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Calcium in PDB 3t8c: Thermolysin in Complex with UBTLN30

Enzymatic activity of Thermolysin in Complex with UBTLN30

All present enzymatic activity of Thermolysin in Complex with UBTLN30:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN30, PDB code: 3t8c 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) 43.63 / 1.66
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.600, 92.600, 130.400, 90.00, 90.00, 120.00
R / Rfree (%) 13.9 / 16.6

Other elements in 3t8c:

The structure of Thermolysin in Complex with UBTLN30 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 UBTLN30 (pdb code 3t8c). 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 UBTLN30, PDB code: 3t8c:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t8c

Go back to Calcium Binding Sites List in 3t8c
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN30


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 UBTLN30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:9.1
occ:1.00
O A:GLU187 2.3 8.1 1.0
OD2 A:ASP138 2.4 7.0 1.0
OE1 A:GLU177 2.4 8.2 1.0
O A:HOH725 2.5 6.8 1.0
OE2 A:GLU190 2.5 8.8 1.0
OE1 A:GLU190 2.5 8.1 1.0
OD1 A:ASP185 2.5 8.7 1.0
OE2 A:GLU177 2.7 8.2 1.0
CD A:GLU190 2.8 9.2 1.0
CD A:GLU177 2.9 8.5 1.0
CG A:ASP138 3.4 8.8 1.0
C A:GLU187 3.4 7.2 1.0
CG A:ASP185 3.5 10.3 1.0
CA A:CA328 3.8 10.4 1.0
OD2 A:ASP185 3.9 9.6 1.0
CB A:ASP138 4.0 5.1 1.0
O A:ASP185 4.1 9.5 1.0
N A:GLU187 4.2 8.2 1.0
OD1 A:ASP138 4.2 9.8 1.0
N A:ILE188 4.3 7.5 1.0
O A:HOH696 4.3 28.9 1.0
CA A:GLU187 4.3 11.1 1.0
CG A:GLU190 4.3 10.5 1.0
CA A:ILE188 4.3 5.9 1.0
CG A:GLU177 4.4 9.1 1.0
N A:GLY189 4.4 8.2 1.0
O A:HOH511 4.5 14.2 1.0
CB A:GLU187 4.5 7.5 1.0
C A:ASP185 4.6 6.8 1.0
C A:ILE188 4.8 7.9 1.0
N A:ASP185 4.8 8.3 1.0
CB A:ASP185 4.8 9.4 1.0
CB A:GLU177 4.9 7.9 1.0
N A:GLU190 4.9 8.4 1.0
O A:HOH729 5.0 12.3 1.0

Calcium binding site 2 out of 4 in 3t8c

Go back to Calcium Binding Sites List in 3t8c
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN30


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 UBTLN30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:10.4
occ:1.00
O A:ASN183 2.3 10.8 1.0
OE2 A:GLU190 2.3 8.8 1.0
OE2 A:GLU177 2.4 8.2 1.0
O A:HOH730 2.4 13.1 1.0
O A:HOH729 2.4 12.3 1.0
OD2 A:ASP185 2.4 9.6 1.0
CD A:GLU177 3.2 8.5 1.0
CG A:ASP185 3.3 10.3 1.0
CD A:GLU190 3.3 9.2 1.0
C A:ASN183 3.5 12.8 1.0
OD1 A:ASP185 3.6 8.7 1.0
OE1 A:GLU177 3.8 8.2 1.0
CA A:CA327 3.8 9.1 1.0
CG A:GLU190 3.8 10.5 1.0
OD2 A:ASP191 4.1 15.6 1.0
CA A:PRO184 4.1 9.7 1.0
CB A:ASN183 4.1 11.6 1.0
N A:ASP185 4.2 8.3 1.0
OD1 A:ASP191 4.2 12.8 1.0
CG A:GLU177 4.2 9.1 1.0
C A:PRO184 4.2 14.2 1.0
OE1 A:GLU190 4.3 8.1 1.0
N A:PRO184 4.3 9.4 1.0
O A:LYS182 4.4 13.4 1.0
O A:HOH696 4.4 28.9 1.0
CB A:ASP185 4.4 9.4 1.0
CG A:ASP191 4.5 11.1 1.0
CA A:ASN183 4.5 12.9 1.0
O A:HOH758 4.6 32.8 1.0
O A:PRO184 4.9 13.8 1.0
CA A:ASP185 4.9 8.2 1.0

Calcium binding site 3 out of 4 in 3t8c

Go back to Calcium Binding Sites List in 3t8c
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN30


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 UBTLN30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca329

b:10.9
occ:1.00
O A:TYR193 2.3 10.5 1.0
O A:ILE197 2.3 14.1 1.0
O A:HOH727 2.4 13.5 1.0
OD1 A:ASP200 2.4 12.8 1.0
O A:HOH732 2.4 18.6 1.0
O A:THR194 2.4 12.9 1.0
OG1 A:THR194 2.4 11.5 1.0
C A:THR194 3.2 12.0 1.0
C A:TYR193 3.3 12.8 1.0
CG A:ASP200 3.5 14.7 1.0
CB A:THR194 3.5 10.7 1.0
C A:ILE197 3.5 16.5 1.0
CA A:THR194 3.7 9.2 1.0
OD2 A:ASP200 3.9 14.3 1.0
N A:THR194 3.9 9.8 1.0
CA A:ILE197 4.2 15.9 1.0
CB A:ILE197 4.3 16.9 1.0
N A:PRO195 4.3 13.3 1.0
N A:ILE197 4.3 17.4 1.0
O A:ASP200 4.5 12.4 1.0
N A:SER198 4.5 19.5 1.0
CA A:TYR193 4.5 10.1 1.0
O A:HOH679 4.6 25.2 1.0
N A:ASP200 4.6 12.0 1.0
O A:HOH531 4.6 34.4 1.0
O A:GLU190 4.6 11.3 1.0
CD2 A:TYR193 4.7 12.4 1.0
CA A:SER198 4.7 21.1 1.0
CA A:PRO195 4.7 13.4 1.0
CB A:TYR193 4.7 9.9 1.0
CG2 A:THR194 4.8 11.9 1.0
CB A:ASP200 4.8 10.6 1.0
C A:ASP200 4.8 9.9 1.0
CG2 A:ILE197 4.9 17.7 1.0
CA A:ASP200 5.0 10.5 1.0
N A:GLY199 5.0 15.9 1.0
C A:SER198 5.0 16.9 1.0

Calcium binding site 4 out of 4 in 3t8c

Go back to Calcium Binding Sites List in 3t8c
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN30


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 UBTLN30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca330

b:8.7
occ:1.00
O A:GLN61 2.3 9.7 1.0
O A:HOH731 2.4 11.2 1.0
OD1 A:ASP57 2.4 8.1 1.0
O A:HOH728 2.4 12.9 1.0
OD1 A:ASP59 2.4 9.5 1.0
O A:HOH726 2.4 11.3 1.0
OD2 A:ASP57 2.5 8.2 1.0
CG A:ASP57 2.8 10.3 1.0
CG A:ASP59 3.4 14.0 1.0
C A:GLN61 3.5 7.2 1.0
OD2 A:ASP59 3.8 13.6 1.0
O A:HOH579 4.0 14.8 1.0
N A:GLN61 4.0 8.9 1.0
CA A:GLN61 4.1 7.0 0.4
CA A:GLN61 4.1 6.0 0.6
CB A:GLN61 4.3 9.0 0.4
CB A:ASP57 4.3 6.8 1.0
N A:ASP59 4.3 9.4 1.0
CB A:GLN61 4.4 8.8 0.6
O A:HOH461 4.4 11.7 1.0
O A:HOH642 4.5 21.6 1.0
N A:PHE62 4.5 6.9 1.0
O A:HOH447 4.6 8.6 1.0
CB A:ASP59 4.6 9.7 1.0
N A:ASN60 4.7 8.2 1.0
OD2 A:ASP67 4.7 8.1 1.0
O A:HOH619 4.7 26.6 1.0
N A:ALA58 4.8 8.3 1.0
CA A:PHE62 4.8 6.9 1.0
O A:HOH397 4.8 33.2 1.0
CA A:ASP59 4.8 7.3 1.0
C A:ASP59 4.9 9.0 1.0

Reference:

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.
Page generated: Sat Dec 12 04:31:13 2020

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