Calcium in PDB 4n4e: Thermolysin in Complex with UBTLN58

Enzymatic activity of Thermolysin in Complex with UBTLN58

All present enzymatic activity of Thermolysin in Complex with UBTLN58:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN58, PDB code: 4n4e 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) 31.81 / 1.13
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.505, 92.505, 131.488, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 13.8

Other elements in 4n4e:

The 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 Thermolysin in Complex with UBTLN58 (pdb code 4n4e). 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 UBTLN58, PDB code: 4n4e:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4n4e

Go back to Calcium Binding Sites List in 4n4e
Calcium binding site 1 out of 4 in the 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 Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:7.8
occ:1.00
 O E:GLU187 2.3 8.6 1.0
OD2 E:ASP138 2.4 8.3 1.0
O E:HOH501 2.4 8.3 1.0
OD1 E:ASP185 2.5 8.9 1.0
OE1 E:GLU177 2.5 8.4 1.0
OE1 E:GLU190 2.5 9.1 1.0
OE2 E:GLU190 2.5 9.5 1.0
OE2 E:GLU177 2.7 9.6 1.0
CD E:GLU190 2.9 9.1 1.0
CD E:GLU177 2.9 8.6 1.0
CG E:ASP138 3.4 7.7 1.0
C E:GLU187 3.4 8.8 1.0
CG E:ASP185 3.5 9.6 1.0
CA E:CA405 3.8 11.2 1.0
OD2 E:ASP185 3.8 11.3 1.0
CB E:ASP138 4.0 7.2 1.0
O E:ASP185 4.1 8.8 1.0
N E:GLU187 4.2 9.1 1.0
O E:HOH802 4.3 16.8 0.5
OD1 E:ASP138 4.3 9.2 1.0
N E:ILE188 4.3 8.2 1.0
CA E:GLU187 4.3 9.3 1.0
CA E:ILE188 4.3 8.0 1.0
CG E:GLU190 4.4 9.8 1.0
O E:HOH567 4.4 13.8 1.0
CG E:GLU177 4.4 8.3 1.0
N E:GLY189 4.4 8.0 1.0
C E:ASP185 4.6 8.7 1.0
CB E:GLU187 4.6 11.0 1.0
N E:ASP185 4.7 9.4 1.0
CB E:ASP185 4.8 9.7 1.0
C E:ILE188 4.8 7.7 1.0
O E:HOH573 4.8 15.8 1.0
CB E:GLU177 4.9 7.9 1.0
CA E:ASP185 5.0 9.1 1.0
N E:GLU190 5.0 8.6 1.0

Calcium binding site 2 out of 4 in 4n4e

Go back to Calcium Binding Sites List in 4n4e
Calcium binding site 2 out of 4 in the 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 Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.4
occ:1.00
 O E:GLN61 2.3 8.7 0.6
O E:GLN61 2.3 8.6 0.4
O E:HOH527 2.3 10.8 1.0
OD1 E:ASP57 2.4 9.1 1.0
O E:HOH552 2.4 11.3 1.0
OD1 E:ASP59 2.4 9.1 1.0
O E:HOH519 2.4 10.2 1.0
OD2 E:ASP57 2.6 8.6 1.0
CG E:ASP57 2.8 8.5 1.0
CG E:ASP59 3.4 10.0 1.0
C E:GLN61 3.5 8.2 0.6
C E:GLN61 3.5 8.1 0.4
OD2 E:ASP59 3.8 11.8 1.0
N E:GLN61 3.9 8.3 0.6
N E:GLN61 3.9 8.2 0.4
O E:HOH596 4.0 15.3 1.0
CA E:GLN61 4.1 8.9 0.6
CA E:GLN61 4.1 8.6 0.4
CB E:GLN61 4.3 10.8 0.6
CB E:ASP57 4.3 8.5 1.0
N E:ASP59 4.3 8.8 1.0
CB E:GLN61 4.4 10.1 0.4
O E:HOH526 4.4 11.0 1.0
N E:PHE62 4.5 7.8 1.0
O E:HOH883 4.6 15.3 1.0
CB E:ASP59 4.6 9.8 1.0
O E:HOH514 4.6 8.3 1.0
OD2 E:ASP67 4.6 8.8 1.0
N E:ASN60 4.6 7.8 1.0
O E:HOH712 4.7 23.1 1.0
N E:ALA58 4.7 8.3 1.0
CA E:PHE62 4.8 8.1 1.0
CA E:ASP59 4.8 9.1 1.0
O E:HOH723 4.8 30.0 1.0
C E:ASP59 4.9 8.2 1.0

Calcium binding site 3 out of 4 in 4n4e

Go back to Calcium Binding Sites List in 4n4e
Calcium binding site 3 out of 4 in the 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 Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:10.6
occ:1.00
 O E:ILE197 2.3 15.1 1.0
OD1 E:ASP200 2.4 11.0 1.0
O E:TYR193 2.4 10.7 1.0
O E:HOH556 2.4 14.6 1.0
O E:THR194 2.4 11.9 1.0
OG1 E:THR194 2.4 11.6 1.0
O E:HOH608 2.4 17.5 1.0
C E:THR194 3.2 11.3 1.0
C E:TYR193 3.4 10.2 1.0
CG E:ASP200 3.4 11.1 1.0
CB E:THR194 3.5 11.3 1.0
C E:ILE197 3.5 15.9 1.0
CA E:THR194 3.7 10.8 1.0
OD2 E:ASP200 3.8 12.0 1.0
N E:THR194 3.9 10.3 1.0
CA E:ILE197 4.2 16.3 1.0
CB E:ILE197 4.2 17.0 1.0
N E:PRO195 4.3 12.4 1.0
N E:ILE197 4.3 16.3 1.0
O E:HOH833 4.4 39.2 1.0
O E:ASP200 4.5 11.6 1.0
N E:SER198 4.5 16.7 0.3
N E:SER198 4.5 16.7 0.7
O E:HOH827 4.5 40.5 1.0
CA E:TYR193 4.6 9.6 1.0
N E:ASP200 4.6 12.9 1.0
CA E:SER198 4.7 17.5 0.3
O E:GLU190 4.7 10.3 1.0
CA E:PRO195 4.7 14.4 1.0
CB E:TYR193 4.7 10.3 1.0
CD2 E:TYR193 4.7 11.3 1.0
CA E:SER198 4.7 17.7 0.7
O E:HOH701 4.7 27.7 1.0
CB E:ASP200 4.7 11.6 1.0
CG2 E:THR194 4.8 11.6 1.0
C E:ASP200 4.8 11.4 1.0
CG2 E:ILE197 4.9 16.9 1.0
C E:SER198 4.9 16.9 0.7
CA E:ASP200 4.9 12.0 1.0
C E:PRO195 5.0 15.8 1.0

Calcium binding site 4 out of 4 in 4n4e

Go back to Calcium Binding Sites List in 4n4e
Calcium binding site 4 out of 4 in the 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 Thermolysin in Complex with UBTLN58 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:11.2
occ:1.00
 O E:ASN183 2.3 12.8 1.0
OE2 E:GLU190 2.3 9.5 1.0
O E:HOH587 2.3 16.2 1.0
O E:HOH573 2.3 15.8 1.0
OD2 E:ASP185 2.4 11.3 1.0
OE2 E:GLU177 2.5 9.6 1.0
CG E:ASP185 3.2 9.6 1.0
CD E:GLU177 3.3 8.6 1.0
CD E:GLU190 3.3 9.1 1.0
C E:ASN183 3.5 13.0 1.0
OD1 E:ASP185 3.6 8.9 1.0
OE1 E:GLU177 3.7 8.4 1.0
CA E:CA402 3.8 7.8 1.0
CG E:GLU190 3.8 9.8 1.0
CA E:PRO184 4.1 10.3 1.0
N E:ASP185 4.2 9.4 1.0
CB E:ASN183 4.2 18.7 1.0
O E:HOH940 4.2 46.9 1.0
OD1 E:ASP191 4.3 13.3 1.0
OD2 E:ASP191 4.3 13.3 1.0
C E:PRO184 4.3 10.1 1.0
OE1 E:GLU190 4.3 9.1 1.0
CG E:GLU177 4.3 8.3 1.0
N E:PRO184 4.3 11.4 1.0
CB E:ASP185 4.4 9.7 1.0
O E:LYS182 4.5 16.3 1.0
CA E:ASN183 4.5 15.9 1.0
O E:HOH802 4.5 16.8 0.5
CG E:ASP191 4.6 11.8 1.0
O E:HOH783 4.6 49.2 1.0
CA E:ASP185 4.9 9.1 1.0
O E:PRO184 5.0 11.5 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 05:00:27 2020

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