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Calcium in PDB 1kr6: Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)

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

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

Protein crystallography data

The structure of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid), PDB code: 1kr6 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) 25.00 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.772, 93.772, 131.359, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.1

Other elements in 1kr6:

The structure of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic 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-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) (pdb code 1kr6). 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-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid), PDB code: 1kr6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1kr6

Go back to Calcium Binding Sites List in 1kr6
Calcium binding site 1 out of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic 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-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:10.8
occ:1.00
 O A:GLU187 2.4 10.7 1.0
O A:HOH1320 2.4 11.5 1.0
OD2 A:ASP138 2.4 12.5 1.0
OE1 A:GLU177 2.4 11.4 1.0
OE1 A:GLU190 2.5 11.7 1.0
OD1 A:ASP185 2.5 12.1 1.0
OE2 A:GLU190 2.6 11.5 1.0
OE2 A:GLU177 2.8 12.0 1.0
CD A:GLU190 2.8 10.8 1.0
CD A:GLU177 2.9 13.1 1.0
C A:GLU187 3.4 11.6 1.0
CG A:ASP138 3.5 11.9 1.0
CG A:ASP185 3.6 14.3 1.0
CA A:CA402 3.8 12.7 1.0
OD2 A:ASP185 3.9 14.2 1.0
CB A:ASP138 4.0 10.4 1.0
N A:GLU187 4.2 14.4 1.0
O A:ASP185 4.2 13.3 1.0
N A:ILE188 4.3 11.7 1.0
CA A:GLU187 4.3 13.9 1.0
CA A:ILE188 4.3 11.8 1.0
CG A:GLU190 4.3 12.0 1.0
OD1 A:ASP138 4.4 12.6 1.0
CG A:GLU177 4.4 11.1 1.0
O A:HOH1416 4.4 29.1 1.0
N A:GLY189 4.5 12.3 1.0
O A:HOH1358 4.6 16.5 1.0
CB A:GLU187 4.6 16.2 1.0
C A:ASP185 4.7 13.8 1.0
C A:ILE188 4.8 11.8 1.0
CB A:ASP185 4.8 14.1 1.0
N A:ASP185 4.9 14.4 1.0
O A:HOH1345 4.9 16.1 1.0
N A:GLU190 4.9 11.6 1.0
CB A:GLU177 4.9 11.2 1.0

Calcium binding site 2 out of 4 in 1kr6

Go back to Calcium Binding Sites List in 1kr6
Calcium binding site 2 out of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic 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-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:12.7
occ:1.00
 OE2 A:GLU190 2.3 11.5 1.0
OD2 A:ASP185 2.3 14.2 1.0
O A:ASN183 2.4 15.6 1.0
O A:HOH1334 2.4 16.0 1.0
OE2 A:GLU177 2.4 12.0 1.0
O A:HOH1345 2.4 16.1 1.0
CG A:ASP185 3.2 14.3 1.0
CD A:GLU190 3.2 10.8 1.0
CD A:GLU177 3.3 13.1 1.0
C A:ASN183 3.5 18.4 1.0
OD1 A:ASP185 3.6 12.1 1.0
CG A:GLU190 3.8 12.0 1.0
CA A:CA401 3.8 10.8 1.0
OE1 A:GLU177 3.8 11.4 1.0
O A:LYS182 3.9 24.6 1.0
OD2 A:ASP191 4.2 16.4 1.0
N A:ASP185 4.2 14.4 1.0
OE1 A:GLU190 4.2 11.7 1.0
CA A:PRO184 4.2 16.9 1.0
CG A:GLU177 4.3 11.1 1.0
CB A:ASN183 4.3 22.8 1.0
N A:PRO184 4.3 18.2 1.0
C A:PRO184 4.3 17.4 1.0
OD1 A:ASP191 4.3 16.4 1.0
CB A:ASP185 4.4 14.1 1.0
CA A:ASN183 4.5 20.5 1.0
CG A:ASP191 4.6 16.5 1.0
O A:HOH1416 4.7 29.1 1.0
CA A:ASP185 4.9 13.9 1.0
C A:LYS182 4.9 23.9 1.0
O A:PRO184 5.0 16.3 1.0

Calcium binding site 3 out of 4 in 1kr6

Go back to Calcium Binding Sites List in 1kr6
Calcium binding site 3 out of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic 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-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:11.5
occ:1.00
 O A:GLN61 2.3 11.9 1.0
O A:HOH1331 2.3 13.7 1.0
OD1 A:ASP57 2.4 12.2 1.0
OD1 A:ASP59 2.4 14.1 1.0
O A:HOH1329 2.5 12.6 1.0
OD2 A:ASP57 2.5 14.0 1.0
O A:HOH1336 2.5 17.1 1.0
CG A:ASP57 2.8 12.9 1.0
CG A:ASP59 3.4 16.7 1.0
C A:GLN61 3.5 11.7 1.0
OD2 A:ASP59 3.8 16.6 1.0
N A:GLN61 4.0 11.6 1.0
O A:HOH1370 4.1 22.9 1.0
CA A:GLN61 4.2 12.9 1.0
CB A:ASP57 4.3 11.1 1.0
N A:ASP59 4.3 13.7 1.0
CB A:GLN61 4.4 15.8 1.0
N A:PHE62 4.5 11.4 1.0
O A:HOH1318 4.6 11.2 1.0
O A:HOH1340 4.6 16.2 1.0
OD2 A:ASP67 4.7 11.1 1.0
CB A:ASP59 4.7 14.9 1.0
CA A:PHE62 4.7 10.6 1.0
N A:ASN60 4.7 13.0 1.0
O A:HOH1418 4.7 35.8 1.0
N A:ALA58 4.7 11.6 1.0
CA A:ASP59 4.8 13.6 1.0
C A:ASP59 4.9 14.4 1.0

Calcium binding site 4 out of 4 in 1kr6

Go back to Calcium Binding Sites List in 1kr6
Calcium binding site 4 out of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic 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-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:14.9
occ:1.00
 O A:ILE197 2.2 28.2 1.0
O A:TYR193 2.3 13.4 1.0
OD1 A:ASP200 2.4 16.1 1.0
OG1 A:THR194 2.4 17.5 1.0
O A:THR194 2.4 20.3 1.0
O A:HOH1324 2.4 17.0 1.0
O A:HOH1366 2.5 22.4 1.0
C A:THR194 3.2 19.6 1.0
C A:TYR193 3.3 15.7 1.0
C A:ILE197 3.4 29.8 1.0
CG A:ASP200 3.4 16.5 1.0
CB A:THR194 3.4 17.0 1.0
CA A:THR194 3.7 18.1 1.0
OD2 A:ASP200 3.7 18.5 1.0
N A:THR194 3.9 16.4 1.0
CA A:ILE197 4.1 29.2 1.0
CB A:ILE197 4.2 29.4 1.0
N A:ILE197 4.2 29.4 1.0
N A:PRO195 4.2 21.0 1.0
N A:SER198 4.4 29.8 1.0
O A:ASP200 4.4 17.9 1.0
CA A:SER198 4.5 30.6 1.0
CA A:TYR193 4.5 14.8 1.0
O A:GLU190 4.6 13.2 1.0
O A:HOH1382 4.6 30.9 1.0
N A:ASP200 4.6 20.9 1.0
CA A:PRO195 4.7 22.9 1.0
CB A:TYR193 4.7 15.6 1.0
CD2 A:TYR193 4.7 20.1 1.0
CG2 A:THR194 4.7 19.2 1.0
CB A:ASP200 4.7 17.6 1.0
C A:ASP200 4.8 17.0 1.0
CG2 A:ILE197 4.9 27.8 1.0
C A:PRO195 5.0 25.1 1.0
C A:SER198 5.0 29.3 1.0
CA A:ASP200 5.0 18.5 1.0

Reference:

M.Senda, T.Senda, S.Kidokoro. Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors. To Be Published.
Page generated: Sat Dec 12 03:04:02 2020

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