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Calcium in PDB 5fxn: Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer

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

All present enzymatic activity of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff 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 Esrf Robodiff Goniometer, PDB code: 5fxn was solved by M.W.Bowler, D.Nurizzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.63 / 1.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.100, 93.100, 130.302, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 18

Other elements in 5fxn:

The structure of Structure of Thermolysin Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff 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 Esrf Robodiff Goniometer (pdb code 5fxn). 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 Esrf Robodiff Goniometer, PDB code: 5fxn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5fxn

Go back to Calcium Binding Sites List in 5fxn
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 Esrf Robodiff 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 Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1320

b:22.6
occ:1.00
 O A:ILE197 2.2 27.1 1.0
O A:TYR193 2.4 20.3 1.0
OD1 A:ASP200 2.4 21.7 1.0
O A:THR194 2.4 23.4 1.0
O A:HOH2197 2.4 22.0 1.0
OG1 A:THR194 2.5 22.9 1.0
O A:HOH2199 2.5 25.1 1.0
C A:THR194 3.2 23.0 1.0
C A:TYR193 3.4 19.2 1.0
C A:ILE197 3.4 26.1 1.0
CG A:ASP200 3.4 22.2 1.0
CB A:THR194 3.5 21.3 1.0
CA A:THR194 3.6 21.7 1.0
OD2 A:ASP200 3.8 25.6 1.0
N A:THR194 3.9 19.3 1.0
CA A:ILE197 4.2 30.8 1.0
N A:ILE197 4.2 32.1 1.0
CB A:ILE197 4.2 32.6 1.0
N A:PRO195 4.3 23.9 1.0
N A:SER198 4.5 32.1 1.0
O A:ASP200 4.5 22.3 1.0
CA A:TYR193 4.6 18.4 1.0
O A:GLU190 4.6 20.4 1.0
O A:HOH2198 4.6 32.9 1.0
CA A:PRO195 4.6 25.3 1.0
CD2 A:TYR193 4.7 22.8 1.0
N A:ASP200 4.7 25.5 1.0
CB A:TYR193 4.7 20.9 1.0
CA A:SER198 4.7 33.0 1.0
CG2 A:THR194 4.8 22.2 1.0
CB A:ASP200 4.8 23.2 1.0
C A:ASP200 4.9 21.0 1.0
CG2 A:ILE197 4.9 31.5 1.0
C A:PRO195 5.0 26.7 1.0
CA A:ASP200 5.0 22.5 1.0
C A:SER198 5.0 31.9 1.0

Calcium binding site 2 out of 4 in 5fxn

Go back to Calcium Binding Sites List in 5fxn
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 Esrf Robodiff 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 Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1321

b:16.4
occ:1.00
 O A:GLU187 2.3 17.9 1.0
OD2 A:ASP138 2.4 16.8 1.0
OE2 A:GLU190 2.4 18.1 1.0
OD1 A:ASP185 2.5 18.3 1.0
O A:HOH2171 2.5 17.5 1.0
OE1 A:GLU177 2.5 17.3 1.0
OE1 A:GLU190 2.5 17.4 1.0
OE2 A:GLU177 2.7 19.2 1.0
CD A:GLU190 2.8 16.7 1.0
CD A:GLU177 2.9 16.4 1.0
C A:GLU187 3.4 16.3 1.0
CG A:ASP138 3.4 18.1 1.0
CG A:ASP185 3.4 18.1 1.0
OD2 A:ASP185 3.8 20.6 1.0
CA A:CA1323 3.8 21.4 1.0
CB A:ASP138 4.0 14.7 1.0
O A:ASP185 4.1 18.0 1.0
N A:GLU187 4.2 18.7 1.0
CA A:GLU187 4.2 19.1 1.0
N A:ILE188 4.3 17.0 1.0
CG A:GLU190 4.3 17.8 1.0
OD1 A:ASP138 4.3 19.6 1.0
CA A:ILE188 4.4 16.2 1.0
CG A:GLU177 4.4 14.9 1.0
O A:HOH2170 4.4 23.3 1.0
N A:GLY189 4.4 14.9 1.0
CB A:GLU187 4.5 20.6 1.0
C A:ASP185 4.6 17.4 1.0
N A:ASP185 4.7 17.5 1.0
CB A:ASP185 4.8 17.6 1.0
O A:HOH2189 4.8 23.1 1.0
C A:ILE188 4.8 15.9 1.0
CB A:GLU177 4.9 14.8 1.0

Calcium binding site 3 out of 4 in 5fxn

Go back to Calcium Binding Sites List in 5fxn
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 Esrf Robodiff 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 Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1322

b:16.9
occ:1.00
 O A:GLN61 2.2 15.4 1.0
OD2 A:ASP57 2.3 14.9 1.0
O A:HOH2093 2.3 19.2 1.0
O A:HOH2094 2.4 17.7 1.0
O A:HOH2096 2.4 19.3 1.0
OD1 A:ASP59 2.4 17.8 1.0
OD1 A:ASP57 2.6 15.6 1.0
CG A:ASP57 2.8 15.9 1.0
CG A:ASP59 3.4 16.3 1.0
C A:GLN61 3.4 14.6 1.0
OD2 A:ASP59 3.8 20.0 1.0
O A:HOH2097 3.9 24.5 1.0
N A:GLN61 4.0 15.0 1.0
CA A:GLN61 4.1 16.3 1.0
CB A:ASP57 4.3 16.1 1.0
CB A:GLN61 4.4 17.6 1.0
N A:ASP59 4.4 15.9 1.0
N A:PHE62 4.5 13.9 1.0
O A:HOH2095 4.5 19.7 1.0
O A:HOH2089 4.6 16.1 1.0
O A:HOH2043 4.6 24.6 1.0
OD2 A:ASP67 4.6 15.3 1.0
CB A:ASP59 4.6 16.8 1.0
N A:ASN60 4.7 15.9 1.0
O A:HOH2044 4.7 36.5 1.0
CA A:PHE62 4.7 15.9 1.0
N A:ALA58 4.8 15.9 1.0
CA A:ASP59 4.8 15.8 1.0
C A:ASP59 4.9 15.7 1.0

Calcium binding site 4 out of 4 in 5fxn

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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 Esrf Robodiff 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 Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1323

b:21.4
occ:1.00
 O A:HOH2189 2.3 23.1 1.0
O A:ASN183 2.3 20.9 1.0
O A:HOH2193 2.3 23.1 1.0
OE2 A:GLU190 2.3 18.1 1.0
OD2 A:ASP185 2.4 20.6 1.0
OE2 A:GLU177 2.5 19.2 1.0
CG A:ASP185 3.3 18.1 1.0
CD A:GLU177 3.3 16.4 1.0
CD A:GLU190 3.3 16.7 1.0
C A:ASN183 3.5 21.4 1.0
OD1 A:ASP185 3.7 18.3 1.0
OE1 A:GLU177 3.8 17.3 1.0
CG A:GLU190 3.8 17.8 1.0
CA A:CA1321 3.8 16.4 1.0
O A:HOH2192 4.1 35.7 1.0
CA A:PRO184 4.1 19.0 1.0
N A:ASP185 4.2 17.5 1.0
CB A:ASN183 4.2 24.3 1.0
OD2 A:ASP191 4.2 26.2 1.0
OD1 A:ASP191 4.2 23.0 1.0
C A:PRO184 4.2 17.9 1.0
N A:PRO184 4.3 20.1 1.0
CG A:GLU177 4.3 14.9 1.0
OE1 A:GLU190 4.3 17.4 1.0
CB A:ASP185 4.4 17.6 1.0
CA A:ASN183 4.5 23.9 1.0
CG A:ASP191 4.5 21.2 1.0
CA A:ASP185 5.0 18.2 1.0
O A:PRO184 5.0 21.7 1.0

Reference:

D.Nurizzo, M.W.Bowler, H.Caserotto, F.Dobias, T.Giraud, J.Surr, N.Guichard, G.Papp, M.Guijarro, C.Mueller-Dieckmann, D.Flot, S.Mcsweeney, F.Cipriani, P.Theveneau, G.A.Leonard. Robodiff: Combining A Sample Changer and Goniometer For Highly Automated Macromolecular Crystallography Experiments. Acta Crystallogr.,Sect.D V. 72 966 2016.
ISSN: ISSN 0907-4449
PubMed: 27487827
DOI: 10.1107/S205979831601158X
Page generated: Sun Jul 14 19:25:05 2024

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