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Calcium in PDB 4n5p: Thermolysin in Complex with UBTLN20

Enzymatic activity of Thermolysin in Complex with UBTLN20

All present enzymatic activity of Thermolysin in Complex with UBTLN20:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with UBTLN20, PDB code: 4n5p 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) 34.16 / 1.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.491, 92.491, 130.891, 90.00, 90.00, 120.00
R / Rfree (%) 11.3 / 13.4

Other elements in 4n5p:

The structure of Thermolysin in Complex with UBTLN20 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 UBTLN20 (pdb code 4n5p). 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 UBTLN20, PDB code: 4n5p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4n5p

Go back to Calcium Binding Sites List in 4n5p
Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN20


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 UBTLN20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:8.7
occ:1.00
 O E:GLU187 2.3 9.3 1.0
OD2 E:ASP138 2.4 8.7 1.0
O E:HOH601 2.4 9.0 1.0
OE1 E:GLU177 2.5 9.1 1.0
OD1 E:ASP185 2.5 9.5 1.0
OE1 E:GLU190 2.5 9.5 1.0
OE2 E:GLU190 2.5 10.1 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 8.7 1.0
CG E:ASP138 3.4 8.8 1.0
C E:GLU187 3.4 9.5 1.0
CG E:ASP185 3.5 9.7 1.0
CA E:CA403 3.8 11.2 1.0
OD2 E:ASP185 3.8 11.1 1.0
CB E:ASP138 4.0 8.0 1.0
O E:ASP185 4.1 9.2 1.0
N E:GLU187 4.2 9.7 1.0
OD1 E:ASP138 4.3 10.5 1.0
N E:ILE188 4.3 8.4 1.0
CA E:GLU187 4.3 9.9 1.0
CA E:ILE188 4.3 8.6 1.0
O E:HOH1059 4.3 19.6 0.5
CG E:GLU190 4.4 10.1 1.0
CG E:GLU177 4.4 9.2 1.0
O E:HOH666 4.4 14.8 1.0
N E:GLY189 4.4 8.7 1.0
CB E:GLU187 4.6 11.7 1.0
C E:ASP185 4.6 9.3 1.0
N E:ASP185 4.8 9.8 1.0
CB E:ASP185 4.8 10.3 1.0
C E:ILE188 4.8 8.3 1.0
CB E:GLU177 4.9 8.4 1.0
O E:HOH974 4.9 14.4 1.0
N E:GLU190 5.0 9.0 1.0
CA E:ASP185 5.0 9.8 1.0

Calcium binding site 2 out of 4 in 4n5p

Go back to Calcium Binding Sites List in 4n5p
Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN20


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 UBTLN20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:9.1
occ:1.00
 O E:GLN61 2.3 9.4 0.5
O E:GLN61 2.3 9.3 0.5
O E:HOH624 2.3 11.5 1.0
OD1 E:ASP59 2.4 9.7 1.0
OD2 E:ASP57 2.4 9.7 1.0
O E:HOH635 2.4 11.5 1.0
O E:HOH620 2.4 10.8 1.0
OD1 E:ASP57 2.6 9.2 1.0
CG E:ASP57 2.8 9.2 1.0
CG E:ASP59 3.4 10.5 1.0
C E:GLN61 3.5 8.8 0.5
C E:GLN61 3.5 8.5 0.5
OD2 E:ASP59 3.8 12.7 1.0
N E:GLN61 3.9 9.1 0.5
N E:GLN61 3.9 8.9 0.5
O E:HOH681 4.0 15.8 1.0
CA E:GLN61 4.1 9.6 0.5
CA E:GLN61 4.1 9.1 0.5
CB E:GLN61 4.3 12.1 0.5
N E:ASP59 4.3 9.6 1.0
CB E:ASP57 4.3 9.4 1.0
CB E:GLN61 4.3 11.2 0.5
O E:HOH629 4.4 11.7 1.0
N E:PHE62 4.5 8.1 1.0
O E:HOH685 4.6 17.0 1.0
CB E:ASP59 4.6 10.4 1.0
O E:HOH606 4.6 8.8 1.0
N E:ASN60 4.6 8.8 1.0
OD2 E:ASP67 4.6 9.1 1.0
O E:HOH806 4.7 26.1 1.0
O E:HOH796 4.7 31.7 1.0
N E:ALA58 4.7 9.2 1.0
CA E:PHE62 4.8 8.6 1.0
CA E:ASP59 4.8 9.7 1.0
C E:ASP59 4.9 9.2 1.0

Calcium binding site 3 out of 4 in 4n5p

Go back to Calcium Binding Sites List in 4n5p
Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN20


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 UBTLN20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:11.2
occ:1.00
 OE2 E:GLU190 2.3 10.1 1.0
O E:ASN183 2.3 12.6 1.0
O E:HOH897 2.3 14.9 1.0
O E:HOH974 2.3 14.4 1.0
OD2 E:ASP185 2.4 11.1 1.0
OE2 E:GLU177 2.4 9.8 1.0
CG E:ASP185 3.2 9.7 1.0
CD E:GLU177 3.2 8.7 1.0
CD E:GLU190 3.3 9.2 1.0
C E:ASN183 3.5 12.7 1.0
OD1 E:ASP185 3.6 9.5 1.0
OE1 E:GLU177 3.8 9.1 1.0
CA E:CA401 3.8 8.7 1.0
CG E:GLU190 3.8 10.1 1.0
CA E:PRO184 4.1 10.8 1.0
CB E:ASN183 4.1 17.5 1.0
N E:ASP185 4.2 9.8 1.0
O E:HOH1001 4.2 42.5 1.0
OD2 E:ASP191 4.2 13.5 1.0
CG E:GLU177 4.3 9.2 1.0
OD1 E:ASP191 4.3 13.6 1.0
C E:PRO184 4.3 10.7 1.0
OE1 E:GLU190 4.3 9.5 1.0
N E:PRO184 4.3 11.4 1.0
CB E:ASP185 4.4 10.3 1.0
O E:LYS182 4.4 16.0 1.0
CA E:ASN183 4.5 15.1 1.0
O E:HOH1059 4.5 19.6 0.5
CG E:ASP191 4.6 12.2 1.0
O E:HOH869 4.6 40.4 1.0
CA E:ASP185 4.9 9.8 1.0
O E:PRO184 4.9 12.2 1.0

Calcium binding site 4 out of 4 in 4n5p

Go back to Calcium Binding Sites List in 4n5p
Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN20


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 UBTLN20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:11.9
occ:1.00
 O E:ILE197 2.3 16.1 1.0
O E:TYR193 2.4 11.3 1.0
OD1 E:ASP200 2.4 12.1 1.0
O E:HOH697 2.4 18.7 1.0
O E:THR194 2.4 13.3 1.0
O E:HOH642 2.4 14.5 1.0
OG1 E:THR194 2.4 12.4 1.0
C E:THR194 3.2 12.6 1.0
C E:TYR193 3.4 11.1 1.0
CG E:ASP200 3.4 12.2 1.0
CB E:THR194 3.5 12.6 1.0
C E:ILE197 3.5 17.5 1.0
CA E:THR194 3.7 11.8 1.0
OD2 E:ASP200 3.8 13.2 1.0
N E:THR194 3.9 11.3 1.0
CA E:ILE197 4.2 17.9 1.0
N E:PRO195 4.2 13.6 1.0
CB E:ILE197 4.3 18.4 1.0
N E:ILE197 4.3 17.6 1.0
O E:HOH924 4.5 36.8 1.0
O E:ASP200 4.5 12.1 1.0
O E:HOH912 4.5 43.6 1.0
N E:SER198 4.5 18.4 0.3
N E:SER198 4.5 18.4 0.7
CA E:TYR193 4.5 10.5 1.0
O E:HOH848 4.6 37.8 1.0
N E:ASP200 4.6 13.6 1.0
CA E:PRO195 4.6 15.6 1.0
O E:GLU190 4.7 10.7 1.0
O E:HOH821 4.7 28.3 1.0
CD2 E:TYR193 4.7 13.0 1.0
CB E:TYR193 4.7 11.5 1.0
CA E:SER198 4.7 19.4 0.3
CA E:SER198 4.7 20.1 0.7
CB E:ASP200 4.7 12.4 1.0
CG2 E:THR194 4.8 13.1 1.0
C E:ASP200 4.8 11.9 1.0
CG2 E:ILE197 4.9 18.3 1.0
C E:SER198 4.9 19.7 0.7
CA E:ASP200 4.9 12.7 1.0
C E:PRO195 5.0 17.4 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: Sun Jul 14 10:52:52 2024

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