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Calcium in PDB 6yi6: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

All present enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6yi6 was solved by M.Kljajic, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.32 / 1.44
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.606, 92.606, 130.637, 90, 90, 120
R / Rfree (%) 11.9 / 14.8

Other elements in 6yi6:

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin also contains other interesting chemical elements:

Caesium (Cs) 2 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin (pdb code 6yi6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6yi6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6yi6

Go back to Calcium Binding Sites List in 6yi6
Calcium binding site 1 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:11.6
occ:1.00
 O E:GLN61 2.3 11.5 1.0
O E:HOH768 2.4 13.5 1.0
OD1 E:ASP59 2.4 11.8 1.0
O E:HOH568 2.4 13.8 1.0
O E:HOH602 2.4 12.8 1.0
OD1 E:ASP57 2.4 12.2 1.0
OD2 E:ASP57 2.6 11.7 1.0
CG E:ASP57 2.8 11.1 1.0
H E:GLN61 3.3 14.1 1.0
CG E:ASP59 3.4 11.7 1.0
C E:GLN61 3.4 10.8 1.0
H E:ASP59 3.5 13.5 1.0
HB2 E:GLN61 3.6 15.8 1.0
OD2 E:ASP59 3.8 14.7 1.0
N E:GLN61 4.0 11.8 1.0
O E:HOH675 4.0 19.2 1.0
HA E:PHE62 4.0 13.0 1.0
CA E:GLN61 4.1 11.2 1.0
H E:ALA58 4.3 13.8 1.0
H E:ASN60 4.3 13.7 1.0
N E:ASP59 4.3 11.3 1.0
CB E:GLN61 4.3 13.2 1.0
CB E:ASP57 4.3 11.7 1.0
N E:PHE62 4.5 10.7 1.0
CB E:ASP59 4.6 11.4 1.0
N E:ASN60 4.6 11.5 1.0
O E:HOH527 4.7 11.5 1.0
OD2 E:ASP67 4.7 11.4 1.0
HB2 E:ASP57 4.7 14.0 1.0
N E:ALA58 4.7 11.5 1.0
CA E:PHE62 4.8 10.9 1.0
O E:HOH846 4.8 27.6 1.0
CA E:ASP59 4.8 11.3 1.0
HB3 E:ASP57 4.8 14.0 1.0
H E:PHE63 4.8 14.2 1.0
HB3 E:GLN61 4.8 15.8 1.0
HA E:ASP57 4.9 13.1 1.0
C E:ASP59 4.9 11.7 1.0
HB3 E:ALA58 4.9 15.4 1.0
HB3 E:ASP59 5.0 13.7 1.0

Calcium binding site 2 out of 4 in 6yi6

Go back to Calcium Binding Sites List in 6yi6
Calcium binding site 2 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:11.4
occ:1.00
 O E:GLU187 2.3 11.8 1.0
OD2 E:ASP138 2.4 11.2 1.0
O E:HOH567 2.4 11.8 1.0
OD1 E:ASP185 2.5 11.4 1.0
OE1 E:GLU177 2.5 11.4 1.0
OE2 E:GLU190 2.5 13.6 1.0
OE1 E:GLU190 2.5 12.4 1.0
OE2 E:GLU177 2.7 12.3 1.0
CD E:GLU190 2.8 12.2 1.0
CD E:GLU177 2.9 10.9 1.0
CG E:ASP138 3.4 11.2 1.0
C E:GLU187 3.4 11.3 1.0
CG E:ASP185 3.5 11.3 1.0
HB3 E:ASP138 3.6 11.9 1.0
HA E:ILE188 3.7 12.9 1.0
H E:GLU187 3.7 14.8 1.0
OD2 E:ASP185 3.8 13.8 1.0
CA E:CA404 3.8 14.1 1.0
H E:GLY189 3.8 14.0 1.0
HB2 E:GLU187 3.9 17.3 1.0
CB E:ASP138 4.0 9.9 1.0
O E:ASP185 4.1 12.1 1.0
H E:GLU190 4.1 15.0 1.0
H E:ASP185 4.2 15.1 1.0
N E:GLU187 4.2 12.3 1.0
N E:ILE188 4.3 10.9 1.0
HB2 E:ASP138 4.3 11.9 1.0
OD1 E:ASP138 4.3 12.2 1.0
CA E:GLU187 4.3 12.6 1.0
CG E:GLU190 4.3 12.8 1.0
CA E:ILE188 4.4 10.8 1.0
CG E:GLU177 4.4 11.1 1.0
O E:HOH573 4.4 16.0 1.0
HD13 E:ILE188 4.4 17.6 1.0
N E:GLY189 4.4 11.7 1.0
HG3 E:GLU190 4.6 15.4 1.0
CB E:GLU187 4.6 14.4 1.0
C E:ASP185 4.6 12.3 1.0
HB2 E:GLU177 4.7 13.2 1.0
CB E:ASP185 4.7 12.5 1.0
HB3 E:GLU177 4.8 13.2 1.0
HG2 E:GLU190 4.8 15.4 1.0
HG2 E:GLU177 4.8 13.3 1.0
C E:ILE188 4.8 11.1 1.0
N E:ASP185 4.8 12.6 1.0
CB E:GLU177 4.9 11.0 1.0
HA E:THR174 4.9 12.0 1.0
HG3 E:GLU177 4.9 13.3 1.0
O E:HOH532 4.9 15.9 1.0
HB3 E:GLU190 4.9 14.3 1.0
N E:GLU190 4.9 12.5 1.0
CA E:ASP185 5.0 12.6 1.0

Calcium binding site 3 out of 4 in 6yi6

Go back to Calcium Binding Sites List in 6yi6
Calcium binding site 3 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:14.1
occ:1.00
 O E:ASN183 2.3 15.4 1.0
OD2 E:ASP185 2.3 13.8 1.0
OE2 E:GLU190 2.3 13.6 1.0
O E:HOH571 2.3 15.9 1.0
O E:HOH532 2.4 15.9 1.0
OE2 E:GLU177 2.4 12.3 1.0
CG E:ASP185 3.2 11.3 1.0
CD E:GLU177 3.2 10.9 1.0
CD E:GLU190 3.3 12.2 1.0
C E:ASN183 3.5 16.1 1.0
HG3 E:GLU190 3.6 15.4 1.0
HA E:PRO184 3.6 16.6 1.0
OD1 E:ASP185 3.6 11.4 1.0
HB2 E:ASN183 3.7 24.1 1.0
HG2 E:GLU190 3.7 15.4 1.0
OE1 E:GLU177 3.8 11.4 1.0
CG E:GLU190 3.8 12.8 1.0
CA E:CA403 3.8 11.4 1.0
HB3 E:ASN183 3.8 24.1 1.0
H E:ASP185 4.1 15.1 1.0
CB E:ASN183 4.1 20.1 1.0
CA E:PRO184 4.2 13.8 1.0
OD2 E:ASP191 4.2 15.5 1.0
O E:HOH710 4.2 43.9 1.0
N E:ASP185 4.2 12.6 1.0
OD1 E:ASP191 4.2 15.6 1.0
HG2 E:GLU177 4.3 13.3 1.0
CG E:GLU177 4.3 11.1 1.0
C E:PRO184 4.3 13.9 1.0
N E:PRO184 4.3 14.4 1.0
OE1 E:GLU190 4.3 12.4 1.0
HB3 E:ASP185 4.3 15.0 1.0
CB E:ASP185 4.3 12.5 1.0
HG3 E:GLU177 4.4 13.3 1.0
O E:LYS182 4.4 18.1 1.0
CA E:ASN183 4.5 19.0 1.0
O E:HOH820 4.5 45.5 1.0
CG E:ASP191 4.5 14.8 1.0
CA E:ASP185 4.9 12.6 1.0
O E:PRO184 5.0 15.0 1.0

Calcium binding site 4 out of 4 in 6yi6

Go back to Calcium Binding Sites List in 6yi6
Calcium binding site 4 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:14.8
occ:1.00
 O E:ILE197 2.3 19.1 1.0
OD1 E:ASP200 2.4 14.6 1.0
OG1 E:THR194 2.4 14.5 1.0
O E:TYR193 2.4 14.0 1.0
O E:HOH591 2.4 17.3 1.0
O E:THR194 2.4 16.8 1.0
O E:HOH753 2.4 22.0 1.0
C E:THR194 3.2 15.8 1.0
C E:TYR193 3.4 14.1 1.0
CG E:ASP200 3.4 14.9 1.0
CB E:THR194 3.5 15.0 1.0
C E:ILE197 3.5 20.5 1.0
HB E:ILE197 3.5 26.9 1.0
H E:ILE197 3.6 25.5 1.0
CA E:THR194 3.7 14.7 1.0
HB E:THR194 3.7 18.0 1.0
OD2 E:ASP200 3.8 16.2 1.0
H E:ASP200 3.8 19.4 1.0
N E:THR194 3.9 14.0 1.0
HB3 E:TYR193 4.0 16.6 1.0
HA E:SER198 4.0 27.7 1.0
HD2 E:TYR193 4.1 19.0 1.0
CA E:ILE197 4.2 21.4 1.0
CB E:ILE197 4.2 22.5 1.0
N E:ILE197 4.3 21.3 1.0
N E:PRO195 4.3 17.2 1.0
HA E:PRO195 4.3 21.8 1.0
HG22 E:ILE197 4.3 26.6 1.0
N E:SER198 4.5 21.6 1.0
O E:HOH680 4.5 39.8 1.0
O E:ASP200 4.5 15.0 1.0
CA E:TYR193 4.6 13.3 1.0
HA E:THR194 4.6 17.6 1.0
O E:HOH773 4.6 33.7 1.0
N E:ASP200 4.6 16.1 1.0
CA E:SER198 4.6 23.1 1.0
CB E:TYR193 4.7 13.8 1.0
H E:GLY199 4.7 25.3 1.0
CD2 E:TYR193 4.7 15.9 1.0
CA E:PRO195 4.7 18.2 1.0
O E:GLU190 4.7 13.6 1.0
CG2 E:THR194 4.7 15.9 1.0
CB E:ASP200 4.7 14.8 1.0
H E:THR194 4.7 16.8 1.0
C E:ASP200 4.8 14.0 1.0
CG2 E:ILE197 4.8 22.2 1.0
HG23 E:THR194 4.8 19.1 1.0
C E:SER198 4.9 22.5 1.0
CA E:ASP200 4.9 15.0 1.0
H E:TYR193 4.9 15.1 1.0
N E:GLY199 5.0 21.1 1.0
C E:PRO195 5.0 21.4 1.0
HG21 E:THR194 5.0 19.1 1.0

Reference:

M.Kljajic, H.-D.Gerber, A.Heine, G.Klebe. Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin To Be Published.
Page generated: Wed Jul 9 20:22:12 2025

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