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Calcium in PDB 5lwd: Thermolysin in Complex with Inhibitor (JC96)

Enzymatic activity of Thermolysin in Complex with Inhibitor (JC96)

All present enzymatic activity of Thermolysin in Complex with Inhibitor (JC96):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor (JC96), PDB code: 5lwd was solved by S.G.Krimmer, J.Cramer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.75 / 1.23
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.795, 92.795, 130.629, 90.00, 90.00, 120.00
R / Rfree (%) 10.4 / 12.3

Other elements in 5lwd:

The structure of Thermolysin in Complex with Inhibitor (JC96) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor (JC96) (pdb code 5lwd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin in Complex with Inhibitor (JC96), PDB code: 5lwd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5lwd

Go back to Calcium Binding Sites List in 5lwd
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Inhibitor (JC96)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with Inhibitor (JC96) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:8.4
occ:1.00
 O E:GLN61 2.3 8.8 1.0
O E:HOH787 2.3 11.0 1.0
OD1 E:ASP59 2.4 9.1 1.0
O E:HOH578 2.4 10.7 1.0
OD1 E:ASP57 2.4 8.9 1.0
O E:HOH582 2.4 9.8 1.0
OD2 E:ASP57 2.6 8.7 1.0
CG E:ASP57 2.8 8.4 1.0
H E:GLN61 3.3 10.1 1.0
CG E:ASP59 3.4 9.6 1.0
C E:GLN61 3.5 8.0 1.0
H E:ASP59 3.5 10.8 1.0
HB2 E:GLN61 3.6 12.9 1.0
OD2 E:ASP59 3.8 11.7 1.0
N E:GLN61 4.0 8.4 1.0
O E:HOH708 4.0 15.0 1.0
HA E:PHE62 4.1 9.3 1.0
CA E:GLN61 4.1 8.7 1.0
CB E:GLN61 4.3 10.7 1.0
N E:ASP59 4.3 9.0 1.0
CB E:ASP57 4.3 8.1 1.0
H E:ASN60 4.3 9.8 1.0
H E:ALA58 4.4 9.9 1.0
N E:PHE62 4.5 7.7 1.0
O E:HOH859 4.6 14.5 1.0
CB E:ASP59 4.6 9.5 1.0
N E:ASN60 4.6 8.1 1.0
OD2 E:ASP67 4.6 8.7 1.0
O E:HOH526 4.7 8.3 1.0
O E:HOH885 4.7 27.3 1.0
HB2 E:ASP57 4.7 9.8 1.0
N E:ALA58 4.8 8.2 1.0
CA E:ASP59 4.8 9.0 1.0
CA E:PHE62 4.8 7.8 1.0
HB3 E:ASP57 4.8 9.8 1.0
H E:PHE63 4.9 10.5 1.0
HA E:ASP57 4.9 9.9 1.0
C E:ASP59 4.9 8.6 1.0
HB3 E:GLN61 4.9 12.9 1.0
HB3 E:ASP59 4.9 11.3 1.0

Calcium binding site 2 out of 4 in 5lwd

Go back to Calcium Binding Sites List in 5lwd
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Inhibitor (JC96)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with Inhibitor (JC96) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.3
occ:1.00
 O E:GLU187 2.3 8.9 1.0
OD2 E:ASP138 2.4 8.2 1.0
O E:HOH588 2.4 8.5 1.0
OE1 E:GLU177 2.5 8.9 1.0
OD1 E:ASP185 2.5 9.0 1.0
OE1 E:GLU190 2.5 9.4 1.0
OE2 E:GLU190 2.5 10.1 1.0
OE2 E:GLU177 2.7 10.3 1.0
CD E:GLU190 2.9 9.6 1.0
CD E:GLU177 2.9 8.8 1.0
CG E:ASP138 3.4 8.0 1.0
C E:GLU187 3.4 9.3 1.0
CG E:ASP185 3.5 9.8 1.0
HB3 E:ASP138 3.6 8.3 1.0
HA E:ILE188 3.6 10.0 1.0
H E:GLU187 3.7 11.7 1.0
CA E:CA404 3.8 12.2 1.0
H E:GLY189 3.8 10.2 1.0
OD2 E:ASP185 3.8 11.6 1.0
HB2 E:GLU187 3.9 13.9 1.0
CB E:ASP138 4.0 6.9 1.0
O E:ASP185 4.1 9.4 1.0
H E:ASP185 4.1 11.6 1.0
H E:GLU190 4.2 10.8 1.0
N E:GLU187 4.2 9.7 1.0
N E:ILE188 4.3 8.7 1.0
HB2 E:ASP138 4.3 8.3 1.0
OD1 E:ASP138 4.3 9.5 1.0
O E:HOH577 4.3 12.9 0.5
CA E:GLU187 4.3 9.9 1.0
CA E:ILE188 4.3 8.3 1.0
CG E:GLU190 4.4 10.3 1.0
HD13 E:ILE188 4.4 13.5 1.0
CG E:GLU177 4.4 8.8 1.0
N E:GLY189 4.4 8.5 1.0
O E:HOH586 4.5 14.6 1.0
C E:ASP185 4.6 9.2 1.0
CB E:GLU187 4.6 11.6 1.0
HG3 E:GLU190 4.6 12.4 1.0
HB2 E:GLU177 4.7 9.6 1.0
HB3 E:GLU177 4.7 9.6 1.0
N E:ASP185 4.8 9.7 1.0
CB E:ASP185 4.8 10.1 1.0
C E:ILE188 4.8 8.5 1.0
HG2 E:GLU190 4.8 12.4 1.0
HG2 E:GLU177 4.8 10.6 1.0
O E:HOH562 4.9 15.8 1.0
HA E:THR174 4.9 8.8 1.0
CB E:GLU177 4.9 8.0 1.0
HG3 E:GLU177 4.9 10.6 1.0
CA E:ASP185 5.0 9.7 1.0
HB3 E:GLU190 5.0 12.4 1.0
N E:GLU190 5.0 9.0 1.0

Calcium binding site 3 out of 4 in 5lwd

Go back to Calcium Binding Sites List in 5lwd
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Inhibitor (JC96)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with Inhibitor (JC96) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:12.2
occ:1.00
 OE2 E:GLU190 2.3 10.1 1.0
O E:ASN183 2.3 13.8 1.0
OD2 E:ASP185 2.3 11.6 1.0
O E:HOH562 2.3 15.8 1.0
O E:HOH583 2.3 15.6 1.0
OE2 E:GLU177 2.5 10.3 1.0
CG E:ASP185 3.2 9.8 1.0
CD E:GLU177 3.3 8.8 1.0
CD E:GLU190 3.3 9.6 1.0
C E:ASN183 3.5 13.7 1.0
HA E:PRO184 3.5 13.4 1.0
HG3 E:GLU190 3.5 12.4 1.0
OD1 E:ASP185 3.6 9.0 1.0
OE1 E:GLU177 3.7 8.9 1.0
HB2 E:ASN183 3.8 22.4 1.0
HG2 E:GLU190 3.8 12.4 1.0
CA E:CA403 3.8 8.3 1.0
CG E:GLU190 3.8 10.3 1.0
HB3 E:ASN183 3.8 22.4 1.0
H E:ASP185 4.0 11.6 1.0
O E:HOH549 4.1 39.0 1.0
CA E:PRO184 4.1 11.2 1.0
N E:ASP185 4.2 9.7 1.0
CB E:ASN183 4.2 18.7 1.0
OD2 E:ASP191 4.2 13.6 1.0
OE1 E:GLU190 4.2 9.4 1.0
C E:PRO184 4.3 10.8 1.0
OD1 E:ASP191 4.3 13.3 1.0
HG2 E:GLU177 4.3 10.6 1.0
CG E:GLU177 4.3 8.8 1.0
N E:PRO184 4.3 12.5 1.0
HB3 E:ASP185 4.3 12.1 1.0
CB E:ASP185 4.4 10.1 1.0
HG3 E:GLU177 4.4 10.6 1.0
O E:LYS182 4.4 16.2 1.0
CA E:ASN183 4.5 16.2 1.0
O E:HOH577 4.5 12.9 0.5
O E:HOH861 4.6 38.1 1.0
CG E:ASP191 4.6 12.1 1.0
CA E:ASP185 4.9 9.7 1.0
O E:PRO184 5.0 12.5 1.0

Calcium binding site 4 out of 4 in 5lwd

Go back to Calcium Binding Sites List in 5lwd
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Inhibitor (JC96)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with Inhibitor (JC96) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:12.6
occ:1.00
 O E:ILE197 2.3 19.4 1.0
O E:HOH761 2.4 19.0 1.0
O E:TYR193 2.4 12.2 1.0
OD1 E:ASP200 2.4 13.7 1.0
OG1 E:THR194 2.4 14.2 1.0
O E:THR194 2.4 15.0 1.0
O E:HOH604 2.4 14.5 1.0
C E:THR194 3.2 14.8 1.0
C E:TYR193 3.4 12.2 1.0
CG E:ASP200 3.4 13.7 1.0
CB E:THR194 3.5 14.5 1.0
C E:ILE197 3.5 20.3 1.0
HB E:ILE197 3.5 26.4 1.0
H E:ILE197 3.6 24.9 1.0
CA E:THR194 3.7 14.1 1.0
HB E:THR194 3.7 17.4 1.0
OD2 E:ASP200 3.8 14.9 1.0
H E:ASP200 3.9 17.7 1.0
N E:THR194 3.9 12.8 1.0
HA E:SER198 4.1 26.3 1.0
HD1 E:TYR193 4.1 18.1 1.0
HB3 E:TYR193 4.1 15.3 1.0
CA E:ILE197 4.2 20.8 1.0
CB E:ILE197 4.3 22.0 1.0
N E:PRO195 4.3 16.3 1.0
N E:ILE197 4.3 20.7 1.0
HA E:PRO195 4.3 22.1 1.0
HG22 E:ILE197 4.4 26.7 1.0
O E:HOH669 4.4 40.4 1.0
N E:SER198 4.5 20.9 1.0
O E:ASP200 4.5 12.7 1.0
O E:HOH597 4.5 43.5 1.0
CA E:TYR193 4.6 11.7 1.0
HA E:THR194 4.6 16.9 1.0
O E:GLU190 4.6 10.9 1.0
CA E:SER198 4.7 21.9 1.0
N E:ASP200 4.7 14.8 1.0
CD1 E:TYR193 4.7 15.1 1.0
H E:GLY199 4.7 22.6 1.0
O E:HOH791 4.7 26.6 1.0
CB E:TYR193 4.7 12.8 1.0
CA E:PRO195 4.7 18.4 1.0
CB E:ASP200 4.7 13.8 1.0
CG2 E:THR194 4.7 15.3 1.0
H E:THR194 4.7 15.3 1.0
C E:ASP200 4.8 12.7 1.0
HG23 E:THR194 4.8 18.3 1.0
CG2 E:ILE197 4.9 22.2 1.0
H E:TYR193 4.9 12.5 1.0
CA E:ASP200 5.0 13.9 1.0
C E:SER198 5.0 20.8 1.0
N E:GLY199 5.0 18.8 1.0
C E:PRO195 5.0 20.3 1.0
HG21 E:THR194 5.0 18.3 1.0

Reference:

J.Cramer, S.G.Krimmer, V.Fridh, T.Wulsdorf, R.Karlsson, A.Heine, G.Klebe. Elucidating the Origin of Long Residence Time Binding For Inhibitors of the Metalloprotease Thermolysin. Acs Chem. Biol. V. 12 225 2017.
ISSN: ESSN 1554-8937
PubMed: 27959500
DOI: 10.1021/ACSCHEMBIO.6B00979
Page generated: Mon Jul 15 07:49:44 2024

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