Atomistry » Calcium » PDB 4n0b-4n5x » 4n5p
Atomistry »
  Calcium »
    PDB 4n0b-4n5x »
      4n5p »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy