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Calcium in PDB 3t8g: Thermolysin in Complex with UBTLN26

Enzymatic activity of Thermolysin in Complex with UBTLN26

All present enzymatic activity of Thermolysin in Complex with UBTLN26:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN26, PDB code: 3t8g 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) 40.14 / 1.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.700, 92.700, 130.800, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 15.6

Other elements in 3t8g:

The structure of Thermolysin in Complex with UBTLN26 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 UBTLN26 (pdb code 3t8g). 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 UBTLN26, PDB code: 3t8g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t8g

Go back to Calcium Binding Sites List in 3t8g
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN26


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 UBTLN26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:9.2
occ:1.00
O A:GLU187 2.3 9.1 1.0
OD2 A:ASP138 2.4 9.0 1.0
O A:HOH907 2.5 9.6 1.0
OD1 A:ASP185 2.5 9.7 1.0
OE1 A:GLU177 2.5 9.8 1.0
OE1 A:GLU190 2.5 10.1 1.0
OE2 A:GLU190 2.5 11.2 1.0
OE2 A:GLU177 2.7 9.8 1.0
CD A:GLU190 2.8 11.6 1.0
CD A:GLU177 2.9 9.6 1.0
CG A:ASP138 3.4 9.5 1.0
C A:GLU187 3.4 9.7 1.0
CG A:ASP185 3.5 9.6 1.0
CA A:CA413 3.8 12.1 1.0
OD2 A:ASP185 3.8 11.9 1.0
CB A:ASP138 4.0 6.8 1.0
O A:ASP185 4.1 9.7 1.0
N A:GLU187 4.2 9.3 1.0
N A:ILE188 4.2 8.8 1.0
CA A:GLU187 4.3 11.1 1.0
OD1 A:ASP138 4.3 11.6 1.0
CA A:ILE188 4.3 9.2 1.0
CG A:GLU190 4.3 11.2 1.0
O A:HOH894 4.4 31.5 1.0
O A:HOH643 4.4 14.8 1.0
N A:GLY189 4.4 9.2 1.0
CG A:GLU177 4.4 9.0 1.0
CB A:GLU187 4.5 11.2 1.0
C A:ASP185 4.6 9.3 1.0
N A:ASP185 4.8 10.6 1.0
CB A:ASP185 4.8 10.8 1.0
C A:ILE188 4.8 9.3 1.0
CB A:GLU177 4.9 8.6 1.0
O A:HOH913 4.9 14.8 1.0
N A:GLU190 4.9 10.2 1.0
CA A:ASP185 5.0 9.6 1.0

Calcium binding site 2 out of 4 in 3t8g

Go back to Calcium Binding Sites List in 3t8g
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN26


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 UBTLN26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:12.1
occ:1.00
O A:ASN183 2.3 13.7 1.0
OE2 A:GLU190 2.3 11.2 1.0
O A:HOH912 2.3 13.9 1.0
O A:HOH913 2.4 14.8 1.0
OE2 A:GLU177 2.4 9.8 1.0
OD2 A:ASP185 2.4 11.9 1.0
CD A:GLU177 3.2 9.6 1.0
CG A:ASP185 3.2 9.6 1.0
CD A:GLU190 3.3 11.6 1.0
C A:ASN183 3.5 13.9 1.0
OD1 A:ASP185 3.6 9.7 1.0
OE1 A:GLU177 3.7 9.8 1.0
CA A:CA412 3.8 9.2 1.0
CG A:GLU190 3.8 11.2 1.0
CA A:PRO184 4.1 10.0 1.0
CB A:ASN183 4.1 15.4 1.0
N A:ASP185 4.1 10.6 1.0
OD2 A:ASP191 4.2 15.8 1.0
O A:HOH891 4.2 37.9 1.0
CG A:GLU177 4.2 9.0 1.0
C A:PRO184 4.2 12.2 1.0
OE1 A:GLU190 4.3 10.1 1.0
OD1 A:ASP191 4.3 15.0 1.0
N A:PRO184 4.3 12.3 1.0
CB A:ASP185 4.4 10.8 1.0
O A:LYS182 4.4 15.3 1.0
CA A:ASN183 4.5 16.6 1.0
CG A:ASP191 4.5 14.1 1.0
O A:HOH894 4.5 31.5 1.0
O A:HOH942 4.6 35.5 1.0
CA A:ASP185 4.9 9.6 1.0
O A:PRO184 4.9 14.9 1.0

Calcium binding site 3 out of 4 in 3t8g

Go back to Calcium Binding Sites List in 3t8g
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN26


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 UBTLN26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca414

b:12.8
occ:1.00
O A:ILE197 2.3 14.1 1.0
O A:TYR193 2.3 13.4 1.0
OD1 A:ASP200 2.4 13.2 1.0
O A:THR194 2.4 14.4 1.0
O A:HOH910 2.4 13.0 1.0
OG1 A:THR194 2.4 13.8 1.0
O A:HOH914 2.4 19.1 1.0
C A:THR194 3.2 14.4 1.0
C A:TYR193 3.3 13.4 1.0
CG A:ASP200 3.5 14.4 1.0
C A:ILE197 3.5 14.1 1.0
CB A:THR194 3.5 13.2 1.0
CA A:THR194 3.7 12.0 1.0
OD2 A:ASP200 3.8 15.6 1.0
N A:THR194 3.9 10.9 1.0
CA A:ILE197 4.2 17.9 1.0
CB A:ILE197 4.2 20.7 1.0
N A:ILE197 4.3 19.8 1.0
N A:PRO195 4.3 14.8 1.0
N A:SER198 4.5 19.2 1.0
O A:ASP200 4.5 13.5 1.0
O A:HOH883 4.5 37.9 1.0
O A:HOH904 4.5 39.3 1.0
CA A:TYR193 4.5 12.0 1.0
N A:ASP200 4.6 13.7 1.0
O A:HOH808 4.6 24.0 1.0
O A:GLU190 4.6 12.5 1.0
CD2 A:TYR193 4.6 13.6 1.0
O A:HOH717 4.6 37.7 1.0
CA A:SER198 4.6 19.5 1.0
CA A:PRO195 4.7 15.2 1.0
CB A:TYR193 4.7 12.3 1.0
CB A:ASP200 4.7 14.6 1.0
CG2 A:THR194 4.8 13.6 1.0
C A:ASP200 4.8 11.4 1.0
CG2 A:ILE197 4.9 19.0 1.0
C A:SER198 4.9 18.4 1.0
CA A:ASP200 4.9 15.1 1.0
N A:GLY199 5.0 16.5 1.0
C A:PRO195 5.0 18.6 1.0

Calcium binding site 4 out of 4 in 3t8g

Go back to Calcium Binding Sites List in 3t8g
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN26


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 UBTLN26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:9.9
occ:1.00
O A:GLN61 2.3 10.1 1.0
OD1 A:ASP57 2.4 10.8 1.0
O A:HOH909 2.4 12.9 1.0
O A:HOH911 2.4 11.8 1.0
OD1 A:ASP59 2.4 9.7 1.0
O A:HOH908 2.4 12.2 1.0
OD2 A:ASP57 2.5 9.1 1.0
CG A:ASP57 2.8 10.4 1.0
CG A:ASP59 3.4 11.2 1.0
C A:GLN61 3.5 9.1 1.0
OD2 A:ASP59 3.8 14.1 1.0
N A:GLN61 4.0 9.8 1.0
O A:HOH677 4.0 17.2 1.0
CA A:GLN61 4.1 9.5 0.5
CA A:GLN61 4.1 9.5 0.5
CB A:ASP57 4.3 9.4 1.0
N A:ASP59 4.3 9.0 1.0
CB A:GLN61 4.3 11.9 0.5
CB A:GLN61 4.3 11.8 0.5
O A:HOH645 4.4 14.1 1.0
N A:PHE62 4.5 7.9 1.0
O A:HOH771 4.5 20.1 1.0
CB A:ASP59 4.6 7.7 1.0
O A:HOH615 4.6 9.9 1.0
OD2 A:ASP67 4.7 10.0 1.0
N A:ASN60 4.7 8.8 1.0
O A:HOH792 4.7 26.6 1.0
N A:ALA58 4.8 9.5 1.0
CA A:PHE62 4.8 7.3 1.0
CA A:ASP59 4.8 8.8 1.0
C A:ASP59 4.9 9.9 1.0

Reference:

A.Biela, M.Betz, A.Heine, G.Klebe. Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding. Chemmedchem V. 7 1423 2012.
ISSN: ISSN 1860-7179
PubMed: 22733601
DOI: 10.1002/CMDC.201200206
Page generated: Sat Dec 12 04:31:15 2020

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