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Calcium in PDB 4mzn: Thermolysin in Complex with UBTLN59

Enzymatic activity of Thermolysin in Complex with UBTLN59

All present enzymatic activity of Thermolysin in Complex with UBTLN59:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN59, PDB code: 4mzn was solved by S.G.Krimmer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.71 / 1.17
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.493, 92.493, 131.183, 90.00, 90.00, 120.00
R / Rfree (%) 11.6 / 13.8

Other elements in 4mzn:

The structure of Thermolysin in Complex with UBTLN59 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 UBTLN59 (pdb code 4mzn). 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 UBTLN59, PDB code: 4mzn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4mzn

Go back to Calcium Binding Sites List in 4mzn
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:8.4
occ:1.00
O E:GLU187 2.3 8.7 1.0
OD2 E:ASP138 2.4 8.9 1.0
O E:HOH501 2.4 8.9 1.0
OD1 E:ASP185 2.5 9.4 1.0
OE1 E:GLU177 2.5 9.0 1.0
OE1 E:GLU190 2.5 9.1 1.0
OE2 E:GLU190 2.5 9.7 1.0
OE2 E:GLU177 2.7 9.8 1.0
CD E:GLU190 2.8 9.2 1.0
CD E:GLU177 2.9 8.8 1.0
CG E:ASP138 3.4 8.4 1.0
C E:GLU187 3.4 9.1 1.0
CG E:ASP185 3.5 9.8 1.0
CA E:CA405 3.8 11.0 1.0
OD2 E:ASP185 3.8 11.2 1.0
CB E:ASP138 4.0 8.3 1.0
O E:ASP185 4.1 9.1 1.0
N E:GLU187 4.2 9.5 1.0
N E:ILE188 4.3 8.5 1.0
OD1 E:ASP138 4.3 9.9 1.0
CA E:GLU187 4.3 9.5 1.0
O E:HOH958 4.3 16.6 0.5
CA E:ILE188 4.3 8.5 1.0
CG E:GLU190 4.4 9.9 1.0
CG E:GLU177 4.4 9.2 1.0
O E:HOH564 4.4 14.3 1.0
N E:GLY189 4.4 8.7 1.0
CB E:GLU187 4.6 11.1 1.0
C E:ASP185 4.6 8.9 1.0
N E:ASP185 4.8 9.5 1.0
CB E:ASP185 4.8 10.3 1.0
C E:ILE188 4.8 8.4 1.0
CB E:GLU177 4.9 8.4 1.0
O E:HOH556 4.9 14.4 1.0
N E:GLU190 5.0 9.1 1.0
CA E:ASP185 5.0 9.1 1.0

Calcium binding site 2 out of 4 in 4mzn

Go back to Calcium Binding Sites List in 4mzn
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.9
occ:1.00
O E:GLN61 2.3 9.3 0.5
O E:GLN61 2.3 9.4 0.5
O E:HOH525 2.4 11.5 1.0
OD1 E:ASP59 2.4 9.6 1.0
OD2 E:ASP57 2.4 9.7 1.0
O E:HOH547 2.4 11.8 1.0
O E:HOH516 2.4 10.6 1.0
OD1 E:ASP57 2.6 9.1 1.0
CG E:ASP57 2.8 9.0 1.0
CG E:ASP59 3.4 10.3 1.0
C E:GLN61 3.5 8.5 0.5
C E:GLN61 3.5 8.4 0.5
OD2 E:ASP59 3.8 12.2 1.0
N E:GLN61 3.9 8.9 0.5
N E:GLN61 3.9 8.8 0.5
O E:HOH585 4.0 16.1 1.0
CA E:GLN61 4.1 9.3 0.5
CA E:GLN61 4.1 9.1 0.5
CB E:GLN61 4.3 11.3 0.5
N E:ASP59 4.3 9.2 1.0
CB E:ASP57 4.3 8.8 1.0
CB E:GLN61 4.4 11.0 0.5
N E:PHE62 4.5 8.2 1.0
O E:HOH949 4.6 15.3 1.0
CB E:ASP59 4.6 10.2 1.0
O E:HOH503 4.6 8.4 1.0
OD2 E:ASP67 4.6 8.8 1.0
N E:ASN60 4.6 8.4 1.0
O E:HOH699 4.7 25.7 1.0
N E:ALA58 4.7 8.9 1.0
O E:HOH698 4.8 35.1 1.0
CA E:PHE62 4.8 8.6 1.0
CA E:ASP59 4.8 9.5 1.0
C E:ASP59 4.9 8.9 1.0

Calcium binding site 3 out of 4 in 4mzn

Go back to Calcium Binding Sites List in 4mzn
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:11.3
occ:1.00
O E:ILE197 2.3 15.8 1.0
OD1 E:ASP200 2.4 12.3 1.0
O E:TYR193 2.4 11.2 1.0
O E:THR194 2.4 12.7 1.0
O E:HOH551 2.4 14.3 1.0
OG1 E:THR194 2.4 11.9 1.0
O E:HOH593 2.4 18.1 1.0
C E:THR194 3.2 12.1 1.0
C E:TYR193 3.4 10.8 1.0
CG E:ASP200 3.4 11.7 1.0
CB E:THR194 3.5 11.9 1.0
C E:ILE197 3.5 17.1 1.0
CA E:THR194 3.7 11.3 1.0
OD2 E:ASP200 3.8 12.6 1.0
N E:THR194 3.9 10.7 1.0
CA E:ILE197 4.2 17.5 1.0
CB E:ILE197 4.2 17.9 1.0
N E:PRO195 4.2 13.2 1.0
N E:ILE197 4.3 17.5 1.0
O E:HOH803 4.4 36.0 1.0
O E:ASP200 4.5 11.5 1.0
N E:SER198 4.5 18.1 0.4
N E:SER198 4.5 17.8 0.6
CA E:TYR193 4.6 10.2 1.0
O E:HOH850 4.6 45.2 1.0
N E:ASP200 4.6 13.3 1.0
CA E:PRO195 4.6 15.2 1.0
CD2 E:TYR193 4.6 12.3 1.0
O E:GLU190 4.7 10.7 1.0
CA E:SER198 4.7 19.2 0.4
CB E:TYR193 4.7 11.2 1.0
O E:HOH720 4.7 27.7 1.0
O E:HOH774 4.7 44.0 1.0
CA E:SER198 4.7 19.1 0.6
CB E:ASP200 4.7 12.5 1.0
CG2 E:THR194 4.7 12.6 1.0
C E:ASP200 4.8 11.5 1.0
CG2 E:ILE197 4.8 18.1 1.0
C E:SER198 4.9 19.0 0.6
CA E:ASP200 4.9 12.5 1.0
C E:PRO195 5.0 16.5 1.0

Calcium binding site 4 out of 4 in 4mzn

Go back to Calcium Binding Sites List in 4mzn
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN59


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 UBTLN59 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:11.0
occ:1.00
O E:ASN183 2.3 12.5 1.0
OE2 E:GLU190 2.3 9.7 1.0
O E:HOH867 2.3 14.5 1.0
OD2 E:ASP185 2.3 11.2 1.0
O E:HOH556 2.4 14.4 1.0
OE2 E:GLU177 2.4 9.8 1.0
CG E:ASP185 3.2 9.8 1.0
CD E:GLU177 3.2 8.8 1.0
CD E:GLU190 3.3 9.2 1.0
C E:ASN183 3.5 12.8 1.0
OD1 E:ASP185 3.6 9.4 1.0
OE1 E:GLU177 3.7 9.0 1.0
CA E:CA402 3.8 8.4 1.0
CG E:GLU190 3.9 9.9 1.0
CA E:PRO184 4.1 10.6 1.0
CB E:ASN183 4.1 17.2 1.0
N E:ASP185 4.2 9.5 1.0
O E:HOH843 4.2 40.4 1.0
OD2 E:ASP191 4.2 13.7 1.0
CG E:GLU177 4.2 9.2 1.0
C E:PRO184 4.3 10.5 1.0
OD1 E:ASP191 4.3 13.7 1.0
OE1 E:GLU190 4.3 9.1 1.0
N E:PRO184 4.3 11.6 1.0
CB E:ASP185 4.4 10.3 1.0
O E:LYS182 4.4 15.5 1.0
CA E:ASN183 4.5 14.8 1.0
O E:HOH958 4.5 16.6 0.5
CG E:ASP191 4.6 12.3 1.0
O E:HOH836 4.6 39.7 1.0
CA E:ASP185 4.9 9.1 1.0
O E:PRO184 4.9 11.9 1.0

Reference:

S.G.Krimmer, M.Betz, A.Heine, G.Klebe. Methyl, Ethyl, Propyl, Butyl: Futile But Not For Water, As the Correlation of Structure and Thermodynamic Signature Shows in A Congeneric Series of Thermolysin Inhibitors. Chemmedchem V. 4 833 2014.
ISSN: ISSN 1860-7179
PubMed: 24623396
DOI: 10.1002/CMDC.201400013
Page generated: Sat Dec 12 04:59:48 2020

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