Calcium in PDB 6fj2: Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B

Enzymatic activity of Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B

All present enzymatic activity of Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B, PDB code: 6fj2 was solved by A.A.Mccarthy, C.Mueller-Dieckmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.30 / 1.43
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.717, 92.717, 128.621, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 16.4

Other elements in 6fj2:

The structure of Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B 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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B (pdb code 6fj2). 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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B, PDB code: 6fj2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6fj2

Go back to Calcium Binding Sites List in 6fj2
Calcium binding site 1 out of 4 in the Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B


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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1402

b:16.1
occ:1.00
 O A:ILE197 2.3 20.9 1.0
O A:TYR193 2.3 15.2 1.0
O A:HOH1739 2.3 23.5 1.0
OD1 A:ASP200 2.3 16.7 1.0
O A:HOH1601 2.4 15.2 1.0
O A:THR194 2.4 18.5 1.0
OG1 A:THR194 2.4 18.5 1.0
C A:THR194 3.2 17.7 1.0
C A:TYR193 3.3 14.2 1.0
CG A:ASP200 3.4 16.9 1.0
CB A:THR194 3.4 18.6 1.0
C A:ILE197 3.5 23.7 1.0
CA A:THR194 3.6 17.2 1.0
OD2 A:ASP200 3.8 19.1 1.0
N A:THR194 3.9 15.7 1.0
CB A:ILE197 4.2 25.8 1.0
CA A:ILE197 4.2 25.0 1.0
N A:ILE197 4.2 27.4 1.0
N A:PRO195 4.3 19.7 1.0
O A:HOH1652 4.4 36.0 1.0
O A:ASP200 4.5 15.6 1.0
O A:HOH1679 4.5 39.7 1.0
N A:SER198 4.5 25.9 1.0
CA A:TYR193 4.5 13.6 1.0
N A:ASP200 4.6 17.7 1.0
O A:GLU190 4.6 12.7 1.0
CB A:TYR193 4.7 14.4 1.0
CA A:PRO195 4.7 21.3 1.0
CD2 A:TYR193 4.7 17.9 1.0
CB A:ASP200 4.7 16.7 1.0
O A:HOH1782 4.7 27.5 1.0
O A:HOH1762 4.7 36.9 1.0
CG2 A:THR194 4.8 19.2 1.0
CG2 A:ILE197 4.8 26.4 1.0
CA A:SER198 4.8 26.1 1.0
C A:ASP200 4.8 15.4 1.0
C A:SER198 5.0 24.4 1.0
N A:GLY199 5.0 21.6 1.0
CA A:ASP200 5.0 16.7 1.0
C A:PRO195 5.0 24.1 1.0

Calcium binding site 2 out of 4 in 6fj2

Go back to Calcium Binding Sites List in 6fj2
Calcium binding site 2 out of 4 in the Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B


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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1403

b:10.4
occ:1.00
 O A:GLU187 2.4 10.9 1.0
OD1 A:ASP185 2.4 11.3 1.0
OD2 A:ASP138 2.4 10.2 1.0
OE2 A:GLU190 2.4 13.1 1.0
O A:HOH1616 2.4 10.6 1.0
OE1 A:GLU177 2.4 11.1 1.0
OE2 A:GLU177 2.5 14.3 1.0
OE1 A:GLU190 2.5 11.7 1.0
CD A:GLU190 2.8 12.1 1.0
CD A:GLU177 2.8 11.7 1.0
CG A:ASP185 3.4 13.1 1.0
CG A:ASP138 3.4 9.9 1.0
C A:GLU187 3.4 11.2 1.0
CA A:CA1405 3.7 33.3 1.0
OD2 A:ASP185 3.8 17.4 1.0
CB A:ASP138 4.0 9.4 1.0
O A:ASP185 4.0 10.9 1.0
N A:GLU187 4.2 12.1 1.0
O A:HOH1614 4.2 12.5 1.0
CA A:GLU187 4.3 11.2 0.3
OD1 A:ASP138 4.3 11.5 1.0
CA A:GLU187 4.3 12.2 0.7
N A:ILE188 4.3 10.5 1.0
CG A:GLU190 4.3 11.9 1.0
CG A:GLU177 4.3 11.4 1.0
CA A:ILE188 4.4 10.2 1.0
O A:HOH1529 4.4 21.6 1.0
N A:GLY189 4.4 10.6 1.0
C A:ASP185 4.5 11.2 1.0
CB A:GLU187 4.5 11.4 0.3
N A:ASP185 4.6 12.4 1.0
CB A:ASP185 4.7 11.6 1.0
CB A:GLU187 4.7 14.4 0.7
CA A:ASP185 4.8 11.7 1.0
C A:ILE188 4.8 10.4 1.0
CB A:GLU177 4.9 10.7 1.0

Calcium binding site 3 out of 4 in 6fj2

Go back to Calcium Binding Sites List in 6fj2
Calcium binding site 3 out of 4 in the Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B


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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1404

b:10.8
occ:1.00
 O A:GLN61 2.3 11.2 1.0
O A:HOH1768 2.3 14.6 1.0
OD1 A:ASP59 2.3 12.6 1.0
OD2 A:ASP57 2.3 12.4 1.0
O A:HOH1621 2.4 13.8 1.0
O A:HOH1613 2.4 11.5 1.0
OD1 A:ASP57 2.6 11.1 1.0
CG A:ASP57 2.9 11.1 1.0
CG A:ASP59 3.4 12.6 1.0
C A:GLN61 3.5 10.4 1.0
OD2 A:ASP59 3.8 15.2 1.0
N A:GLN61 4.0 11.4 1.0
O A:HOH1680 4.0 15.3 1.0
CA A:GLN61 4.1 11.3 0.5
CA A:GLN61 4.1 11.7 0.5
CB A:GLN61 4.3 12.4 0.5
N A:ASP59 4.3 12.3 1.0
CB A:ASP57 4.4 11.0 1.0
CB A:GLN61 4.4 13.4 0.5
O A:HOH1705 4.5 15.6 1.0
N A:PHE62 4.5 9.8 1.0
O A:HOH1852 4.5 15.9 1.0
CB A:ASP59 4.6 13.1 1.0
OD2 A:ASP67 4.6 10.3 1.0
N A:ASN60 4.6 11.8 1.0
O A:HOH1548 4.6 11.3 1.0
O A:HOH1857 4.7 26.3 1.0
CA A:ASP59 4.8 12.5 1.0
N A:ALA58 4.8 12.2 1.0
CA A:PHE62 4.8 9.7 1.0
O A:HOH1829 4.8 37.0 1.0
C A:ASP59 4.9 11.9 1.0

Calcium binding site 4 out of 4 in 6fj2

Go back to Calcium Binding Sites List in 6fj2
Calcium binding site 4 out of 4 in the Structure of Thermolysin Solved From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B


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 From Sad Data Collected at the Peak of the Zn Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1405

b:33.3
occ:1.00
 OE2 A:GLU190 2.4 13.1 1.0
OD2 A:ASP185 2.4 17.4 1.0
O A:ASN183 2.4 25.8 1.0
OE2 A:GLU177 2.5 14.3 1.0
O A:HOH1529 2.7 21.6 1.0
CG A:ASP185 3.1 13.1 1.0
CD A:GLU177 3.2 11.7 1.0
O A:HOH1551 3.3 28.4 1.0
CD A:GLU190 3.3 12.1 1.0
OD1 A:ASP185 3.5 11.3 1.0
OE1 A:GLU177 3.6 11.1 1.0
CA A:CA1403 3.7 10.4 1.0
C A:ASN183 3.7 21.4 1.0
N A:ASP185 3.8 12.4 1.0
CG A:GLU190 3.9 11.9 1.0
CA A:PRO184 3.9 14.5 1.0
C A:PRO184 4.0 14.7 1.0
CB A:ASP185 4.1 11.6 1.0
CG A:GLU177 4.2 11.4 1.0
OE1 A:GLU190 4.3 11.7 1.0
O A:HOH1504 4.3 24.3 1.0
N A:PRO184 4.3 17.2 1.0
OD1 A:ASP191 4.5 16.6 1.0
OD2 A:ASP191 4.5 15.6 1.0
CA A:ASP185 4.6 11.7 1.0
O A:LYS182 4.6 26.2 1.0
CG A:ASP191 4.8 14.9 1.0
O A:PRO184 4.9 16.2 1.0
CA A:ASN183 5.0 25.7 1.0
O A:HOH1614 5.0 12.5 1.0

Reference:

A.A.Mccarthy, R.Barrett, A.Beteva, H.Caserotto, F.Dobias, F.Felisaz, T.Giraud, M.Guijarro, R.Janocha, A.Khadrouche, M.Lentini, G.A.Leonard, M.Lopez Marrero, S.Malbet-Monaco, S.Mcsweeney, D.Nurizzo, G.Papp, C.Rossi, J.Sinoir, C.Sorez, J.Surr, O.Svensson, U.Zander, F.Cipriani, P.Theveneau, C.Mueller-Dieckmann. ID30B - A Versatile Beamline For Macromolecular Crystallography Experiments at the Esrf. J Synchrotron Radiat V. 25 1249 2018.
ISSN: ESSN 1600-5775
PubMed: 29979188
DOI: 10.1107/S1600577518007166
Page generated: Sat Dec 12 06:06:57 2020

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