9 9.2 1.0

Reference:

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.
Page generated: Sat Dec 12 04:31:16 2020

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