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Calcium in PDB 4oi5: Glycerol-Free Structure of Thermolysin in Complex with UBTLN58

Enzymatic activity of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58

All present enzymatic activity of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58:
3.4.24.27;

Protein crystallography data

The structure of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58, PDB code: 4oi5 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) 19.65 / 1.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.373, 92.373, 130.270, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 14.6

Other elements in 4oi5:

The structure of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 (pdb code 4oi5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58, PDB code: 4oi5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4oi5

Go back to Calcium Binding Sites List in 4oi5
Calcium binding site 1 out of 4 in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:7.5
occ:1.00
 O E:GLU187 2.3 7.7 1.0
OD2 E:ASP138 2.4 7.9 1.0
O E:HOH501 2.4 7.7 1.0
OE1 E:GLU177 2.5 7.9 1.0
OD1 E:ASP185 2.5 8.5 1.0
OE1 E:GLU190 2.5 8.7 1.0
OE2 E:GLU190 2.5 9.0 1.0
OE2 E:GLU177 2.7 9.4 1.0
CD E:GLU190 2.8 8.3 1.0
CD E:GLU177 2.9 8.0 1.0
CG E:ASP138 3.4 8.1 1.0
C E:GLU187 3.4 7.2 1.0
CG E:ASP185 3.5 9.0 1.0
OD2 E:ASP185 3.8 10.4 1.0
CA E:CA404 3.8 11.4 1.0
CB E:ASP138 4.0 7.5 1.0
O E:ASP185 4.1 8.0 1.0
N E:GLU187 4.2 8.0 1.0
O E:HOH950 4.2 13.5 0.5
OD1 E:ASP138 4.3 9.4 1.0
N E:ILE188 4.3 7.4 1.0
CA E:GLU187 4.3 8.3 1.0
CA E:ILE188 4.3 7.6 1.0
CG E:GLU190 4.4 10.0 1.0
CG E:GLU177 4.4 8.4 1.0
O E:HOH571 4.4 14.1 1.0
N E:GLY189 4.4 7.6 1.0
CB E:GLU187 4.6 10.0 1.0
C E:ASP185 4.6 8.0 1.0
CB E:ASP185 4.8 9.7 1.0
N E:ASP185 4.8 9.1 1.0
C E:ILE188 4.8 7.4 1.0
O E:HOH574 4.9 14.1 1.0
CB E:GLU177 4.9 7.6 1.0
N E:GLU190 5.0 8.4 1.0
CA E:ASP185 5.0 8.7 1.0

Calcium binding site 2 out of 4 in 4oi5

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Calcium binding site 2 out of 4 in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.2
occ:1.00
 O E:GLN61 2.3 8.2 0.5
O E:GLN61 2.3 8.3 0.5
O E:HOH799 2.3 10.6 1.0
OD2 E:ASP57 2.4 8.7 1.0
O E:HOH525 2.4 10.2 1.0
OD1 E:ASP59 2.4 8.6 1.0
O E:HOH519 2.4 9.6 1.0
OD1 E:ASP57 2.6 8.6 1.0
CG E:ASP57 2.8 8.4 1.0
CG E:ASP59 3.4 9.6 1.0
C E:GLN61 3.4 7.9 0.5
C E:GLN61 3.5 8.0 0.5
OD2 E:ASP59 3.8 11.7 1.0
N E:GLN61 4.0 8.7 0.5
N E:GLN61 4.0 8.8 0.5
O E:HOH567 4.0 15.4 1.0
CA E:GLN61 4.1 8.9 0.5
CA E:GLN61 4.2 9.1 0.5
CB E:GLN61 4.3 10.9 0.5
N E:ASP59 4.3 8.6 1.0
CB E:ASP57 4.3 8.2 1.0
CB E:GLN61 4.4 11.5 0.5
O E:HOH518 4.4 10.5 1.0
N E:PHE62 4.5 7.8 1.0
O E:HOH556 4.6 14.1 1.0
CB E:ASP59 4.6 9.2 1.0
OD2 E:ASP67 4.6 8.0 1.0
O E:HOH503 4.6 7.6 1.0
N E:ASN60 4.6 7.9 1.0
N E:ALA58 4.7 7.6 1.0
O E:HOH648 4.7 22.4 1.0
CA E:PHE62 4.8 8.3 1.0
CA E:ASP59 4.8 8.6 1.0
C E:ASP59 4.9 8.0 1.0

Calcium binding site 3 out of 4 in 4oi5

Go back to Calcium Binding Sites List in 4oi5
Calcium binding site 3 out of 4 in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:11.4
occ:1.00
 O E:HOH878 2.3 15.5 1.0
O E:ASN183 2.3 13.4 1.0
OE2 E:GLU190 2.3 9.0 1.0
O E:HOH574 2.3 14.1 1.0
OD2 E:ASP185 2.3 10.4 1.0
OE2 E:GLU177 2.4 9.4 1.0
CG E:ASP185 3.2 9.0 1.0
CD E:GLU177 3.2 8.0 1.0
CD E:GLU190 3.3 8.3 1.0
C E:ASN183 3.5 13.3 1.0
OD1 E:ASP185 3.6 8.5 1.0
OE1 E:GLU177 3.8 7.9 1.0
CA E:CA402 3.8 7.5 1.0
CG E:GLU190 3.9 10.0 1.0
CB E:ASN183 4.1 18.4 1.0
CA E:PRO184 4.1 10.3 1.0
N E:ASP185 4.2 9.1 1.0
OD1 E:ASP191 4.2 14.0 1.0
OD2 E:ASP191 4.2 13.2 1.0
CG E:GLU177 4.3 8.4 1.0
C E:PRO184 4.3 9.9 1.0
OE1 E:GLU190 4.3 8.7 1.0
O E:HOH928 4.3 47.7 1.0
N E:PRO184 4.3 11.7 1.0
CB E:ASP185 4.4 9.7 1.0
O E:LYS182 4.5 17.4 1.0
CA E:ASN183 4.5 15.6 1.0
O E:HOH950 4.5 13.5 0.5
CG E:ASP191 4.6 12.3 1.0
O E:HOH915 4.6 42.0 1.0
CA E:ASP185 4.9 8.7 1.0
O E:PRO184 5.0 12.2 1.0

Calcium binding site 4 out of 4 in 4oi5

Go back to Calcium Binding Sites List in 4oi5
Calcium binding site 4 out of 4 in the Glycerol-Free Structure of Thermolysin in Complex with UBTLN58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Glycerol-Free Structure of Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:12.4
occ:1.00
 O E:ILE197 2.3 18.0 1.0
OD1 E:ASP200 2.4 13.0 1.0
O E:TYR193 2.4 11.6 1.0
O E:THR194 2.4 14.5 1.0
OG1 E:THR194 2.4 12.3 1.0
O E:HOH843 2.4 19.4 1.0
O E:HOH555 2.4 14.7 1.0
C E:THR194 3.2 14.1 1.0
C E:TYR193 3.4 11.2 1.0
CG E:ASP200 3.4 12.5 1.0
CB E:THR194 3.5 12.9 1.0
C E:ILE197 3.5 18.6 1.0
CA E:THR194 3.7 12.7 1.0
OD2 E:ASP200 3.8 13.1 1.0
N E:THR194 3.9 11.8 1.0
CA E:ILE197 4.2 18.9 1.0
CB E:ILE197 4.2 19.5 1.0
N E:PRO195 4.2 15.1 1.0
N E:ILE197 4.3 18.1 1.0
O E:HOH789 4.4 40.2 1.0
O E:HOH830 4.4 34.7 1.0
O E:ASP200 4.5 12.7 1.0
N E:SER198 4.5 19.6 1.0
O E:HOH854 4.5 28.6 1.0
CA E:TYR193 4.6 10.3 1.0
N E:ASP200 4.6 15.5 1.0
O E:GLU190 4.7 10.8 1.0
CA E:SER198 4.7 21.6 1.0
CA E:PRO195 4.7 16.6 1.0
CD2 E:TYR193 4.7 13.2 1.0
CB E:TYR193 4.7 11.0 1.0
CB E:ASP200 4.7 12.6 1.0
CG2 E:THR194 4.8 13.6 1.0
C E:ASP200 4.8 12.3 1.0
CG2 E:ILE197 4.9 19.3 1.0
C E:SER198 4.9 21.1 1.0
CA E:ASP200 4.9 13.6 1.0
N E:GLY199 4.9 19.7 1.0
C E:PRO195 5.0 18.1 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. 9 833 2014.
ISSN: ISSN 1860-7179
PubMed: 24623396
DOI: 10.1002/CMDC.201400013
Page generated: Sun Jul 14 11:22:47 2024

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