Atomistry » Calcium » PDB 3dcq-3dsw » 3dnz
Atomistry »
  Calcium »
    PDB 3dcq-3dsw »
      3dnz »

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 Jul 13 09:04:15 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy