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Calcium in PDB 6sc0: Thermolysin in Complex with Fragment J22

Enzymatic activity of Thermolysin in Complex with Fragment J22

All present enzymatic activity of Thermolysin in Complex with Fragment J22:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Fragment J22, PDB code: 6sc0 was solved by F.Magari, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 1.53
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.572, 92.572, 129.113, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 16.6

Other elements in 6sc0:

The structure of Thermolysin in Complex with Fragment J22 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with Fragment J22 (pdb code 6sc0). 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 Fragment J22, PDB code: 6sc0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6sc0

Go back to Calcium Binding Sites List in 6sc0
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Fragment J22


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 Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:14.0
occ:1.00
O E:GLU187 2.2 15.7 0.6
OD1 E:ASP138 2.3 13.5 1.0
OD2 E:ASP185 2.4 15.6 1.0
O E:GLU187 2.4 11.4 0.4
OE1 E:GLU177 2.5 14.4 1.0
OE2 E:GLU190 2.5 15.3 1.0
O E:HOH557 2.5 14.6 1.0
OE1 E:GLU190 2.5 14.5 1.0
OE2 E:GLU177 2.7 15.5 1.0
CD E:GLU190 2.8 13.3 1.0
CD E:GLU177 2.9 15.1 1.0
CG E:ASP138 3.4 15.0 1.0
C E:GLU187 3.4 13.8 0.6
C E:GLU187 3.4 10.7 0.4
CG E:ASP185 3.4 14.0 1.0
HB3 E:ASP138 3.6 13.9 1.0
HA E:ILE188 3.6 18.5 1.0
H E:GLU187 3.7 19.4 0.6
H E:GLU187 3.8 18.4 0.4
HB2 E:GLU187 3.8 13.0 0.4
H E:GLY189 3.8 15.6 1.0
OD1 E:ASP185 3.8 16.2 1.0
CA E:CA402 3.8 15.6 1.0
CB E:ASP138 4.0 11.6 1.0
O E:ASP185 4.1 15.0 1.0
H E:GLU190 4.2 18.2 1.0
N E:GLU187 4.2 16.1 0.6
O E:HOH612 4.2 36.8 1.0
N E:GLU187 4.2 15.3 0.4
N E:ILE188 4.2 14.0 1.0
H E:ASP185 4.2 17.1 1.0
CA E:GLU187 4.3 17.2 0.4
HB2 E:ASP138 4.3 13.9 1.0
OD2 E:ASP138 4.3 16.6 1.0
HD13 E:ILE188 4.3 24.3 1.0
HB2 E:GLU187 4.3 24.4 0.6
CA E:ILE188 4.3 15.4 1.0
CA E:GLU187 4.3 13.9 0.6
CG E:GLU190 4.3 14.4 1.0
CG E:GLU177 4.4 13.8 1.0
O E:HOH568 4.4 17.8 1.0
N E:GLY189 4.4 13.0 1.0
CB E:GLU187 4.5 10.9 0.4
HG3 E:GLU190 4.6 17.2 1.0
C E:ASP185 4.6 14.2 1.0
HB2 E:GLU177 4.7 17.3 1.0
CB E:ASP185 4.7 13.4 1.0
N E:ASP185 4.8 14.2 1.0
HG2 E:GLU190 4.8 17.2 1.0
C E:ILE188 4.8 13.7 1.0
HB3 E:GLU177 4.8 17.3 1.0
HG2 E:GLU177 4.8 16.5 1.0
CB E:GLU187 4.9 20.3 0.6
HA E:THR174 4.9 16.0 1.0
HG3 E:GLU177 4.9 16.5 1.0
CB E:GLU177 4.9 14.4 1.0
O E:HOH547 5.0 18.4 1.0
H E:ILE188 5.0 16.8 0.4
CA E:ASP185 5.0 15.1 1.0
HB3 E:GLU190 5.0 18.4 1.0
N E:GLU190 5.0 15.2 1.0
H E:ILE188 5.0 16.8 0.6

Calcium binding site 2 out of 4 in 6sc0

Go back to Calcium Binding Sites List in 6sc0
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Fragment J22


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 Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:15.6
occ:1.00
O E:ASN183 2.3 17.8 1.0
OD1 E:ASP185 2.3 16.2 1.0
OE2 E:GLU190 2.3 15.3 1.0
O E:HOH573 2.4 19.4 1.0
O E:HOH547 2.4 18.4 1.0
OE2 E:GLU177 2.4 15.5 1.0
CG E:ASP185 3.2 14.0 1.0
CD E:GLU177 3.3 15.1 1.0
CD E:GLU190 3.3 13.3 1.0
C E:ASN183 3.5 17.1 1.0
HG3 E:GLU190 3.5 17.2 1.0
HA E:PRO184 3.6 20.6 1.0
OD2 E:ASP185 3.6 15.6 1.0
HB2 E:ASN183 3.7 24.1 1.0
HG2 E:GLU190 3.8 17.2 1.0
OE1 E:GLU177 3.8 14.4 1.0
CG E:GLU190 3.8 14.4 1.0
HB3 E:ASN183 3.8 24.1 1.0
CA E:CA401 3.8 14.0 1.0
H E:ASP185 4.1 17.1 1.0
OD1 E:ASP191 4.1 20.6 1.0
CA E:PRO184 4.1 17.1 1.0
CB E:ASN183 4.1 20.0 1.0
N E:ASP185 4.2 14.2 1.0
HG2 E:GLU177 4.2 16.5 1.0
CG E:GLU177 4.2 13.8 1.0
OD2 E:ASP191 4.2 18.4 1.0
O E:HOH691 4.2 40.5 1.0
C E:PRO184 4.3 18.9 1.0
N E:PRO184 4.3 16.1 1.0
OE1 E:GLU190 4.3 14.5 1.0
HG3 E:GLU177 4.3 16.5 1.0
O E:LYS182 4.4 20.6 1.0
HB3 E:ASP185 4.4 16.1 1.0
CB E:ASP185 4.4 13.4 1.0
O E:HOH612 4.4 36.8 1.0
CA E:ASN183 4.5 19.6 1.0
CG E:ASP191 4.5 20.0 1.0
O E:PRO184 4.9 20.0 1.0
CA E:ASP185 4.9 15.1 1.0

Calcium binding site 3 out of 4 in 6sc0

Go back to Calcium Binding Sites List in 6sc0
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Fragment J22


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 Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:14.4
occ:1.00
O E:GLN61 2.2 14.5 1.0
OD1 E:ASP57 2.4 13.9 1.0
O E:HOH556 2.4 17.2 1.0
O E:HOH713 2.4 16.5 1.0
OD1 E:ASP59 2.4 14.4 1.0
O E:HOH581 2.4 16.2 1.0
OD2 E:ASP57 2.6 14.0 1.0
CG E:ASP57 2.8 15.2 1.0
H E:GLN61 3.3 16.6 1.0
CG E:ASP59 3.4 15.9 1.0
C E:GLN61 3.4 12.9 1.0
H E:ASP59 3.6 15.4 1.0
HB2 E:GLN61 3.7 16.5 1.0
OD2 E:ASP59 3.8 18.0 1.0
O E:HOH616 4.0 21.5 1.0
N E:GLN61 4.0 13.8 1.0
HA E:PHE62 4.0 15.1 1.0
CA E:GLN61 4.2 13.6 1.0
H E:ALA58 4.3 16.6 1.0
CB E:ASP57 4.3 12.2 1.0
N E:ASP59 4.3 12.8 1.0
H E:ASN60 4.4 16.6 1.0
CB E:GLN61 4.4 13.8 1.0
O E:HOH669 4.5 16.0 1.0
N E:PHE62 4.5 11.8 1.0
O E:HOH756 4.6 33.9 1.0
OD2 E:ASP67 4.6 13.3 1.0
CB E:ASP59 4.6 14.1 1.0
O E:HOH531 4.6 14.3 1.0
N E:ASN60 4.7 13.8 1.0
HB2 E:ASP57 4.7 14.6 1.0
CA E:PHE62 4.7 12.6 1.0
H E:PHE63 4.7 16.6 1.0
N E:ALA58 4.8 13.8 1.0
HB3 E:ASP57 4.8 14.6 1.0
CA E:ASP59 4.8 13.3 1.0
HA E:ASP57 4.8 15.3 1.0
O E:HOH746 4.9 28.6 1.0
C E:ASP59 4.9 14.7 1.0
HB3 E:GLN61 4.9 16.5 1.0
HB3 E:ASP59 5.0 17.0 1.0

Calcium binding site 4 out of 4 in 6sc0

Go back to Calcium Binding Sites List in 6sc0
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Fragment J22


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 Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:16.7
occ:1.00
O E:ILE197 2.3 18.9 1.0
O E:TYR193 2.3 16.5 1.0
O E:HOH564 2.4 16.9 1.0
OD1 E:ASP200 2.4 17.7 1.0
O E:HOH688 2.4 26.9 1.0
OG1 E:THR194 2.4 17.8 1.0
O E:THR194 2.4 20.3 1.0
C E:THR194 3.3 18.1 1.0
C E:TYR193 3.3 17.1 1.0
C E:ILE197 3.5 19.7 1.0
CG E:ASP200 3.5 17.9 1.0
HB E:ILE197 3.5 28.1 1.0
CB E:THR194 3.5 19.2 1.0
H E:ILE197 3.6 30.3 1.0
CA E:THR194 3.7 16.5 1.0
HB E:THR194 3.7 23.1 1.0
H E:ASP200 3.8 22.3 1.0
OD2 E:ASP200 3.9 19.8 1.0
N E:THR194 3.9 17.1 1.0
HB3 E:TYR193 4.1 20.0 1.0
HA E:SER198 4.1 22.5 0.7
HD2 E:TYR193 4.1 21.0 1.0
HA E:SER198 4.1 30.7 0.3
CA E:ILE197 4.2 21.1 1.0
N E:ILE197 4.2 25.2 1.0
CB E:ILE197 4.2 23.4 1.0
O E:HOH627 4.3 31.4 1.0
N E:PRO195 4.3 19.2 1.0
HA E:PRO195 4.3 22.2 1.0
O E:ASP200 4.5 18.2 1.0
HG22 E:ILE197 4.5 29.6 1.0
N E:SER198 4.5 24.2 0.7
N E:SER198 4.5 25.0 0.3
CA E:TYR193 4.5 16.3 1.0
N E:ASP200 4.6 18.6 1.0
H E:GLY199 4.6 24.6 0.3
HA E:THR194 4.6 19.8 1.0
O E:GLU190 4.7 15.6 1.0
CA E:SER198 4.7 18.8 0.7
H E:GLY199 4.7 24.6 0.7
CB E:TYR193 4.7 16.6 1.0
CD2 E:TYR193 4.7 17.5 1.0
CA E:SER198 4.7 25.6 0.3
CA E:PRO195 4.7 18.5 1.0
H E:THR194 4.7 20.5 1.0
CG2 E:THR194 4.8 18.8 1.0
CB E:ASP200 4.8 18.3 1.0
C E:ASP200 4.8 17.4 1.0
CG2 E:ILE197 4.9 24.6 1.0
HG23 E:THR194 4.9 22.6 1.0
C E:SER198 4.9 18.8 0.7
N E:GLY199 4.9 20.5 1.0
H E:TYR193 5.0 15.8 1.0
CA E:ASP200 5.0 18.0 1.0
HG21 E:THR194 5.0 22.6 1.0
C E:PRO195 5.0 21.7 1.0

Reference:

F.Magari, A.Heine, G.Klebe. Thermolysin in Complex with Fragment J22 To Be Published.
Page generated: Wed Jul 9 17:46:43 2025

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