Atomistry » Calcium » PDB 1k9u-1kre » 1kr6
Atomistry »
  Calcium »
    PDB 1k9u-1kre »
      1kr6 »

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

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy