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Calcium in PDB 3t8f: Thermolysin in Complex with UBTLN34

Enzymatic activity of Thermolysin in Complex with UBTLN34

All present enzymatic activity of Thermolysin in Complex with UBTLN34:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN34, PDB code: 3t8f 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) 30.35 / 1.44
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.400, 92.400, 131.200, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 15.9

Other elements in 3t8f:

The structure of Thermolysin in Complex with UBTLN34 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 UBTLN34 (pdb code 3t8f). 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 UBTLN34, PDB code: 3t8f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t8f

Go back to Calcium Binding Sites List in 3t8f
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:11.0
occ:1.00
OE2 A:GLU190 2.3 9.7 1.0
O A:HOH684 2.3 13.6 1.0
O A:ASN183 2.3 11.8 1.0
O A:HOH705 2.4 13.3 1.0
OD2 A:ASP185 2.4 10.8 1.0
OE2 A:GLU177 2.4 8.5 1.0
CG A:ASP185 3.2 8.6 1.0
CD A:GLU177 3.2 7.5 1.0
CD A:GLU190 3.3 8.6 1.0
C A:ASN183 3.5 13.4 1.0
OD1 A:ASP185 3.6 9.7 1.0
OE1 A:GLU177 3.7 7.9 1.0
CA A:CA413 3.8 8.2 1.0
CG A:GLU190 3.8 10.4 1.0
CB A:ASN183 4.1 14.2 1.0
CA A:PRO184 4.1 9.4 1.0
N A:ASP185 4.2 9.7 1.0
O A:HOH875 4.2 34.4 1.0
OD2 A:ASP191 4.2 14.2 1.0
CG A:GLU177 4.2 7.9 1.0
OE1 A:GLU190 4.2 8.5 1.0
OD1 A:ASP191 4.3 12.2 1.0
C A:PRO184 4.3 12.4 1.0
N A:PRO184 4.3 10.1 1.0
CB A:ASP185 4.4 8.5 1.0
O A:LYS182 4.4 14.0 1.0
CA A:ASN183 4.5 15.1 1.0
CG A:ASP191 4.6 12.2 1.0
O A:HOH851 4.6 31.6 1.0
CA A:ASP185 4.9 8.8 1.0
O A:PRO184 5.0 12.7 1.0

Calcium binding site 2 out of 4 in 3t8f

Go back to Calcium Binding Sites List in 3t8f
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:8.2
occ:1.00
O A:GLU187 2.4 7.8 1.0
OD2 A:ASP138 2.4 7.6 1.0
O A:HOH522 2.4 8.4 1.0
OE1 A:GLU177 2.4 7.9 1.0
OD1 A:ASP185 2.4 9.7 1.0
OE1 A:GLU190 2.5 8.5 1.0
OE2 A:GLU190 2.5 9.7 1.0
OE2 A:GLU177 2.7 8.5 1.0
CD A:GLU190 2.8 8.6 1.0
CD A:GLU177 2.9 7.5 1.0
CG A:ASP138 3.4 7.5 1.0
C A:GLU187 3.4 7.9 1.0
CG A:ASP185 3.5 8.6 1.0
CA A:CA412 3.8 11.0 1.0
OD2 A:ASP185 3.8 10.8 1.0
CB A:ASP138 4.0 6.8 1.0
O A:ASP185 4.1 8.3 1.0
N A:GLU187 4.2 8.6 1.0
OD1 A:ASP138 4.2 9.6 1.0
N A:ILE188 4.3 6.2 1.0
CA A:GLU187 4.3 9.1 1.0
CA A:ILE188 4.3 6.8 1.0
CG A:GLU190 4.3 10.4 1.0
CG A:GLU177 4.4 7.9 1.0
N A:GLY189 4.4 7.9 1.0
O A:HOH717 4.4 12.1 1.0
CB A:GLU187 4.6 10.1 1.0
C A:ASP185 4.6 8.0 1.0
N A:ASP185 4.7 9.7 1.0
CB A:ASP185 4.8 8.5 1.0
C A:ILE188 4.8 8.0 1.0
CB A:GLU177 4.9 8.2 1.0
O A:HOH705 4.9 13.3 1.0
N A:GLU190 5.0 8.3 1.0
CA A:ASP185 5.0 8.8 1.0

Calcium binding site 3 out of 4 in 3t8f

Go back to Calcium Binding Sites List in 3t8f
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca414

b:11.1
occ:1.00
O A:ILE197 2.2 12.8 1.0
O A:TYR193 2.3 11.0 1.0
O A:THR194 2.4 12.1 1.0
OD1 A:ASP200 2.4 11.0 1.0
OG1 A:THR194 2.4 10.9 1.0
O A:HOH682 2.4 11.9 1.0
O A:HOH725 2.5 17.0 1.0
C A:THR194 3.2 10.8 1.0
C A:TYR193 3.3 8.7 1.0
C A:ILE197 3.4 15.2 1.0
CG A:ASP200 3.5 11.3 1.0
CB A:THR194 3.5 10.8 1.0
CA A:THR194 3.6 10.6 1.0
OD2 A:ASP200 3.8 13.4 1.0
N A:THR194 3.9 9.3 1.0
CA A:ILE197 4.2 16.1 1.0
CB A:ILE197 4.2 18.5 1.0
N A:PRO195 4.3 12.3 1.0
N A:ILE197 4.3 17.8 1.0
N A:SER198 4.5 17.3 1.0
O A:ASP200 4.5 11.3 1.0
O A:HOH546 4.5 32.8 1.0
CA A:TYR193 4.5 10.0 1.0
CD2 A:TYR193 4.6 11.8 1.0
N A:ASP200 4.6 12.5 1.0
O A:GLU190 4.6 10.1 1.0
O A:HOH864 4.6 23.0 1.0
CA A:SER198 4.6 19.4 1.0
CA A:PRO195 4.7 13.3 1.0
CB A:TYR193 4.7 10.1 1.0
O A:HOH503 4.7 39.7 1.0
CG2 A:THR194 4.7 10.8 1.0
CB A:ASP200 4.8 11.3 1.0
C A:ASP200 4.8 10.6 1.0
CG2 A:ILE197 4.9 17.6 1.0
CA A:ASP200 4.9 11.3 1.0
C A:PRO195 5.0 17.6 1.0
C A:SER198 5.0 15.3 1.0
N A:GLY199 5.0 13.8 1.0

Calcium binding site 4 out of 4 in 3t8f

Go back to Calcium Binding Sites List in 3t8f
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN34


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 UBTLN34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:8.6
occ:1.00
O A:GLN61 2.3 8.7 1.0
O A:HOH663 2.3 10.6 1.0
OD1 A:ASP59 2.4 9.1 1.0
OD1 A:ASP57 2.4 9.7 1.0
O A:HOH683 2.4 11.5 1.0
O A:HOH636 2.4 10.0 1.0
OD2 A:ASP57 2.6 8.5 1.0
CG A:ASP57 2.8 9.4 1.0
CG A:ASP59 3.4 10.4 1.0
C A:GLN61 3.4 7.6 1.0
OD2 A:ASP59 3.8 12.9 1.0
N A:GLN61 3.9 8.6 1.0
O A:HOH745 4.0 16.4 1.0
CA A:GLN61 4.1 7.2 1.0
N A:ASP59 4.3 8.6 1.0
CB A:GLN61 4.3 9.5 1.0
CB A:ASP57 4.3 8.9 1.0
N A:PHE62 4.5 7.8 1.0
O A:HOH740 4.6 16.1 1.0
CB A:ASP59 4.6 7.6 1.0
OD2 A:ASP67 4.6 9.3 1.0
O A:HOH595 4.6 8.6 1.0
N A:ASN60 4.6 7.6 1.0
O A:HOH879 4.7 24.2 1.0
N A:ALA58 4.7 8.4 1.0
CA A:PHE62 4.7 8.1 1.0
CA A:ASP59 4.8 8.9 1.0
C A:ASP59 4.9 8.9 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 04:31:14 2020

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