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Calcium in PDB 3dnz: Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline

Enzymatic activity of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline

All present enzymatic activity of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3dnz was solved by E.Pechkova, S.K.Tripathi, C.Nicolini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.04 / 1.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.535, 92.535, 128.628, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 26.7

Other elements in 3dnz:

The structure of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline (pdb code 3dnz). 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 By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3dnz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3dnz

Go back to Calcium Binding Sites List in 3dnz
Calcium binding site 1 out of 4 in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.8
occ:1.00
 OD2 A:ASP138 2.4 10.8 1.0
OE1 A:GLU177 2.4 9.3 1.0
O A:GLU187 2.4 12.9 1.0
OD1 A:ASP185 2.4 12.4 1.0
O A:HOH1005 2.4 11.1 1.0
OE1 A:GLU190 2.5 10.5 1.0
OE2 A:GLU190 2.6 15.4 1.0
OE2 A:GLU177 2.8 12.5 1.0
CD A:GLU177 2.9 12.9 1.0
CD A:GLU190 2.9 14.7 1.0
CG A:ASP138 3.4 13.4 1.0
C A:GLU187 3.4 13.7 1.0
CG A:ASP185 3.5 14.2 1.0
CA A:CA402 3.8 15.2 1.0
OD2 A:ASP185 3.8 15.3 1.0
CB A:ASP138 4.0 11.0 1.0
O A:HOH1143 4.1 26.1 1.0
O A:ASP185 4.1 13.5 1.0
N A:GLU187 4.2 14.3 1.0
N A:ILE188 4.3 12.9 1.0
OD1 A:ASP138 4.3 12.4 1.0
CA A:ILE188 4.3 13.3 1.0
CA A:GLU187 4.3 14.0 1.0
O A:HOH1043 4.4 17.9 1.0
CG A:GLU177 4.4 12.8 1.0
CG A:GLU190 4.4 13.5 1.0
N A:GLY189 4.4 12.6 1.0
C A:ASP185 4.6 14.6 1.0
CB A:GLU187 4.6 15.1 1.0
CB A:ASP185 4.7 13.7 1.0
N A:ASP185 4.8 14.5 1.0
C A:ILE188 4.8 12.6 1.0
O A:HOH1030 4.8 18.0 1.0
CB A:GLU177 4.9 12.7 1.0
CA A:ASP185 5.0 14.0 1.0

Calcium binding site 2 out of 4 in 3dnz

Go back to Calcium Binding Sites List in 3dnz
Calcium binding site 2 out of 4 in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.2
occ:1.00
 O A:ASN183 2.3 17.4 1.0
OE2 A:GLU190 2.3 15.4 1.0
OD2 A:ASP185 2.4 15.3 1.0
O A:HOH1030 2.4 18.0 1.0
OE2 A:GLU177 2.4 12.5 1.0
O A:HOH1019 2.5 19.2 1.0
CG A:ASP185 3.2 14.2 1.0
CD A:GLU177 3.2 12.9 1.0
CD A:GLU190 3.3 14.7 1.0
C A:ASN183 3.5 17.3 1.0
OD1 A:ASP185 3.6 12.4 1.0
OE1 A:GLU177 3.8 9.3 1.0
CA A:CA401 3.8 11.8 1.0
CG A:GLU190 3.8 13.5 1.0
CA A:PRO184 4.1 15.3 1.0
N A:ASP185 4.2 14.5 1.0
OD2 A:ASP191 4.2 14.6 1.0
C A:PRO184 4.2 15.5 1.0
OD1 A:ASP191 4.2 14.5 1.0
CG A:GLU177 4.2 12.8 1.0
OE1 A:GLU190 4.2 10.5 1.0
CB A:ASN183 4.3 19.4 1.0
N A:PRO184 4.3 16.1 1.0
O A:HOH1143 4.3 26.1 1.0
O A:LYS182 4.3 21.8 1.0
CB A:ASP185 4.3 13.7 1.0
CG A:ASP191 4.5 14.1 1.0
CA A:ASN183 4.5 18.9 1.0
O A:PRO184 4.8 16.0 1.0
CA A:ASP185 4.9 14.0 1.0

Calcium binding site 3 out of 4 in 3dnz

Go back to Calcium Binding Sites List in 3dnz
Calcium binding site 3 out of 4 in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.2
occ:1.00
 O A:HOH1021 2.3 15.6 1.0
O A:HOH1016 2.3 11.7 1.0
O A:GLN61 2.3 11.1 1.0
O A:HOH1014 2.4 11.1 1.0
OD1 A:ASP57 2.4 14.6 1.0
OD1 A:ASP59 2.4 12.8 1.0
OD2 A:ASP57 2.6 12.0 1.0
CG A:ASP57 2.8 14.4 1.0
CG A:ASP59 3.4 14.4 1.0
C A:GLN61 3.5 12.1 1.0
OD2 A:ASP59 3.8 13.0 1.0
N A:GLN61 4.0 11.9 1.0
O A:HOH1055 4.0 16.2 1.0
CA A:GLN61 4.2 12.5 1.0
N A:ASP59 4.3 12.5 1.0
CB A:ASP57 4.3 11.8 1.0
CB A:GLN61 4.4 13.3 1.0
O A:HOH1025 4.4 14.3 1.0
O A:HOH1133 4.5 19.7 1.0
N A:PHE62 4.6 11.6 1.0
OD2 A:ASP67 4.6 12.4 1.0
O A:HOH1003 4.6 12.2 1.0
CB A:ASP59 4.7 12.5 1.0
N A:ALA58 4.7 12.1 1.0
N A:ASN60 4.7 11.2 1.0
CA A:PHE62 4.8 12.1 1.0
CA A:ASP59 4.8 12.3 1.0
O A:HOH1154 4.9 22.0 1.0
C A:ASP59 4.9 12.5 1.0

Calcium binding site 4 out of 4 in 3dnz

Go back to Calcium Binding Sites List in 3dnz
Calcium binding site 4 out of 4 in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:15.3
occ:1.00
 O A:ILE197 2.3 20.9 1.0
O A:TYR193 2.4 15.0 1.0
O A:HOH1009 2.4 14.7 1.0
OD1 A:ASP200 2.4 14.2 1.0
O A:THR194 2.4 16.2 1.0
OG1 A:THR194 2.5 15.6 1.0
O A:HOH1051 2.5 22.0 1.0
C A:THR194 3.3 17.0 1.0
C A:TYR193 3.4 15.8 1.0
CB A:THR194 3.4 16.9 1.0
CG A:ASP200 3.4 17.1 1.0
C A:ILE197 3.5 22.3 1.0
CA A:THR194 3.6 16.3 1.0
OD2 A:ASP200 3.8 17.9 1.0
N A:THR194 3.9 15.5 1.0
CA A:ILE197 4.2 21.8 1.0
CB A:ILE197 4.2 22.2 1.0
N A:ILE197 4.3 22.5 1.0
N A:PRO195 4.4 18.2 1.0
O A:ASP200 4.4 16.7 1.0
O A:HOH1067 4.5 31.6 1.0
CA A:TYR193 4.5 15.4 1.0
N A:SER198 4.6 22.3 1.0
O A:GLU190 4.6 14.3 1.0
N A:ASP200 4.7 19.0 1.0
CB A:TYR193 4.7 16.1 1.0
CA A:SER198 4.8 22.7 1.0
CA A:PRO195 4.8 19.2 1.0
CB A:ASP200 4.8 17.1 1.0
CD2 A:TYR193 4.8 18.0 1.0
CG2 A:THR194 4.8 16.7 1.0
C A:ASP200 4.8 17.2 1.0
CG2 A:ILE197 4.8 22.6 1.0
CA A:ASP200 5.0 17.7 1.0

Reference:

E.Pechkova, S.K.Tripathi, C.Nicolini. Radiation Damage in Protein Structural Characterization By Synchrotron Radiation: State of the Art and Nanotechnology-Based Perspective To Be Published.
Page generated: Sat Dec 12 04:09:00 2020

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