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Calcium in PDB 6qf3: X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

Enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

All present enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip:
3.4.24.27;

Protein crystallography data

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3 was solved by J.Lieske, M.Cerv, S.Kreida, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.58 / 1.52
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.154, 93.154, 129.294, 90.00, 90.00, 120.00
R / Rfree (%) 12.3 / 15

Other elements in 6qf3:

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip (pdb code 6qf3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6qf3

Go back to Calcium Binding Sites List in 6qf3
Calcium binding site 1 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:9.9
occ:1.00
 O A:GLU187 2.4 9.8 1.0
OD2 A:ASP138 2.4 10.1 1.0
OD1 A:ASP185 2.4 11.9 1.0
O A:HOH665 2.4 11.5 1.0
OE2 A:GLU190 2.5 13.1 1.0
OE1 A:GLU177 2.5 10.8 1.0
OE1 A:GLU190 2.5 10.9 1.0
OE2 A:GLU177 2.7 11.6 1.0
CD A:GLU190 2.8 12.2 1.0
CD A:GLU177 2.9 10.8 1.0
CG A:ASP138 3.4 10.1 1.0
CG A:ASP185 3.4 12.6 1.0
C A:GLU187 3.4 10.4 1.0
HB3 A:ASP138 3.6 10.0 1.0
HA A:ILE188 3.7 12.6 1.0
H A:GLY189 3.7 11.5 1.0
CA A:CA403 3.8 10.2 0.7
OD2 A:ASP185 3.8 13.6 1.0
H A:GLU187 3.8 14.2 1.0
CB A:ASP138 4.0 8.3 1.0
H A:ASP185 4.0 13.2 1.0
HB2 A:GLU187 4.1 14.5 0.3
O A:ASP185 4.1 11.6 1.0
H A:GLU190 4.2 13.3 1.0
N A:GLU187 4.2 11.9 1.0
HB2 A:ASP138 4.3 10.0 1.0
N A:ILE188 4.3 10.2 1.0
OD1 A:ASP138 4.3 11.4 1.0
O A:HOH648 4.3 11.6 1.0
CG A:GLU190 4.3 11.9 1.0
CA A:GLU187 4.3 12.2 0.3
HD13 A:ILE188 4.4 16.1 1.0
CA A:GLU187 4.4 12.6 0.7
HB2 A:GLU187 4.4 16.0 0.7
CG A:GLU177 4.4 10.8 1.0
CA A:ILE188 4.4 10.5 1.0
N A:GLY189 4.4 9.6 1.0
C A:ASP185 4.5 11.7 1.0
O A:HOH572 4.6 16.6 1.0
HG3 A:GLU190 4.6 14.3 1.0
N A:ASP185 4.6 11.0 1.0
HB2 A:GLU177 4.7 10.6 1.0
CB A:ASP185 4.7 12.2 1.0
CB A:GLU187 4.7 12.1 0.3
HB3 A:GLU177 4.8 10.6 1.0
HG2 A:GLU190 4.8 14.3 1.0
HG2 A:GLU177 4.8 12.9 1.0
CB A:GLU187 4.8 13.3 0.7
CA A:ASP185 4.9 10.4 1.0
C A:ILE188 4.9 12.3 1.0
HG3 A:GLU177 4.9 12.9 1.0
CB A:GLU177 4.9 8.8 1.0
HA A:THR174 4.9 10.2 1.0
N A:GLU190 5.0 11.1 1.0

Calcium binding site 2 out of 4 in 6qf3

Go back to Calcium Binding Sites List in 6qf3
Calcium binding site 2 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:10.2
occ:0.67
 O A:ASN183 2.3 13.9 1.0
O A:HOH572 2.3 16.6 1.0
OE2 A:GLU190 2.3 13.1 1.0
O A:HOH587 2.4 16.7 1.0
OD2 A:ASP185 2.4 13.6 1.0
OE2 A:GLU177 2.6 11.6 1.0
CG A:ASP185 3.2 12.6 1.0
CD A:GLU190 3.3 12.2 1.0
CD A:GLU177 3.3 10.8 1.0
HG3 A:GLU190 3.5 14.3 1.0
C A:ASN183 3.5 14.7 1.0
HA A:PRO184 3.5 14.5 1.0
OD1 A:ASP185 3.6 11.9 1.0
HB2 A:ASN183 3.6 20.8 1.0
OE1 A:GLU177 3.7 10.8 1.0
HG2 A:GLU190 3.7 14.3 1.0
CG A:GLU190 3.8 11.9 1.0
CA A:CA402 3.8 9.9 1.0
H A:ASP185 4.0 13.2 1.0
O A:HOH613 4.0 24.1 1.0
CA A:PRO184 4.1 12.1 1.0
N A:ASP185 4.1 11.0 1.0
OD2 A:ASP191 4.2 15.3 1.0
HB3 A:ASN183 4.2 20.8 1.0
C A:PRO184 4.2 12.2 1.0
OD1 A:ASP191 4.2 15.9 1.0
OE1 A:GLU190 4.3 10.9 1.0
CB A:ASN183 4.3 17.3 1.0
O A:HOH816 4.3 21.5 1.0
N A:PRO184 4.3 12.1 1.0
CG A:GLU177 4.3 10.8 1.0
HG2 A:GLU177 4.3 12.9 1.0
HB3 A:ASP185 4.3 14.6 1.0
CB A:ASP185 4.4 12.2 1.0
O A:HOH869 4.4 37.6 1.0
HG3 A:GLU177 4.4 12.9 1.0
H12 A:EDO411 4.5 30.3 0.5
CG A:ASP191 4.5 14.3 1.0
CA A:ASN183 4.5 17.4 1.0
H11 A:EDO411 4.5 31.1 0.5
O A:HOH648 4.8 11.6 1.0
H A:ASN183 4.8 23.3 1.0
CA A:ASP185 4.9 10.4 1.0
O A:PRO184 4.9 16.0 1.0

Calcium binding site 3 out of 4 in 6qf3

Go back to Calcium Binding Sites List in 6qf3
Calcium binding site 3 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:10.0
occ:1.00
 O A:GLN61 2.3 10.2 1.0
O A:HOH844 2.3 12.8 1.0
OD1 A:ASP57 2.4 10.7 1.0
O A:HOH629 2.4 12.6 1.0
OD1 A:ASP59 2.4 11.0 1.0
O A:HOH597 2.5 12.4 1.0
OD2 A:ASP57 2.6 9.3 1.0
CG A:ASP57 2.8 10.2 1.0
H A:GLN61 3.3 10.9 0.4
H A:GLN61 3.3 10.9 0.6
CG A:ASP59 3.4 12.2 1.0
C A:GLN61 3.4 9.5 1.0
H A:ASP59 3.5 11.6 1.0
HB2 A:GLN61 3.6 13.3 0.4
HB2 A:GLN61 3.6 11.5 0.6
OD2 A:ASP59 3.8 14.4 1.0
O A:HOH769 3.9 16.3 1.0
N A:GLN61 4.0 9.1 1.0
HA A:PHE62 4.1 9.8 1.0
CA A:GLN61 4.1 8.5 0.4
CA A:GLN61 4.1 8.3 0.6
H A:ALA58 4.3 12.9 1.0
CB A:GLN61 4.3 11.1 0.4
CB A:ASP57 4.3 9.3 1.0
N A:ASP59 4.3 9.7 1.0
H A:ASN60 4.3 11.0 1.0
CB A:GLN61 4.4 9.6 0.6
N A:PHE62 4.5 9.7 1.0
O A:HOH938 4.5 20.2 1.0
O A:HOH545 4.6 9.9 1.0
OD2 A:ASP67 4.6 9.9 1.0
CB A:ASP59 4.6 11.3 1.0
O A:HOH945 4.6 30.9 1.0
N A:ASN60 4.6 9.1 1.0
HB2 A:ASP57 4.7 11.2 1.0
N A:ALA58 4.7 10.7 1.0
HB3 A:ASP57 4.8 11.2 1.0
CA A:PHE62 4.8 8.2 1.0
CA A:ASP59 4.8 9.9 1.0
H A:PHE63 4.8 12.0 1.0
HA A:ASP57 4.9 11.7 1.0
HB3 A:GLN61 4.9 13.3 0.4
HB3 A:GLN61 4.9 11.5 0.6
C A:ASP59 4.9 10.8 1.0
HB3 A:ASP59 5.0 13.6 1.0

Calcium binding site 4 out of 4 in 6qf3

Go back to Calcium Binding Sites List in 6qf3
Calcium binding site 4 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:13.6
occ:1.00
 O A:ILE197 2.3 15.1 1.0
O A:TYR193 2.3 14.3 1.0
OD1 A:ASP200 2.4 15.4 1.0
O A:HOH565 2.4 14.1 1.0
O A:THR194 2.4 17.0 1.0
OG1 A:THR194 2.4 15.6 1.0
O A:HOH829 2.5 20.7 1.0
C A:THR194 3.2 17.8 1.0
C A:TYR193 3.3 14.0 1.0
HB A:ILE197 3.4 23.4 1.0
CG A:ASP200 3.4 15.3 1.0
C A:ILE197 3.5 16.9 1.0
CB A:THR194 3.5 15.3 1.0
H A:ILE197 3.5 25.0 1.0
CA A:THR194 3.7 13.2 1.0
HB A:THR194 3.8 18.4 1.0
OD2 A:ASP200 3.8 16.2 1.0
H A:ASP200 3.9 17.7 1.0
N A:THR194 3.9 13.9 1.0
HB3 A:TYR193 4.0 16.0 1.0
HD2 A:TYR193 4.0 21.4 1.0
HA A:SER198 4.1 24.4 1.0
CA A:ILE197 4.2 18.1 1.0
CB A:ILE197 4.2 19.5 1.0
N A:ILE197 4.2 20.9 1.0
HA A:PRO195 4.3 22.6 1.0
N A:PRO195 4.3 16.3 1.0
O A:HOH663 4.3 32.4 1.0
O A:HOH781 4.3 26.8 1.0
HG22 A:ILE197 4.3 24.7 1.0
O A:ASP200 4.4 16.0 1.0
N A:SER198 4.5 21.6 1.0
CA A:TYR193 4.5 12.4 1.0
O A:GLU190 4.6 12.9 1.0
HA A:THR194 4.6 15.9 1.0
O A:HOH706 4.6 37.3 1.0
H A:GLY199 4.6 19.3 1.0
CB A:TYR193 4.6 13.3 1.0
N A:ASP200 4.6 14.7 1.0
CD2 A:TYR193 4.7 17.8 1.0
CA A:PRO195 4.7 18.9 1.0
CA A:SER198 4.7 20.4 1.0
O A:HOH850 4.7 32.4 1.0
H A:THR194 4.7 16.6 1.0
CG2 A:THR194 4.7 16.9 1.0
CB A:ASP200 4.8 15.8 1.0
CG2 A:ILE197 4.8 20.6 1.0
C A:ASP200 4.8 14.0 1.0
HG23 A:THR194 4.8 20.3 1.0
H A:TYR193 4.9 14.0 1.0
C A:PRO195 4.9 22.4 1.0
N A:GLY199 5.0 16.1 1.0
CA A:ASP200 5.0 15.1 1.0
C A:SER198 5.0 17.0 1.0
HG21 A:THR194 5.0 20.3 1.0

Reference:

J.Lieske, M.Cerv, S.Kreida, D.Komadina, J.Fischer, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents. On-Chip Crystallization For Serial Crystallography Experiments and on-Chip Ligand-Binding Studies. Iucrj V. 6 714 2019.
ISSN: ESSN 2052-2525
PubMed: 31316815
DOI: 10.1107/S2052252519007395
Page generated: Wed Jul 9 17:10:26 2025

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