Calcium in PDB 1lnf: A Structural Analysis of Metal Substitutions in Thermolysin

All present enzymatic activity of A Structural Analysis of Metal Substitutions in Thermolysin:
3.4.24.27;

The structure of A Structural Analysis of Metal Substitutions in Thermolysin, PDB code: 1lnf was solved by D.R.Holland, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.850, 93.850, 131.400, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of A Structural Analysis of Metal Substitutions in Thermolysin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the A Structural Analysis of Metal Substitutions in Thermolysin (pdb code 1lnf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Structural Analysis of Metal Substitutions in Thermolysin, PDB code: 1lnf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A Structural Analysis of Metal Substitutions in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Structural Analysis of Metal Substitutions in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca901 b:11.8 occ:1.00 O E:GLU187 2.2 11.1 1.0 OD2 E:ASP138 2.3 14.6 1.0 OD1 E:ASP185 2.4 12.2 1.0 OE1 E:GLU190 2.4 11.8 1.0 OE1 E:GLU177 2.5 14.0 1.0 OE2 E:GLU190 2.5 15.4 1.0 O E:HOH925 2.6 13.2 1.0 CD E:GLU190 2.8 12.5 1.0 OE2 E:GLU177 2.8 16.2 1.0 CD E:GLU177 3.0 13.1 1.0 CG E:ASP138 3.3 17.9 1.0 C E:GLU187 3.3 15.4 1.0 CG E:ASP185 3.4 16.0 1.0 OD2 E:ASP185 3.7 14.3 1.0 CA E:CA902 3.8 14.1 1.0 CB E:ASP138 4.1 10.2 1.0 N E:GLU187 4.2 16.6 1.0 N E:ILE188 4.2 12.0 1.0 CA E:GLU187 4.2 15.7 1.0 O E:ASP185 4.3 17.1 1.0 CG E:GLU190 4.3 9.4 1.0 OD1 E:ASP138 4.3 14.9 1.0 CA E:ILE188 4.3 11.6 1.0 O E:HOH983 4.3 46.4 1.0 N E:GLY189 4.4 17.4 1.0 CG E:GLU177 4.4 13.6 1.0 O E:HOH929 4.5 22.8 1.0 CB E:GLU187 4.5 16.8 1.0 C E:ASP185 4.6 16.1 1.0 CB E:ASP185 4.7 19.6 1.0 C E:ILE188 4.8 14.4 1.0 N E:ASP185 4.8 14.2 1.0 N E:GLU190 4.9 13.3 1.0 O E:HOH905 4.9 17.9 1.0 CB E:GLU177 4.9 11.1 1.0 CA E:ASP185 5.0 11.8 1.0

Calcium binding site 2 out of 4 in the A Structural Analysis of Metal Substitutions in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Structural Analysis of Metal Substitutions in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca902 b:14.1 occ:1.00 OD2 E:ASP185 2.2 14.3 1.0 OE2 E:GLU190 2.3 15.4 1.0 O E:HOH908 2.3 18.1 1.0 OE2 E:GLU177 2.3 16.2 1.0 O E:HOH905 2.4 17.9 1.0 O E:ASN183 2.4 17.5 1.0 CG E:ASP185 3.1 16.0 1.0 CD E:GLU177 3.3 13.1 1.0 CD E:GLU190 3.4 12.5 1.0 C E:ASN183 3.6 18.4 1.0 OD1 E:ASP185 3.7 12.2 1.0 CA E:CA901 3.8 11.8 1.0 CG E:GLU190 3.8 9.4 1.0 OE1 E:GLU177 3.9 14.0 1.0 O E:LYS182 3.9 25.2 1.0 N E:ASP185 4.1 14.2 1.0 CA E:PRO184 4.2 13.6 1.0 CB E:ASN183 4.2 21.4 1.0 C E:PRO184 4.2 33.1 1.0 CG E:GLU177 4.2 13.6 1.0 OD2 E:ASP191 4.2 14.4 1.0 OE1 E:GLU190 4.3 11.8 1.0 OD1 E:ASP191 4.3 18.9 1.0 CB E:ASP185 4.3 19.6 1.0 N E:PRO184 4.4 23.2 1.0 CA E:ASN183 4.6 12.1 1.0 CG E:ASP191 4.7 19.0 1.0 O E:HOH983 4.7 46.4 1.0 O E:PRO184 4.8 24.1 1.0 CA E:ASP185 4.9 11.8 1.0 C E:LYS182 5.0 29.2 1.0

Calcium binding site 3 out of 4 in the A Structural Analysis of Metal Substitutions in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Structural Analysis of Metal Substitutions in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca903 b:13.7 occ:1.00 O E:GLN61 2.2 14.4 1.0 OD1 E:ASP59 2.3 17.2 1.0 O E:HOH911 2.3 15.5 1.0 O E:HOH910 2.3 18.8 1.0 OD1 E:ASP57 2.4 16.8 1.0 O E:HOH966 2.5 14.1 1.0 OD2 E:ASP57 2.6 15.9 1.0 CG E:ASP57 2.8 19.1 1.0 CG E:ASP59 3.3 18.4 1.0 C E:GLN61 3.4 20.1 1.0 OD2 E:ASP59 3.8 20.1 1.0 O E:HOH991 3.9 32.9 1.0 N E:GLN61 4.0 11.8 1.0 CA E:GLN61 4.2 15.2 1.0 N E:ASP59 4.3 14.7 1.0 CB E:ASP57 4.3 8.8 1.0 O E:HOH1046 4.4 47.6 1.0 CB E:GLN61 4.4 11.9 1.0 N E:PHE62 4.5 12.4 1.0 O E:HOH1002 4.5 19.3 1.0 CA E:PHE62 4.6 15.5 1.0 O E:HOH934 4.6 13.2 1.0 CB E:ASP59 4.6 11.4 1.0 OD2 E:ASP67 4.7 14.0 1.0 O E:HOH1061 4.7 62.2 1.0 N E:ALA58 4.7 11.3 1.0 N E:ASN60 4.7 15.3 1.0 CA E:ASP59 4.8 12.8 1.0 C E:ASP59 4.9 19.4 1.0

Calcium binding site 4 out of 4 in the A Structural Analysis of Metal Substitutions in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Structural Analysis of Metal Substitutions in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca904 b:18.6 occ:1.00 OD1 E:ASP200 2.2 17.1 1.0 O E:ILE197 2.2 29.9 1.0 OG1 E:THR194 2.2 13.4 1.0 O E:HOH909 2.3 29.3 1.0 O E:THR194 2.3 15.2 1.0 O E:TYR193 2.4 13.4 1.0 O E:HOH932 2.4 13.0 1.0 C E:THR194 3.1 22.6 1.0 CG E:ASP200 3.2 14.1 1.0 C E:TYR193 3.4 14.1 1.0 CB E:THR194 3.4 15.3 1.0 C E:ILE197 3.4 31.2 1.0 CA E:THR194 3.6 9.9 1.0 OD2 E:ASP200 3.6 17.5 1.0 N E:THR194 3.9 17.3 1.0 N E:ILE197 4.1 48.6 1.0 CA E:ILE197 4.1 21.9 1.0 CB E:ILE197 4.1 32.1 1.0 N E:PRO195 4.1 19.1 1.0 O E:ASP200 4.4 18.9 1.0 N E:SER198 4.5 30.5 1.0 N E:ASP200 4.6 19.2 1.0 CA E:TYR193 4.6 13.5 1.0 CB E:ASP200 4.6 11.5 1.0 CA E:SER198 4.6 35.6 1.0 CG2 E:THR194 4.6 16.0 1.0 CD2 E:TYR193 4.6 19.0 1.0 CA E:PRO195 4.6 21.9 1.0 O E:GLU190 4.6 14.4 1.0 O E:HOH985 4.7 52.1 1.0 C E:ASP200 4.8 12.5 1.0 CB E:TYR193 4.8 17.4 1.0 CG2 E:ILE197 4.9 21.1 1.0 C E:PRO195 4.9 37.8 1.0 CA E:ASP200 4.9 17.6 1.0 C E:SER198 4.9 33.8 1.0

D.R.Holland, A.C.Hausrath, D.Juers, B.W.Matthews. Structural Analysis of Zinc Substitutions in the Active Site of Thermolysin. Protein Sci. V. 4 1955 1995.
ISSN: ISSN 0961-8368
PubMed: 8535232