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Calcium in PDB 3t73: Thermolysin in Complex with UBTLN22

Enzymatic activity of Thermolysin in Complex with UBTLN22

All present enzymatic activity of Thermolysin in Complex with UBTLN22:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN22, PDB code: 3t73 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) 43.66 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.700, 92.700, 130.100, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 16.6

Other elements in 3t73:

The structure of Thermolysin in Complex with UBTLN22 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 UBTLN22 (pdb code 3t73). 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 UBTLN22, PDB code: 3t73:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t73

Go back to Calcium Binding Sites List in 3t73
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN22


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 UBTLN22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca411

b:11.7
occ:1.00
O A:GLU187 2.3 11.9 1.0
OD2 A:ASP138 2.3 10.1 1.0
O A:HOH850 2.4 11.2 1.0
OE1 A:GLU177 2.4 11.4 1.0
OD1 A:ASP185 2.5 11.5 1.0
OE2 A:GLU190 2.5 13.3 1.0
OE1 A:GLU190 2.5 12.0 1.0
OE2 A:GLU177 2.7 12.2 1.0
CD A:GLU190 2.8 14.7 1.0
CD A:GLU177 2.9 12.0 1.0
CG A:ASP138 3.3 12.5 1.0
C A:GLU187 3.4 12.1 1.0
CG A:ASP185 3.5 13.0 1.0
CA A:CA412 3.8 13.0 1.0
OD2 A:ASP185 3.9 13.5 1.0
CB A:ASP138 4.0 8.4 1.0
O A:ASP185 4.1 12.4 1.0
N A:GLU187 4.2 10.8 1.0
OD1 A:ASP138 4.2 13.5 1.0
N A:ILE188 4.2 10.7 1.0
CA A:GLU187 4.3 13.4 1.0
CA A:ILE188 4.3 11.8 1.0
CG A:GLU190 4.3 13.5 1.0
O A:HOH617 4.4 18.1 1.0
CG A:GLU177 4.4 12.5 1.0
N A:GLY189 4.4 12.0 1.0
CB A:GLU187 4.6 10.7 1.0
C A:ASP185 4.6 11.3 1.0
N A:ASP185 4.8 12.2 1.0
C A:ILE188 4.8 12.6 1.0
CB A:ASP185 4.8 12.4 1.0
CB A:GLU177 4.9 11.9 1.0
N A:GLU190 4.9 12.4 1.0
O A:HOH856 5.0 15.4 1.0

Calcium binding site 2 out of 4 in 3t73

Go back to Calcium Binding Sites List in 3t73
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN22


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 UBTLN22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:13.0
occ:1.00
O A:ASN183 2.3 15.3 1.0
OE2 A:GLU190 2.3 13.3 1.0
O A:HOH855 2.4 15.8 1.0
OE2 A:GLU177 2.4 12.2 1.0
O A:HOH856 2.4 15.4 1.0
OD2 A:ASP185 2.4 13.5 1.0
CD A:GLU177 3.2 12.0 1.0
CG A:ASP185 3.2 13.0 1.0
CD A:GLU190 3.3 14.7 1.0
C A:ASN183 3.5 15.1 1.0
OD1 A:ASP185 3.6 11.5 1.0
OE1 A:GLU177 3.8 11.4 1.0
CG A:GLU190 3.8 13.5 1.0
CA A:CA411 3.8 11.7 1.0
CA A:PRO184 4.1 12.8 1.0
OD2 A:ASP191 4.1 19.3 1.0
N A:ASP185 4.2 12.2 1.0
CB A:ASN183 4.2 14.8 1.0
CG A:GLU177 4.2 12.5 1.0
C A:PRO184 4.2 16.6 1.0
OD1 A:ASP191 4.3 17.8 1.0
N A:PRO184 4.3 13.6 1.0
OE1 A:GLU190 4.3 12.0 1.0
O A:HOH559 4.3 41.0 1.0
O A:LYS182 4.4 17.2 1.0
CB A:ASP185 4.4 12.4 1.0
CA A:ASN183 4.5 17.7 1.0
CG A:ASP191 4.5 16.8 1.0
O A:HOH834 4.7 36.6 1.0
O A:PRO184 4.9 15.7 1.0
CA A:ASP185 4.9 11.9 1.0

Calcium binding site 3 out of 4 in 3t73

Go back to Calcium Binding Sites List in 3t73
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN22


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 UBTLN22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:13.9
occ:1.00
O A:ILE197 2.3 15.7 1.0
O A:TYR193 2.3 14.2 1.0
O A:THR194 2.3 16.1 1.0
OD1 A:ASP200 2.4 14.7 1.0
O A:HOH852 2.4 16.1 1.0
OG1 A:THR194 2.4 16.1 1.0
O A:HOH836 2.4 21.3 1.0
C A:THR194 3.2 15.8 1.0
C A:TYR193 3.3 13.9 1.0
CG A:ASP200 3.5 16.2 1.0
CB A:THR194 3.5 15.7 1.0
C A:ILE197 3.5 16.6 1.0
CA A:THR194 3.7 12.9 1.0
OD2 A:ASP200 3.8 17.5 1.0
N A:THR194 3.9 12.4 1.0
CA A:ILE197 4.2 19.3 1.0
CB A:ILE197 4.2 20.0 1.0
N A:PRO195 4.3 16.6 1.0
N A:ILE197 4.3 21.1 1.0
O A:HOH548 4.5 37.6 1.0
O A:ASP200 4.5 16.6 1.0
N A:SER198 4.5 21.7 1.0
CA A:TYR193 4.5 12.0 1.0
N A:ASP200 4.6 15.3 1.0
O A:HOH760 4.6 27.4 1.0
CA A:SER198 4.6 22.4 1.0
O A:HOH650 4.7 34.7 1.0
O A:GLU190 4.7 14.2 1.0
CD2 A:TYR193 4.7 14.1 1.0
CB A:TYR193 4.7 12.8 1.0
CA A:PRO195 4.7 16.8 1.0
CG2 A:THR194 4.7 15.1 1.0
CB A:ASP200 4.8 14.8 1.0
C A:ASP200 4.8 13.5 1.0
CG2 A:ILE197 4.8 20.7 1.0
C A:SER198 4.9 21.0 1.0
CA A:ASP200 5.0 14.1 1.0
N A:GLY199 5.0 20.2 1.0
C A:PRO195 5.0 19.2 1.0

Calcium binding site 4 out of 4 in 3t73

Go back to Calcium Binding Sites List in 3t73
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN22


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 UBTLN22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca414

b:11.5
occ:1.00
O A:GLN61 2.3 12.4 1.0
O A:HOH853 2.3 16.2 1.0
OD1 A:ASP57 2.4 11.9 1.0
O A:HOH854 2.4 14.8 1.0
OD1 A:ASP59 2.4 11.7 1.0
O A:HOH851 2.4 13.5 1.0
OD2 A:ASP57 2.5 11.2 1.0
CG A:ASP57 2.8 11.9 1.0
CG A:ASP59 3.4 14.4 1.0
C A:GLN61 3.5 11.3 1.0
OD2 A:ASP59 3.8 16.7 1.0
N A:GLN61 4.0 11.9 1.0
O A:HOH674 4.0 19.1 1.0
CA A:GLN61 4.2 9.7 0.5
CA A:GLN61 4.2 9.5 0.5
CB A:ASP57 4.3 10.7 1.0
N A:ASP59 4.3 11.5 1.0
CB A:GLN61 4.3 12.4 0.5
CB A:GLN61 4.4 12.2 0.5
O A:HOH600 4.4 14.8 1.0
O A:HOH736 4.5 23.1 1.0
N A:PHE62 4.5 8.5 1.0
CB A:ASP59 4.6 10.9 1.0
N A:ASN60 4.6 11.2 1.0
O A:HOH507 4.6 12.4 1.0
OD2 A:ASP67 4.7 11.1 1.0
O A:HOH764 4.8 31.8 1.0
N A:ALA58 4.8 11.9 1.0
CA A:PHE62 4.8 8.7 1.0
CA A:ASP59 4.8 10.7 1.0
C A:ASP59 4.9 13.8 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 04:31:10 2020

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