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Calcium in PDB 1kkk: Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)

Enzymatic activity of Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)

All present enzymatic activity of Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid), PDB code: 1kkk 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) 25.13 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.676, 93.676, 131.515, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 18.9

Other elements in 1kkk:

The structure of Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) 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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) (pdb code 1kkk). 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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid), PDB code: 1kkk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1kkk

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Calcium binding site 1 out of 4 in the Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)


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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.4
occ:1.00
 O A:GLU187 2.3 12.6 1.0
OD2 A:ASP138 2.4 12.4 1.0
O A:HOH1320 2.5 11.6 1.0
OE1 A:GLU177 2.5 11.3 1.0
OE1 A:GLU190 2.5 12.7 1.0
OD1 A:ASP185 2.5 13.6 1.0
OE2 A:GLU190 2.5 13.3 1.0
OE2 A:GLU177 2.8 13.1 1.0
CD A:GLU190 2.8 12.3 1.0
CD A:GLU177 3.0 13.8 1.0
C A:GLU187 3.4 12.9 1.0
CG A:ASP138 3.4 12.7 1.0
CG A:ASP185 3.5 14.9 1.0
CA A:CA402 3.8 14.3 1.0
OD2 A:ASP185 3.9 14.9 1.0
CB A:ASP138 4.0 11.0 1.0
N A:GLU187 4.2 14.0 1.0
N A:ILE188 4.2 11.6 1.0
O A:ASP185 4.3 14.4 1.0
CA A:ILE188 4.3 12.2 1.0
CA A:GLU187 4.3 13.9 1.0
CG A:GLU190 4.3 13.1 1.0
OD1 A:ASP138 4.4 14.9 1.0
O A:HOH1419 4.4 27.2 1.0
CG A:GLU177 4.4 12.3 1.0
N A:GLY189 4.5 12.0 1.0
O A:HOH1358 4.6 17.5 1.0
CB A:GLU187 4.6 16.8 1.0
C A:ASP185 4.7 14.0 1.0
C A:ILE188 4.8 12.1 1.0
CB A:ASP185 4.8 13.9 1.0
N A:ASP185 4.9 14.9 1.0
O A:HOH1345 4.9 17.1 1.0
N A:GLU190 5.0 12.5 1.0
CB A:GLU177 5.0 11.8 1.0

Calcium binding site 2 out of 4 in 1kkk

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Calcium binding site 2 out of 4 in the Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)


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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.3
occ:1.00
 O A:ASN183 2.3 17.9 1.0
OE2 A:GLU190 2.4 13.3 1.0
OD2 A:ASP185 2.4 14.9 1.0
OE2 A:GLU177 2.4 13.1 1.0
O A:HOH1334 2.4 16.5 1.0
O A:HOH1345 2.4 17.1 1.0
CG A:ASP185 3.2 14.9 1.0
CD A:GLU177 3.3 13.8 1.0
CD A:GLU190 3.3 12.3 1.0
C A:ASN183 3.5 19.3 1.0
OD1 A:ASP185 3.6 13.6 1.0
O A:LYS182 3.8 25.9 1.0
CG A:GLU190 3.8 13.1 1.0
OE1 A:GLU177 3.8 11.3 1.0
CA A:CA401 3.8 11.4 1.0
O A:HOH1480 4.2 35.0 1.0
OD2 A:ASP191 4.2 19.0 1.0
CB A:ASN183 4.2 24.2 1.0
N A:ASP185 4.2 14.9 1.0
CA A:PRO184 4.2 17.4 1.0
CG A:GLU177 4.2 12.3 1.0
OE1 A:GLU190 4.3 12.7 1.0
N A:PRO184 4.3 18.4 1.0
C A:PRO184 4.3 17.3 1.0
OD1 A:ASP191 4.3 17.0 1.0
CB A:ASP185 4.4 13.9 1.0
CA A:ASN183 4.5 21.9 1.0
CG A:ASP191 4.6 16.3 1.0
O A:HOH1419 4.6 27.2 1.0
C A:LYS182 4.8 25.1 1.0
CA A:ASP185 4.9 14.5 1.0
O A:PRO184 5.0 17.6 1.0

Calcium binding site 3 out of 4 in 1kkk

Go back to Calcium Binding Sites List in 1kkk
Calcium binding site 3 out of 4 in the Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)


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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.6
occ:1.00
 O A:GLN61 2.3 13.5 1.0
O A:HOH1331 2.3 18.4 1.0
O A:HOH1329 2.4 14.9 1.0
OD1 A:ASP57 2.4 13.8 1.0
OD1 A:ASP59 2.4 15.1 1.0
O A:HOH1336 2.5 19.2 1.0
OD2 A:ASP57 2.5 14.5 1.0
CG A:ASP57 2.8 13.5 1.0
CG A:ASP59 3.4 16.9 1.0
C A:GLN61 3.5 12.7 1.0
OD2 A:ASP59 3.8 18.5 1.0
N A:GLN61 4.0 12.8 1.0
O A:HOH1370 4.1 27.5 1.0
CA A:GLN61 4.2 14.2 1.0
N A:ASP59 4.3 15.4 1.0
CB A:ASP57 4.3 11.8 1.0
CB A:GLN61 4.4 17.8 1.0
N A:PHE62 4.5 12.3 1.0
O A:HOH1318 4.6 13.9 1.0
O A:HOH1340 4.6 19.8 1.0
OD2 A:ASP67 4.6 13.2 1.0
CB A:ASP59 4.7 15.7 1.0
N A:ASN60 4.7 14.2 1.0
CA A:PHE62 4.7 12.1 1.0
N A:ALA58 4.8 13.1 1.0
O A:HOH1435 4.8 31.6 1.0
CA A:ASP59 4.8 14.8 1.0
C A:ASP59 4.9 14.6 1.0

Calcium binding site 4 out of 4 in 1kkk

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Calcium binding site 4 out of 4 in the Thermolysin Complexed with Z-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid)


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-L-Aspartic Acid (Benzyloxycarbonyl-L- Aspartic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:16.9
occ:1.00
 O A:ILE197 2.2 28.8 1.0
O A:THR194 2.3 21.0 1.0
O A:TYR193 2.3 16.5 1.0
OD1 A:ASP200 2.3 19.0 1.0
O A:HOH1324 2.4 19.0 1.0
OG1 A:THR194 2.4 19.9 1.0
O A:HOH1366 2.6 28.0 1.0
C A:THR194 3.2 20.8 1.0
C A:TYR193 3.4 16.4 1.0
C A:ILE197 3.4 30.5 1.0
CG A:ASP200 3.4 19.1 1.0
CB A:THR194 3.5 18.3 1.0
CA A:THR194 3.7 18.6 1.0
OD2 A:ASP200 3.7 21.2 1.0
N A:THR194 3.9 17.1 1.0
CA A:ILE197 4.2 29.9 1.0
CB A:ILE197 4.2 30.4 1.0
N A:PRO195 4.2 22.3 1.0
N A:ILE197 4.2 30.2 1.0
N A:SER198 4.4 30.6 0.5
N A:SER198 4.4 30.6 0.5
O A:ASP200 4.5 18.5 1.0
CA A:SER198 4.5 31.1 0.5
CA A:SER198 4.5 31.0 0.5
O A:HOH1381 4.5 33.2 1.0
CA A:TYR193 4.6 15.8 1.0
O A:GLU190 4.6 15.6 1.0
CA A:PRO195 4.6 24.5 1.0
N A:ASP200 4.7 21.5 1.0
CB A:ASP200 4.7 19.6 1.0
CB A:TYR193 4.7 16.1 1.0
CD2 A:TYR193 4.7 19.5 1.0
CG2 A:THR194 4.8 19.9 1.0
C A:ASP200 4.8 17.5 1.0
CG2 A:ILE197 4.9 30.0 1.0
C A:PRO195 5.0 26.2 1.0
C A:SER198 5.0 30.2 0.5
CA A:ASP200 5.0 18.9 1.0
C A:SER198 5.0 30.1 0.5

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 11:24:27 2024

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