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Calcium in PDB 3zi6: Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer

Enzymatic activity of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer

All present enzymatic activity of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer, PDB code: 3zi6 was solved by M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.754, 92.754, 129.224, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 20.4

Other elements in 3zi6:

The structure of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer (pdb code 3zi6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer, PDB code: 3zi6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3zi6

Go back to Calcium Binding Sites List in 3zi6
Calcium binding site 1 out of 4 in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1320

b:14.3
occ:1.00
 O A:HOH2146 2.2 21.0 1.0
OG1 A:THR194 2.3 17.5 1.0
O A:TYR193 2.3 11.4 1.0
O A:THR194 2.3 15.9 1.0
OD1 A:ASP200 2.4 12.1 1.0
O A:ILE197 2.5 23.1 1.0
O A:HOH2142 2.5 15.8 1.0
C A:THR194 3.1 17.1 1.0
C A:TYR193 3.3 13.4 1.0
CB A:THR194 3.4 16.8 1.0
CG A:ASP200 3.4 12.6 1.0
CA A:THR194 3.6 16.2 1.0
C A:ILE197 3.6 28.8 1.0
OD2 A:ASP200 3.7 11.7 1.0
N A:THR194 3.8 13.8 1.0
N A:PRO195 4.2 18.1 1.0
CA A:ILE197 4.3 28.3 1.0
CB A:ILE197 4.3 28.9 1.0
N A:ILE197 4.3 30.4 1.0
O A:ASP200 4.5 14.0 1.0
CA A:TYR193 4.5 13.8 1.0
CA A:PRO195 4.6 21.0 1.0
CG2 A:THR194 4.6 17.9 1.0
CB A:TYR193 4.7 14.8 1.0
O A:GLU190 4.7 12.7 1.0
N A:SER198 4.7 26.1 1.0
O A:HOH2143 4.7 24.6 1.0
CD2 A:TYR193 4.7 17.2 1.0
CG2 A:ILE197 4.7 29.2 1.0
N A:ASP200 4.7 19.1 1.0
CB A:ASP200 4.8 13.4 1.0
C A:PRO195 4.9 25.3 1.0
C A:ASP200 4.9 15.2 1.0
N A:TYR193 4.9 13.1 1.0
CA A:SER198 4.9 28.7 1.0

Calcium binding site 2 out of 4 in 3zi6

Go back to Calcium Binding Sites List in 3zi6
Calcium binding site 2 out of 4 in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1321

b:10.7
occ:1.00
 O A:HOH2119 2.4 9.7 1.0
OD2 A:ASP138 2.4 9.7 1.0
O A:GLU187 2.4 10.4 1.0
OE2 A:GLU190 2.4 12.2 1.0
OE1 A:GLU177 2.4 10.6 1.0
OD1 A:ASP185 2.5 11.6 1.0
OE1 A:GLU190 2.6 9.9 1.0
OE2 A:GLU177 2.7 12.5 1.0
CD A:GLU190 2.8 11.8 1.0
CD A:GLU177 2.9 12.3 1.0
CG A:ASP138 3.3 9.6 1.0
CG A:ASP185 3.4 13.1 1.0
C A:GLU187 3.5 12.1 1.0
OD2 A:ASP185 3.7 14.5 1.0
CA A:CA1323 3.9 30.5 1.0
CB A:ASP138 3.9 8.7 1.0
O A:ASP185 4.1 11.1 1.0
OD1 A:ASP138 4.2 9.6 1.0
N A:GLU187 4.3 13.4 1.0
N A:ILE188 4.3 11.0 1.0
CG A:GLU190 4.3 12.1 1.0
CA A:ILE188 4.3 10.5 1.0
O A:HOH2118 4.3 13.0 1.0
CA A:GLU187 4.4 14.0 1.0
CG A:GLU177 4.4 11.3 1.0
N A:GLY189 4.4 10.8 1.0
C A:ASP185 4.6 13.7 1.0
N A:ASP185 4.6 13.2 1.0
CB A:GLU187 4.6 16.1 1.0
CB A:ASP185 4.8 13.3 1.0
C A:ILE188 4.8 11.2 1.0
CB A:GLU177 4.9 11.2 1.0
CA A:ASP185 4.9 13.1 1.0
N A:GLU190 5.0 11.4 1.0

Calcium binding site 3 out of 4 in 3zi6

Go back to Calcium Binding Sites List in 3zi6
Calcium binding site 3 out of 4 in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1322

b:10.8
occ:1.00
 O A:GLN61 2.2 9.2 1.0
OD1 A:ASP59 2.3 10.7 1.0
OD2 A:ASP57 2.4 9.5 1.0
O A:HOH2066 2.4 12.4 1.0
O A:HOH2067 2.4 12.3 1.0
O A:HOH2069 2.5 13.6 1.0
OD1 A:ASP57 2.6 9.0 1.0
CG A:ASP57 2.8 9.2 1.0
CG A:ASP59 3.4 11.4 1.0
C A:GLN61 3.4 10.5 1.0
OD2 A:ASP59 3.8 10.1 1.0
O A:HOH2070 3.9 11.0 1.0
N A:GLN61 3.9 11.8 1.0
CA A:GLN61 4.1 13.5 1.0
CB A:ASP57 4.3 8.7 1.0
CB A:GLN61 4.3 16.6 1.0
N A:ASP59 4.4 10.2 1.0
N A:PHE62 4.4 10.0 1.0
O A:HOH2063 4.5 7.8 1.0
O A:HOH2068 4.5 8.8 1.0
OD2 A:ASP67 4.6 9.4 1.0
CB A:ASP59 4.6 10.9 1.0
N A:ASN60 4.6 9.6 1.0
O A:HOH2029 4.7 17.2 1.0
CA A:PHE62 4.7 10.7 1.0
N A:ALA58 4.8 9.3 1.0
CA A:ASP59 4.8 10.5 1.0
C A:ASP59 4.9 10.6 1.0

Calcium binding site 4 out of 4 in 3zi6

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Calcium binding site 4 out of 4 in the Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1323

b:30.5
occ:1.00
 OE2 A:GLU190 2.4 12.2 1.0
O A:ASN183 2.6 16.1 1.0
OD2 A:ASP185 2.7 14.5 1.0
OE2 A:GLU177 2.7 12.5 1.0
CD A:GLU177 3.3 12.3 1.0
CD A:GLU190 3.4 11.8 1.0
CG A:ASP185 3.5 13.1 1.0
C A:ASN183 3.6 18.5 1.0
CG A:GLU190 3.7 12.1 1.0
OE1 A:GLU177 3.8 10.6 1.0
CA A:CA1321 3.9 10.7 1.0
OD1 A:ASP185 3.9 11.6 1.0
CA A:PRO184 4.0 15.0 1.0
OD2 A:ASP191 4.1 10.8 1.0
N A:ASP185 4.1 13.2 1.0
OD1 A:ASP191 4.2 12.5 1.0
C A:PRO184 4.2 15.0 1.0
N A:PRO184 4.3 15.7 1.0
CG A:GLU177 4.3 11.3 1.0
CB A:ASN183 4.3 26.3 1.0
CG A:ASP191 4.4 11.8 1.0
OE1 A:GLU190 4.5 9.9 1.0
CB A:ASP185 4.5 13.3 1.0
CA A:ASN183 4.6 24.0 1.0
O A:HOH2145 4.8 26.9 1.0
CA A:ASP185 5.0 13.1 1.0

Reference:

J.L.Ferrer, N.A.Larive, M.W.Bowler, D.Nurizzo. Recent Progress in Robot-Based Systems For Crystallography and Their Contribution to Drug Discovery. Expert Opin.Drug Discov. V. 8 835 2013.
ISSN: ISSN 1746-0441
PubMed: 23656378
DOI: 10.1517/17460441.2013.793666
Page generated: Sat Jul 13 21:40:41 2024

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