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Calcium in PDB 1kto: Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)

Enzymatic activity of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)

All present enzymatic activity of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine), PDB code: 1kto was solved by M.Senda, T.Senda, S.Kidokoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.607, 93.607, 131.332, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 18.5

Other elements in 1kto:

The structure of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) (pdb code 1kto). 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 Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine), PDB code: 1kto:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1kto

Go back to Calcium Binding Sites List in 1kto
Calcium binding site 1 out of 4 in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.3
occ:1.00
 O A:GLU187 2.4 12.5 1.0
OE1 A:GLU177 2.4 13.5 1.0
O A:HOH1320 2.4 10.9 1.0
OD2 A:ASP138 2.5 13.6 1.0
OE1 A:GLU190 2.5 12.7 1.0
OD1 A:ASP185 2.5 12.9 1.0
OE2 A:GLU190 2.5 12.4 1.0
OE2 A:GLU177 2.8 12.4 1.0
CD A:GLU190 2.8 13.6 1.0
CD A:GLU177 2.9 14.6 1.0
CG A:ASP138 3.5 13.7 1.0
C A:GLU187 3.5 13.9 1.0
CG A:ASP185 3.5 15.9 1.0
CA A:CA402 3.7 14.8 1.0
OD2 A:ASP185 3.8 14.6 1.0
CB A:ASP138 4.0 12.2 1.0
O A:ASP185 4.2 15.4 1.0
N A:GLU187 4.2 16.3 1.0
O A:HOH1408 4.3 31.9 1.0
N A:ILE188 4.3 12.0 1.0
CG A:GLU190 4.3 12.5 1.0
CA A:ILE188 4.4 13.3 1.0
CA A:GLU187 4.4 15.8 1.0
OD1 A:ASP138 4.4 14.7 1.0
CG A:GLU177 4.4 12.9 1.0
N A:GLY189 4.4 12.4 1.0
O A:HOH1358 4.6 18.0 1.0
C A:ASP185 4.6 16.0 1.0
CB A:GLU187 4.7 17.1 1.0
CB A:ASP185 4.8 15.7 1.0
N A:ASP185 4.8 16.0 1.0
C A:ILE188 4.9 13.3 1.0
N A:GLU190 4.9 12.7 1.0
CB A:GLU177 4.9 13.7 1.0
O A:HOH1345 4.9 19.7 1.0

Calcium binding site 2 out of 4 in 1kto

Go back to Calcium Binding Sites List in 1kto
Calcium binding site 2 out of 4 in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.8
occ:1.00
 OE2 A:GLU190 2.2 12.4 1.0
OD2 A:ASP185 2.3 14.6 1.0
O A:ASN183 2.4 19.3 1.0
OE2 A:GLU177 2.4 12.4 1.0
O A:HOH1334 2.4 14.2 1.0
O A:HOH1345 2.5 19.7 1.0
CG A:ASP185 3.2 15.9 1.0
CD A:GLU190 3.2 13.6 1.0
CD A:GLU177 3.3 14.6 1.0
C A:ASN183 3.5 20.9 1.0
OD1 A:ASP185 3.6 12.9 1.0
CA A:CA401 3.7 13.3 1.0
CG A:GLU190 3.8 12.5 1.0
OE1 A:GLU177 3.8 13.5 1.0
O A:LYS182 3.8 24.4 1.0
OE1 A:GLU190 4.2 12.7 1.0
N A:ASP185 4.2 16.0 1.0
OD2 A:ASP191 4.2 16.4 1.0
CB A:ASN183 4.2 25.5 1.0
CA A:PRO184 4.3 18.8 1.0
CG A:GLU177 4.3 12.9 1.0
OD1 A:ASP191 4.3 17.5 1.0
C A:PRO184 4.3 18.8 1.0
N A:PRO184 4.3 20.7 1.0
CB A:ASP185 4.3 15.7 1.0
O A:HOH1408 4.5 31.9 1.0
CA A:ASN183 4.5 22.7 1.0
CG A:ASP191 4.6 16.4 1.0
C A:LYS182 4.9 25.0 1.0
CA A:ASP185 4.9 15.5 1.0
O A:PRO184 5.0 16.9 1.0

Calcium binding site 3 out of 4 in 1kto

Go back to Calcium Binding Sites List in 1kto
Calcium binding site 3 out of 4 in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:13.2
occ:1.00
 O A:GLN61 2.3 13.3 1.0
O A:HOH1331 2.3 16.2 1.0
O A:HOH1329 2.4 12.9 1.0
OD1 A:ASP57 2.4 14.7 1.0
OD1 A:ASP59 2.4 17.1 1.0
O A:HOH1336 2.5 20.8 1.0
OD2 A:ASP57 2.6 15.1 1.0
CG A:ASP57 2.8 14.6 1.0
C A:GLN61 3.4 14.7 1.0
CG A:ASP59 3.4 18.1 1.0
OD2 A:ASP59 3.8 18.0 1.0
N A:GLN61 4.0 14.2 1.0
O A:HOH1370 4.1 26.0 1.0
CA A:GLN61 4.2 16.3 1.0
CB A:ASP57 4.3 13.4 1.0
N A:ASP59 4.3 14.4 1.0
CB A:GLN61 4.3 19.9 1.0
N A:PHE62 4.5 14.4 1.0
O A:HOH1440 4.5 42.4 1.0
O A:HOH1340 4.6 18.5 1.0
O A:HOH1318 4.6 12.1 1.0
CA A:PHE62 4.7 13.2 1.0
OD2 A:ASP67 4.7 13.6 1.0
CB A:ASP59 4.7 15.2 1.0
N A:ASN60 4.7 14.2 1.0
N A:ALA58 4.8 12.8 1.0
CA A:ASP59 4.8 14.9 1.0
C A:ASP59 5.0 14.6 1.0

Calcium binding site 4 out of 4 in 1kto

Go back to Calcium Binding Sites List in 1kto
Calcium binding site 4 out of 4 in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:16.8
occ:1.00
 O A:ILE197 2.2 30.9 1.0
OG1 A:THR194 2.3 18.5 1.0
OD1 A:ASP200 2.3 18.0 1.0
O A:TYR193 2.3 13.9 1.0
O A:THR194 2.4 20.8 1.0
O A:HOH1366 2.4 23.6 1.0
O A:HOH1324 2.5 21.4 1.0
C A:THR194 3.2 20.8 1.0
C A:TYR193 3.4 16.3 1.0
C A:ILE197 3.4 31.8 1.0
CG A:ASP200 3.4 18.8 1.0
CB A:THR194 3.5 18.4 1.0
CA A:THR194 3.7 19.0 1.0
OD2 A:ASP200 3.7 18.4 1.0
N A:THR194 3.9 17.4 1.0
CA A:ILE197 4.2 31.7 1.0
N A:ILE197 4.2 32.5 1.0
CB A:ILE197 4.2 32.1 1.0
N A:PRO195 4.3 22.7 1.0
N A:SER198 4.4 31.3 1.0
O A:ASP200 4.4 19.1 1.0
CA A:SER198 4.5 31.8 1.0
CA A:TYR193 4.5 15.7 1.0
O A:GLU190 4.6 13.7 1.0
CD2 A:TYR193 4.7 19.4 1.0
N A:ASP200 4.7 22.5 1.0
CA A:PRO195 4.7 25.0 1.0
CB A:TYR193 4.7 16.9 1.0
CG2 A:THR194 4.7 19.4 1.0
CB A:ASP200 4.7 19.7 1.0
O A:HOH1381 4.7 33.0 1.0
C A:ASP200 4.8 19.0 1.0
C A:SER198 5.0 30.5 1.0
CA A:ASP200 5.0 19.5 1.0
C A:PRO195 5.0 27.6 1.0
CG2 A:ILE197 5.0 31.2 1.0

Reference:

M.Senda, T.Senda, S.Kidokoro. Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors. To Be Published.
Page generated: Thu Jul 11 11:29:02 2024

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