Atomistry » Calcium » PDB 5l0v-5lia » 5l8p
Atomistry »
  Calcium »
    PDB 5l0v-5lia »
      5l8p »

Calcium in PDB 5l8p: Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)

Enzymatic activity of Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)

All present enzymatic activity of Thermolysin in Complex with JC114 (PEG400 Cryo Protectant):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with JC114 (PEG400 Cryo Protectant), PDB code: 5l8p 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) 40.10 / 1.29
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.596, 92.596, 130.427, 90.00, 90.00, 120.00
R / Rfree (%) 10.7 / 13.3

Other elements in 5l8p:

The structure of Thermolysin in Complex with JC114 (PEG400 Cryo Protectant) 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 JC114 (PEG400 Cryo Protectant) (pdb code 5l8p). 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 JC114 (PEG400 Cryo Protectant), PDB code: 5l8p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5l8p

Go back to Calcium Binding Sites List in 5l8p
Calcium binding site 1 out of 4 in the Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)


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 JC114 (PEG400 Cryo Protectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:7.6
occ:1.00
O E:GLU187 2.4 7.5 1.0
OD2 E:ASP138 2.4 7.8 1.0
O E:HOH593 2.4 8.2 1.0
OE1 E:GLU177 2.5 8.1 1.0
OD1 E:ASP185 2.5 8.2 1.0
OE1 E:GLU190 2.5 8.7 1.0
OE2 E:GLU190 2.5 8.7 1.0
OE2 E:GLU177 2.8 9.1 1.0
CD E:GLU190 2.9 8.5 1.0
CD E:GLU177 2.9 7.8 1.0
CG E:ASP138 3.4 7.6 1.0
C E:GLU187 3.4 7.4 1.0
CG E:ASP185 3.5 8.9 1.0
HB3 E:ASP138 3.6 8.6 1.0
HA E:ILE188 3.7 9.0 1.0
H E:GLU187 3.7 10.1 1.0
OD2 E:ASP185 3.8 10.6 1.0
H E:GLY189 3.8 9.6 1.0
CA E:CA404 3.8 11.0 1.0
HB2 E:GLU187 3.9 12.6 1.0
CB E:ASP138 4.0 7.2 1.0
O E:ASP185 4.1 8.5 1.0
H E:ASP185 4.1 10.8 1.0
H E:GLU190 4.2 9.9 1.0
N E:GLU187 4.2 8.4 1.0
HB2 E:ASP138 4.3 8.6 1.0
N E:ILE188 4.3 7.4 1.0
OD1 E:ASP138 4.3 9.1 1.0
CA E:GLU187 4.3 8.3 1.0
CA E:ILE188 4.4 7.5 1.0
CG E:GLU190 4.4 10.0 1.0
CG E:GLU177 4.4 8.1 1.0
O E:HOH594 4.4 13.3 1.0
N E:GLY189 4.4 8.0 1.0
HD13 E:ILE188 4.4 11.9 1.0
CB E:GLU187 4.6 10.5 1.0
C E:ASP185 4.6 8.0 1.0
HG3 E:GLU190 4.6 11.9 1.0
HB2 E:GLU177 4.7 9.5 1.0
HB3 E:GLU177 4.7 9.5 1.0
N E:ASP185 4.8 9.0 1.0
CB E:ASP185 4.8 9.2 1.0
C E:ILE188 4.8 7.6 1.0
HG2 E:GLU190 4.8 11.9 1.0
HG2 E:GLU177 4.8 9.7 1.0
HA E:THR174 4.9 8.4 1.0
O E:HOH553 4.9 14.1 1.0
CB E:GLU177 4.9 7.9 1.0
HG3 E:GLU177 4.9 9.7 1.0
HB3 E:GLU190 5.0 10.8 1.0
CA E:ASP185 5.0 8.9 1.0
N E:GLU190 5.0 8.3 1.0
HB3 E:GLU187 5.0 12.6 1.0

Calcium binding site 2 out of 4 in 5l8p

Go back to Calcium Binding Sites List in 5l8p
Calcium binding site 2 out of 4 in the Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)


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 JC114 (PEG400 Cryo Protectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:8.2
occ:1.00
O E:GLN61 2.3 8.2 1.0
O E:HOH797 2.3 10.7 1.0
OD1 E:ASP59 2.4 9.2 1.0
OD1 E:ASP57 2.4 8.6 1.0
O E:HOH587 2.4 10.4 1.0
O E:HOH602 2.4 9.8 1.0
OD2 E:ASP57 2.6 8.4 1.0
CG E:ASP57 2.8 8.1 1.0
H E:GLN61 3.3 10.0 1.0
CG E:ASP59 3.4 9.9 1.0
C E:GLN61 3.5 7.6 1.0
H E:ASP59 3.5 10.4 1.0
HB2 E:GLN61 3.6 14.0 1.0
OD2 E:ASP59 3.8 12.4 1.0
N E:GLN61 4.0 8.3 1.0
O E:HOH705 4.0 14.8 1.0
HA E:PHE62 4.0 9.6 1.0
CA E:GLN61 4.2 8.8 1.0
H E:ALA58 4.2 9.6 1.0
N E:ASP59 4.3 8.7 1.0
H E:ASN60 4.4 9.5 1.0
CB E:GLN61 4.4 11.7 1.0
CB E:ASP57 4.4 7.8 1.0
O E:HOH739 4.4 10.0 1.0
N E:PHE62 4.5 7.3 1.0
O E:HOH874 4.6 13.2 1.0
CB E:ASP59 4.6 9.0 1.0
O E:HOH540 4.6 8.1 1.0
N E:ASN60 4.7 7.9 1.0
OD2 E:ASP67 4.7 8.0 1.0
N E:ALA58 4.7 8.0 1.0
HB2 E:ASP57 4.7 9.3 1.0
CA E:PHE62 4.8 8.0 1.0
O E:HOH898 4.8 21.9 1.0
CA E:ASP59 4.8 8.5 1.0
HB3 E:ASP57 4.8 9.3 1.0
O E:HOH876 4.8 21.4 1.0
H E:PHE63 4.8 10.5 1.0
C E:ASP59 4.9 8.4 1.0
HA E:ASP57 4.9 8.8 1.0
HB3 E:ASP59 5.0 10.8 1.0
HB3 E:ALA58 5.0 11.9 1.0
HB3 E:GLN61 5.0 14.0 1.0

Calcium binding site 3 out of 4 in 5l8p

Go back to Calcium Binding Sites List in 5l8p
Calcium binding site 3 out of 4 in the Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)


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 JC114 (PEG400 Cryo Protectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:11.0
occ:1.00
O E:HOH564 2.2 15.4 1.0
OE2 E:GLU190 2.3 8.7 1.0
O E:ASN183 2.3 13.7 1.0
OD2 E:ASP185 2.3 10.6 1.0
O E:HOH553 2.3 14.1 1.0
OE2 E:GLU177 2.4 9.1 1.0
CG E:ASP185 3.2 8.9 1.0
CD E:GLU177 3.3 7.8 1.0
CD E:GLU190 3.3 8.5 1.0
C E:ASN183 3.5 13.7 1.0
HA E:PRO184 3.6 12.9 1.0
HG3 E:GLU190 3.6 11.9 1.0
OD1 E:ASP185 3.7 8.2 1.0
HB2 E:ASN183 3.7 23.1 1.0
OE1 E:GLU177 3.8 8.1 1.0
HB3 E:ASN183 3.8 23.1 1.0
CA E:CA402 3.8 7.6 1.0
HG2 E:GLU190 3.9 11.9 1.0
CG E:GLU190 3.9 10.0 1.0
H E:ASP185 4.0 10.8 1.0
CB E:ASN183 4.2 19.3 1.0
CA E:PRO184 4.2 10.8 1.0
N E:ASP185 4.2 9.0 1.0
OD1 E:ASP191 4.2 13.3 1.0
OD2 E:ASP191 4.3 13.7 1.0
CG E:GLU177 4.3 8.1 1.0
HG2 E:GLU177 4.3 9.7 1.0
OE1 E:GLU190 4.3 8.7 1.0
C E:PRO184 4.3 10.4 1.0
N E:PRO184 4.3 11.7 1.0
HB3 E:ASP185 4.3 11.1 1.0
HG3 E:GLU177 4.4 9.7 1.0
CB E:ASP185 4.4 9.2 1.0
O E:LYS182 4.5 16.8 1.0
CA E:ASN183 4.5 16.0 1.0
CG E:ASP191 4.6 12.1 1.0
CA E:ASP185 4.9 8.9 1.0
O E:PRO184 5.0 12.3 1.0

Calcium binding site 4 out of 4 in 5l8p

Go back to Calcium Binding Sites List in 5l8p
Calcium binding site 4 out of 4 in the Thermolysin in Complex with JC114 (PEG400 Cryo Protectant)


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 JC114 (PEG400 Cryo Protectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:12.0
occ:1.00
O E:ILE197 2.3 17.2 1.0
O E:TYR193 2.4 11.5 1.0
OD1 E:ASP200 2.4 12.8 1.0
OG1 E:THR194 2.4 11.6 1.0
O E:THR194 2.4 13.1 1.0
O E:HOH599 2.4 14.2 1.0
O E:HOH775 2.4 18.4 1.0
C E:THR194 3.2 12.4 1.0
C E:TYR193 3.4 11.0 1.0
CG E:ASP200 3.4 12.4 1.0
CB E:THR194 3.4 11.9 1.0
HB E:ILE197 3.5 23.5 1.0
C E:ILE197 3.5 18.2 1.0
H E:ILE197 3.6 21.4 1.0
CA E:THR194 3.6 11.4 1.0
HB E:THR194 3.7 14.3 1.0
H E:ASP200 3.8 17.8 1.0
OD2 E:ASP200 3.8 12.9 1.0
N E:THR194 3.9 11.2 1.0
HB3 E:TYR193 4.0 12.8 1.0
HA E:SER198 4.0 25.7 1.0
HD2 E:TYR193 4.0 15.3 1.0
CA E:ILE197 4.2 18.1 1.0
CB E:ILE197 4.2 19.6 1.0
HA E:PRO195 4.2 18.7 1.0
N E:PRO195 4.2 14.0 1.0
N E:ILE197 4.3 17.9 1.0
HG22 E:ILE197 4.3 23.6 1.0
O E:HOH740 4.4 38.1 1.0
O E:ASP200 4.5 12.4 1.0
O E:HOH563 4.5 39.2 1.0
N E:SER198 4.5 19.4 1.0
O E:HOH597 4.5 40.9 1.0
CA E:TYR193 4.6 10.2 1.0
HA E:THR194 4.6 13.7 1.0
N E:ASP200 4.6 14.8 1.0
O E:HOH792 4.6 24.8 1.0
CA E:SER198 4.6 21.4 1.0
CA E:PRO195 4.6 15.6 1.0
CB E:TYR193 4.7 10.7 1.0
CD2 E:TYR193 4.7 12.7 1.0
O E:GLU190 4.7 10.7 1.0
H E:THR194 4.7 13.4 1.0
CB E:ASP200 4.7 13.0 1.0
CG2 E:THR194 4.7 12.8 1.0
CG2 E:ILE197 4.8 19.7 1.0
C E:ASP200 4.8 11.5 1.0
HG23 E:THR194 4.9 15.4 1.0
H E:TYR193 4.9 11.4 1.0
N E:GLY199 4.9 19.3 1.0
C E:PRO195 4.9 17.2 1.0
CA E:ASP200 4.9 13.3 1.0
C E:SER198 5.0 21.2 1.0
HG21 E:THR194 5.0 15.4 1.0

Reference:

S.G.Krimmer, J.Cramer, M.Betz, V.Fridh, R.Karlsson, A.Heine, G.Klebe. Rational Design of Thermodynamic and Kinetic Binding Profiles By Optimizing Surface Water Networks Coating Protein-Bound Ligands. J. Med. Chem. V. 59 10530 2016.
ISSN: ISSN 1520-4804
PubMed: 27933956
DOI: 10.1021/ACS.JMEDCHEM.6B00998
Page generated: Wed Jul 9 07:45:13 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy