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Calcium in PDB 4d91: Thermolysin in Complex with Dmso and Acetate

Enzymatic activity of Thermolysin in Complex with Dmso and Acetate

All present enzymatic activity of Thermolysin in Complex with Dmso and Acetate:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Dmso and Acetate, PDB code: 4d91 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) 34.34 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.425, 93.425, 129.923, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18.4

Other elements in 4d91:

The structure of Thermolysin in Complex with Dmso and Acetate 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 Dmso and Acetate (pdb code 4d91). 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 Dmso and Acetate, PDB code: 4d91:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4d91

Go back to Calcium Binding Sites List in 4d91
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Dmso and Acetate


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 Dmso and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:19.6
occ:1.00
OE2 A:GLU190 2.3 16.9 1.0
O A:ASN183 2.3 19.8 1.0
O A:HOH532 2.4 17.7 1.0
O A:HOH616 2.4 20.4 1.0
OD2 A:ASP185 2.4 19.7 1.0
OE1 A:GLU177 2.4 16.0 1.0
CD A:GLU177 3.3 15.1 1.0
CG A:ASP185 3.3 20.5 1.0
CD A:GLU190 3.3 18.4 1.0
C A:ASN183 3.5 25.8 1.0
OD1 A:ASP185 3.7 15.3 1.0
CA A:CA406 3.8 16.8 1.0
OE2 A:GLU177 3.8 14.3 1.0
CG A:GLU190 3.8 19.3 1.0
OD2 A:ASP191 4.1 21.8 1.0
CB A:ASN183 4.1 26.6 1.0
CA A:PRO184 4.1 20.4 1.0
N A:ASP185 4.2 16.1 1.0
OD1 A:ASP191 4.2 22.0 1.0
C A:PRO184 4.2 23.9 1.0
CG A:GLU177 4.2 15.0 1.0
O A:HOH706 4.3 32.2 1.0
N A:PRO184 4.3 24.3 1.0
OE1 A:GLU190 4.3 16.1 1.0
O A:LYS182 4.3 29.6 1.0
CB A:ASP185 4.4 17.2 1.0
CA A:ASN183 4.5 27.1 1.0
CG A:ASP191 4.5 17.8 1.0
O A:HOH733 4.7 38.2 1.0
O A:PRO184 4.9 19.6 1.0
CA A:ASP185 4.9 18.9 1.0

Calcium binding site 2 out of 4 in 4d91

Go back to Calcium Binding Sites List in 4d91
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Dmso and Acetate


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 Dmso and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:16.8
occ:1.00
O A:GLU187 2.4 15.9 1.0
OD2 A:ASP138 2.4 16.1 1.0
OD1 A:ASP185 2.4 15.3 1.0
OE2 A:GLU177 2.5 14.3 1.0
OE1 A:GLU190 2.5 16.1 1.0
O A:HOH542 2.5 15.9 1.0
OE2 A:GLU190 2.5 16.9 1.0
OE1 A:GLU177 2.7 16.0 1.0
CD A:GLU190 2.8 18.4 1.0
CD A:GLU177 2.9 15.1 1.0
CG A:ASP138 3.4 19.0 1.0
C A:GLU187 3.4 14.3 1.0
CG A:ASP185 3.4 20.5 1.0
OD2 A:ASP185 3.8 19.7 1.0
CA A:CA405 3.8 19.6 1.0
CB A:ASP138 4.0 12.1 1.0
O A:ASP185 4.2 16.6 1.0
N A:GLU187 4.2 17.2 1.0
N A:ILE188 4.3 13.4 1.0
CA A:GLU187 4.3 21.1 1.0
CA A:ILE188 4.3 13.6 1.0
CG A:GLU190 4.3 19.3 1.0
OD1 A:ASP138 4.4 20.1 1.0
CG A:GLU177 4.4 15.0 1.0
N A:GLY189 4.5 14.4 1.0
O A:HOH506 4.5 20.0 1.0
CB A:GLU187 4.5 23.8 1.0
C A:ASP185 4.6 20.9 1.0
N A:ASP185 4.7 16.1 1.0
CB A:ASP185 4.7 17.2 1.0
C A:ILE188 4.8 17.0 1.0
O A:HOH616 4.9 20.4 1.0
N A:GLU190 4.9 16.2 1.0
CB A:GLU177 4.9 10.0 1.0
CA A:ASP185 5.0 18.9 1.0

Calcium binding site 3 out of 4 in 4d91

Go back to Calcium Binding Sites List in 4d91
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Dmso and Acetate


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 Dmso and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:19.9
occ:1.00
O A:ILE197 2.3 23.0 1.0
O A:THR194 2.3 22.5 1.0
O A:TYR193 2.3 17.7 1.0
OG1 A:THR194 2.4 21.4 1.0
O A:HOH575 2.4 22.3 1.0
O A:HOH527 2.4 19.2 1.0
OD1 A:ASP200 2.4 22.6 1.0
C A:THR194 3.2 24.3 1.0
C A:TYR193 3.3 18.9 1.0
CB A:THR194 3.5 20.7 1.0
CG A:ASP200 3.5 20.8 1.0
C A:ILE197 3.5 31.1 1.0
CA A:THR194 3.7 17.9 1.0
OD2 A:ASP200 3.8 21.0 1.0
N A:THR194 3.9 16.7 1.0
CA A:ILE197 4.2 31.5 1.0
N A:ILE197 4.2 27.8 1.0
N A:PRO195 4.2 22.0 1.0
CB A:ILE197 4.3 31.0 1.0
O A:ASP200 4.5 20.4 1.0
N A:SER198 4.5 25.7 1.0
CA A:TYR193 4.5 18.1 1.0
O A:HOH837 4.6 44.1 1.0
O A:GLU190 4.6 17.5 1.0
CB A:TYR193 4.7 19.0 1.0
N A:ASP200 4.7 22.4 1.0
CD2 A:TYR193 4.7 19.3 1.0
CA A:PRO195 4.7 24.1 1.0
CA A:SER198 4.7 30.6 1.0
O A:HOH681 4.7 28.1 1.0
CG2 A:THR194 4.7 23.0 1.0
CB A:ASP200 4.8 23.0 1.0
C A:ASP200 4.9 22.6 1.0
CG2 A:ILE197 4.9 25.3 1.0
C A:PRO195 4.9 28.2 1.0

Calcium binding site 4 out of 4 in 4d91

Go back to Calcium Binding Sites List in 4d91
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Dmso and Acetate


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 Dmso and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:18.0
occ:1.00
O A:GLN61 2.3 13.4 1.0
O A:HOH548 2.4 17.7 1.0
O A:HOH618 2.4 16.2 1.0
OD1 A:ASP59 2.4 19.9 1.0
O A:HOH566 2.4 21.2 1.0
OD2 A:ASP57 2.5 20.4 1.0
OD1 A:ASP57 2.5 17.1 1.0
CG A:ASP57 2.8 15.9 1.0
CG A:ASP59 3.4 18.6 1.0
C A:GLN61 3.4 14.5 1.0
OD2 A:ASP59 3.8 23.4 1.0
N A:GLN61 3.9 15.5 1.0
O A:HOH640 4.0 22.0 1.0
CA A:GLN61 4.1 13.9 1.0
CB A:GLN61 4.3 17.9 1.0
CB A:ASP57 4.3 14.1 1.0
N A:ASP59 4.3 19.7 1.0
O A:HOH525 4.5 21.7 1.0
O A:HOH700 4.5 29.5 1.0
N A:PHE62 4.5 14.5 1.0
O A:HOH503 4.6 13.6 1.0
CB A:ASP59 4.6 22.8 1.0
N A:ASN60 4.6 18.2 1.0
OD2 A:ASP67 4.7 17.4 1.0
CA A:PHE62 4.7 15.0 1.0
O A:HOH630 4.7 36.0 1.0
N A:ALA58 4.7 14.0 1.0
O A:HOH712 4.8 34.5 1.0
CA A:ASP59 4.8 17.6 1.0
C A:ASP59 4.9 21.9 1.0

Reference:

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.
Page generated: Sat Dec 12 04:43:15 2020

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