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Calcium in PDB 3do1: Thermolysin By Classical Hanging Drop Method Before High X- Ray Dose on Esrf ID14-2 Beamline

Enzymatic activity of Thermolysin By Classical Hanging Drop Method Before High X- Ray Dose on Esrf ID14-2 Beamline

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

Protein crystallography data

The structure of Thermolysin By Classical Hanging Drop Method Before High X- Ray Dose on Esrf ID14-2 Beamline, PDB code: 3do1 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 / 1.33
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.526, 92.526, 128.553, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 27.7

Other elements in 3do1:

The structure of Thermolysin By Classical Hanging Drop 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 Classical Hanging Drop Method Before High X- Ray Dose on Esrf ID14-2 Beamline (pdb code 3do1). 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 Classical Hanging Drop Method Before High X- Ray Dose on Esrf ID14-2 Beamline, PDB code: 3do1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3do1

Go back to Calcium Binding Sites List in 3do1
Calcium binding site 1 out of 4 in the Thermolysin By Classical Hanging Drop 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 Classical Hanging Drop 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:17.2
occ:1.00
 O A:GLU187 2.4 19.6 1.0
OD2 A:ASP138 2.4 16.6 1.0
O A:HOH1005 2.4 15.9 1.0
OE1 A:GLU177 2.5 17.7 1.0
OD1 A:ASP185 2.5 14.7 1.0
OE2 A:GLU190 2.5 20.5 1.0
OE1 A:GLU190 2.6 16.9 1.0
OE2 A:GLU177 2.9 16.1 1.0
CD A:GLU190 2.9 19.7 1.0
CD A:GLU177 3.0 17.0 1.0
CG A:ASP138 3.4 16.4 1.0
C A:GLU187 3.5 20.0 1.0
CG A:ASP185 3.5 19.1 1.0
CA A:CA402 3.8 19.7 1.0
OD2 A:ASP185 3.8 18.1 1.0
CB A:ASP138 4.0 15.7 1.0
O A:ASP185 4.1 19.1 1.0
N A:GLU187 4.2 20.3 1.0
OD1 A:ASP138 4.3 20.4 1.0
N A:ILE188 4.3 19.6 1.0
CA A:GLU187 4.3 20.7 1.0
CA A:ILE188 4.4 19.3 1.0
CG A:GLU190 4.4 18.7 1.0
O A:HOH1143 4.4 34.5 1.0
CG A:GLU177 4.4 17.6 1.0
N A:GLY189 4.5 18.8 1.0
O A:HOH1043 4.6 22.8 1.0
C A:ASP185 4.6 19.8 1.0
CB A:GLU187 4.6 21.5 1.0
N A:ASP185 4.8 20.2 1.0
CB A:ASP185 4.8 18.9 1.0
C A:ILE188 4.8 19.0 1.0
CB A:GLU177 4.9 19.0 1.0
O A:HOH1030 4.9 19.7 1.0
OG1 A:THR174 5.0 15.8 1.0
CA A:ASP185 5.0 19.8 1.0

Calcium binding site 2 out of 4 in 3do1

Go back to Calcium Binding Sites List in 3do1
Calcium binding site 2 out of 4 in the Thermolysin By Classical Hanging Drop 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 Classical Hanging Drop 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:19.7
occ:1.00
 OE2 A:GLU190 2.3 20.5 1.0
OE2 A:GLU177 2.3 16.1 1.0
O A:HOH1030 2.4 19.7 1.0
O A:ASN183 2.4 24.1 1.0
OD2 A:ASP185 2.4 18.1 1.0
O A:HOH1019 2.5 20.7 1.0
CD A:GLU177 3.2 17.0 1.0
CG A:ASP185 3.2 19.1 1.0
CD A:GLU190 3.3 19.7 1.0
C A:ASN183 3.6 24.6 1.0
OD1 A:ASP185 3.6 14.7 1.0
OE1 A:GLU177 3.7 17.7 1.0
CA A:CA401 3.8 17.2 1.0
CG A:GLU190 3.8 18.7 1.0
O A:LYS182 4.1 28.6 1.0
CA A:PRO184 4.1 22.1 1.0
N A:ASP185 4.2 20.2 1.0
OD1 A:ASP191 4.2 20.7 1.0
CG A:GLU177 4.2 17.6 1.0
OD2 A:ASP191 4.2 18.7 1.0
C A:PRO184 4.3 21.5 1.0
OE1 A:GLU190 4.3 16.9 1.0
CB A:ASN183 4.3 26.5 1.0
N A:PRO184 4.3 23.3 1.0
CB A:ASP185 4.4 18.9 1.0
CG A:ASP191 4.6 19.7 1.0
CA A:ASN183 4.6 25.8 1.0
O A:HOH1143 4.6 34.5 1.0
O A:PRO184 4.9 20.6 1.0
CA A:ASP185 4.9 19.8 1.0

Calcium binding site 3 out of 4 in 3do1

Go back to Calcium Binding Sites List in 3do1
Calcium binding site 3 out of 4 in the Thermolysin By Classical Hanging Drop 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 Classical Hanging Drop 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:17.6
occ:1.00
 O A:HOH1021 2.3 18.6 1.0
O A:GLN61 2.4 18.1 1.0
O A:HOH1016 2.4 20.7 1.0
OD1 A:ASP57 2.4 18.3 1.0
OD1 A:ASP59 2.4 17.9 1.0
O A:HOH1014 2.4 15.3 1.0
OD2 A:ASP57 2.6 16.4 1.0
CG A:ASP57 2.8 18.2 1.0
CG A:ASP59 3.4 17.2 1.0
C A:GLN61 3.5 17.6 1.0
OD2 A:ASP59 3.9 16.2 1.0
O A:HOH1055 3.9 20.9 1.0
N A:GLN61 4.0 16.1 1.0
CA A:GLN61 4.2 18.2 1.0
N A:ASP59 4.3 15.6 1.0
CB A:ASP57 4.3 16.8 1.0
CB A:GLN61 4.4 18.4 1.0
O A:HOH1025 4.5 20.3 1.0
O A:HOH1003 4.5 16.8 1.0
N A:PHE62 4.6 17.1 1.0
OD2 A:ASP67 4.6 16.4 1.0
CB A:ASP59 4.6 15.5 1.0
N A:ALA58 4.7 15.8 1.0
N A:ASN60 4.7 15.2 1.0
CA A:PHE62 4.7 17.0 1.0
CA A:ASP59 4.8 15.7 1.0
O A:HOH1133 4.8 26.8 1.0
C A:ASP59 4.9 15.9 1.0
O A:HOH1154 5.0 23.9 1.0

Calcium binding site 4 out of 4 in 3do1

Go back to Calcium Binding Sites List in 3do1
Calcium binding site 4 out of 4 in the Thermolysin By Classical Hanging Drop 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 Classical Hanging Drop 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:22.1
occ:1.00
 O A:ILE197 2.3 28.0 1.0
O A:TYR193 2.3 20.3 1.0
O A:HOH1009 2.4 23.9 1.0
OD1 A:ASP200 2.4 22.2 1.0
O A:THR194 2.4 22.6 1.0
OG1 A:THR194 2.4 21.1 1.0
O A:HOH1051 2.5 25.3 1.0
C A:THR194 3.2 22.7 1.0
C A:TYR193 3.3 20.7 1.0
CG A:ASP200 3.5 22.4 1.0
CB A:THR194 3.5 21.8 1.0
C A:ILE197 3.5 29.0 1.0
CA A:THR194 3.7 21.7 1.0
OD2 A:ASP200 3.9 22.7 1.0
N A:THR194 3.9 21.1 1.0
O A:HOH1067 4.2 30.5 1.0
CA A:ILE197 4.3 28.8 1.0
CB A:ILE197 4.3 28.7 1.0
O A:ASP200 4.3 23.7 1.0
N A:ILE197 4.3 29.2 1.0
N A:PRO195 4.3 24.0 1.0
N A:SER198 4.5 29.1 1.0
CA A:TYR193 4.5 20.8 1.0
O A:GLU190 4.5 19.3 1.0
CA A:SER198 4.7 29.5 1.0
N A:ASP200 4.7 25.9 1.0
CB A:TYR193 4.7 21.5 1.0
C A:ASP200 4.8 24.1 1.0
CG2 A:THR194 4.8 20.9 1.0
CB A:ASP200 4.8 23.6 1.0
CD2 A:TYR193 4.8 22.5 1.0
CA A:PRO195 4.8 25.1 1.0
C A:SER198 5.0 29.0 1.0
CA A:ASP200 5.0 24.4 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 Jul 13 09:04:59 2024

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