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Calcium in PDB 3eim: Metal Exchange in Thermolysin

Enzymatic activity of Metal Exchange in Thermolysin

All present enzymatic activity of Metal Exchange in Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Metal Exchange in Thermolysin, PDB code: 3eim was solved by L.Englert, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.88
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.710, 92.710, 128.650, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 25.2

Other elements in 3eim:

The structure of Metal Exchange in Thermolysin also contains other interesting chemical elements:

Copper (Cu) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Metal Exchange in Thermolysin (pdb code 3eim). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Metal Exchange in Thermolysin, PDB code: 3eim:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3eim

Go back to Calcium Binding Sites List in 3eim
Calcium binding site 1 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metal Exchange in Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:16.9
occ:1.00
O A:GLU187 2.3 18.7 1.0
OD1 A:ASP185 2.4 19.5 1.0
OE2 A:GLU190 2.4 15.7 1.0
O A:HOH2036 2.4 15.0 1.0
OE1 A:GLU190 2.5 16.8 1.0
OD2 A:ASP138 2.5 17.1 1.0
OE1 A:GLU177 2.5 19.5 1.0
CD A:GLU190 2.8 18.0 1.0
OE2 A:GLU177 2.8 14.5 1.0
CD A:GLU177 3.0 20.4 1.0
C A:GLU187 3.4 14.9 1.0
CG A:ASP185 3.4 22.2 1.0
CG A:ASP138 3.4 17.0 1.0
CA A:CA2002 3.8 18.5 1.0
OD2 A:ASP185 3.8 17.5 1.0
CB A:ASP138 4.1 14.8 1.0
O A:ASP185 4.1 14.5 1.0
N A:GLU187 4.2 15.1 1.0
CA A:GLU187 4.2 15.8 1.0
CG A:GLU190 4.3 15.1 1.0
OD1 A:ASP138 4.3 18.6 1.0
N A:ILE188 4.3 15.9 1.0
CA A:ILE188 4.3 14.0 1.0
CG A:GLU177 4.4 13.1 1.0
O A:HOH2168 4.4 16.5 1.0
N A:GLY189 4.4 16.1 1.0
CB A:GLU187 4.5 22.5 1.0
C A:ASP185 4.6 23.3 1.0
N A:ASP185 4.7 15.8 1.0
CB A:ASP185 4.7 15.4 1.0
C A:ILE188 4.8 15.8 1.0
CA A:ASP185 4.9 16.6 1.0
N A:GLU190 4.9 22.6 1.0
CB A:GLU177 4.9 12.1 1.0

Calcium binding site 2 out of 4 in 3eim

Go back to Calcium Binding Sites List in 3eim
Calcium binding site 2 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metal Exchange in Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:18.5
occ:1.00
O A:HOH2169 2.2 19.9 1.0
O A:ASN183 2.3 17.7 1.0
OE2 A:GLU177 2.3 14.5 1.0
OE2 A:GLU190 2.3 15.7 1.0
OD2 A:ASP185 2.3 17.5 1.0
O A:HOH2189 2.3 18.6 1.0
CD A:GLU177 3.2 20.4 1.0
CG A:ASP185 3.2 22.2 1.0
CD A:GLU190 3.3 18.0 1.0
C A:ASN183 3.4 12.7 1.0
OD1 A:ASP185 3.6 19.5 1.0
OE1 A:GLU177 3.7 19.5 1.0
CA A:CA2001 3.8 16.9 1.0
CG A:GLU190 3.8 15.1 1.0
CA A:PRO184 4.0 16.6 1.0
N A:ASP185 4.1 15.8 1.0
C A:PRO184 4.1 23.0 1.0
N A:PRO184 4.2 14.5 1.0
OD2 A:ASP191 4.2 24.2 1.0
CB A:ASN183 4.2 21.6 1.0
CG A:GLU177 4.2 13.1 1.0
O A:LYS182 4.2 24.2 1.0
OD1 A:ASP191 4.3 22.7 1.0
OE1 A:GLU190 4.3 16.8 1.0
CB A:ASP185 4.4 15.4 1.0
O A:HOH2147 4.4 35.8 1.0
CA A:ASN183 4.5 16.8 1.0
CG A:ASP191 4.5 21.7 1.0
O A:PRO184 4.8 20.9 1.0
CA A:ASP185 4.9 16.6 1.0

Calcium binding site 3 out of 4 in 3eim

Go back to Calcium Binding Sites List in 3eim
Calcium binding site 3 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metal Exchange in Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:17.0
occ:1.00
O A:GLN61 2.2 11.8 1.0
OD1 A:ASP57 2.3 17.7 1.0
O A:HOH2190 2.4 21.4 1.0
OD1 A:ASP59 2.4 16.3 1.0
O A:HOH2161 2.4 22.1 1.0
O A:HOH2138 2.5 16.3 1.0
OD2 A:ASP57 2.5 15.8 1.0
CG A:ASP57 2.7 19.2 1.0
CG A:ASP59 3.4 21.2 1.0
C A:GLN61 3.4 9.6 1.0
OD2 A:ASP59 3.8 22.6 1.0
N A:GLN61 3.9 17.1 1.0
O A:HOH2024 3.9 22.0 1.0
CA A:GLN61 4.1 14.0 1.0
CB A:ASP57 4.2 15.1 1.0
N A:ASP59 4.3 21.7 1.0
CB A:GLN61 4.4 20.9 1.0
O A:HOH2170 4.4 25.4 1.0
N A:PHE62 4.5 13.6 1.0
O A:HOH2085 4.5 18.0 1.0
O A:HOH2031 4.6 15.8 1.0
OD2 A:ASP67 4.6 20.2 1.0
CB A:ASP59 4.6 19.2 1.0
CA A:PHE62 4.7 15.5 1.0
N A:ASN60 4.7 16.3 1.0
N A:ALA58 4.7 16.7 1.0
CA A:ASP59 4.9 21.6 1.0
C A:ASP59 4.9 19.7 1.0

Calcium binding site 4 out of 4 in 3eim

Go back to Calcium Binding Sites List in 3eim
Calcium binding site 4 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Metal Exchange in Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2004

b:20.8
occ:1.00
O A:ILE197 2.2 20.5 1.0
O A:HOH2166 2.2 31.6 1.0
O A:TYR193 2.3 17.6 1.0
O A:THR194 2.3 28.6 1.0
OG1 A:THR194 2.4 19.6 1.0
O A:HOH2164 2.4 20.2 1.0
OD1 A:ASP200 2.5 20.3 1.0
C A:THR194 3.2 18.9 1.0
C A:TYR193 3.3 19.1 1.0
C A:ILE197 3.4 27.9 1.0
CB A:THR194 3.5 17.7 1.0
CG A:ASP200 3.5 24.2 1.0
CA A:THR194 3.7 17.5 1.0
N A:THR194 3.8 21.4 1.0
OD2 A:ASP200 3.9 27.8 1.0
N A:PRO195 4.2 16.1 1.0
CA A:ILE197 4.2 27.1 1.0
N A:ILE197 4.3 31.7 1.0
CB A:ILE197 4.3 29.5 1.0
N A:SER198 4.4 23.0 1.0
CA A:TYR193 4.5 15.6 1.0
CD2 A:TYR193 4.5 21.2 1.0
CA A:SER198 4.5 29.3 1.0
CB A:TYR193 4.6 16.2 1.0
O A:ASP200 4.6 17.5 1.0
CA A:PRO195 4.6 20.4 1.0
O A:GLU190 4.7 20.2 1.0
N A:ASP200 4.7 21.6 1.0
CG2 A:THR194 4.7 28.0 1.0
CB A:ASP200 4.8 21.8 1.0
CG A:TYR193 4.9 21.5 1.0
C A:SER198 4.9 26.2 1.0
C A:ASP200 4.9 19.7 1.0
C A:PRO195 5.0 25.6 1.0
CG2 A:ILE197 5.0 30.0 1.0
N A:TYR193 5.0 17.5 1.0

Reference:

L.Englert, A.Heine, G.Klebe. Metal Exchange in Thermolysin To Be Published.
Page generated: Wed Oct 28 08:09:20 2020

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