Calcium in PDB 1lnd: 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: 1lnd was solved by D.R.Holland, A.C.Hausrath, D.Juers, 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 (°)	93.852, 93.852, 131.322, 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)

2 atoms

The binding sites of Calcium atom in the A Structural Analysis of Metal Substitutions in Thermolysin (pdb code 1lnd). 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: 1lnd:
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:13.6 occ:1.00 O E:GLU187 2.2 13.3 1.0 OD2 E:ASP138 2.3 15.2 1.0 OD1 E:ASP185 2.4 13.5 1.0 OE1 E:GLU190 2.5 13.0 1.0 OE1 E:GLU177 2.5 14.7 1.0 O E:HOH924 2.5 12.6 1.0 OE2 E:GLU190 2.6 16.1 1.0 CD E:GLU190 2.8 14.1 1.0 OE2 E:GLU177 2.8 14.1 1.0 CD E:GLU177 3.0 15.6 1.0 CG E:ASP138 3.3 18.2 1.0 C E:GLU187 3.3 18.8 1.0 CG E:ASP185 3.4 19.6 1.0 CA E:CA902 3.7 13.8 1.0 OD2 E:ASP185 3.7 18.7 1.0 CB E:ASP138 4.0 9.0 1.0 N E:GLU187 4.1 18.0 1.0 N E:ILE188 4.2 13.9 1.0 O E:ASP185 4.2 19.2 1.0 CA E:GLU187 4.2 17.3 1.0 CA E:ILE188 4.3 11.1 1.0 O E:HOH980 4.3 49.0 1.0 OD1 E:ASP138 4.3 15.0 1.0 CG E:GLU190 4.3 11.1 1.0 N E:GLY189 4.4 18.1 1.0 CG E:GLU177 4.4 11.9 1.0 CB E:GLU187 4.5 18.4 1.0 O E:HOH928 4.6 21.2 1.0 C E:ASP185 4.6 17.9 1.0 CB E:ASP185 4.7 21.2 1.0 C E:ILE188 4.7 18.0 1.0 N E:ASP185 4.7 15.9 1.0 O E:HOH905 4.7 20.8 1.0 N E:GLU190 4.9 14.4 1.0 CB E:GLU177 4.9 10.8 1.0 CA E:ASP185 5.0 10.8 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:13.8 occ:1.00 OE2 E:GLU190 2.1 16.1 1.0 O E:HOH906 2.1 20.5 1.0 OD2 E:ASP185 2.2 18.7 1.0 OE2 E:GLU177 2.2 14.1 1.0 O E:HOH905 2.2 20.8 1.0 O E:ASN183 2.4 25.3 1.0 CG E:ASP185 3.1 19.6 1.0 CD E:GLU177 3.2 15.6 1.0 CD E:GLU190 3.2 14.1 1.0 C E:ASN183 3.6 19.1 1.0 OD1 E:ASP185 3.6 13.5 1.0 CG E:GLU190 3.7 11.1 1.0 CA E:CA901 3.7 13.6 1.0 OE1 E:GLU177 3.7 14.7 1.0 O E:LYS182 3.9 27.4 1.0 N E:ASP185 4.1 15.9 1.0 OD2 E:ASP191 4.1 18.5 1.0 CA E:PRO184 4.2 18.0 1.0 OE1 E:GLU190 4.2 13.0 1.0 CG E:GLU177 4.2 11.9 1.0 OD1 E:ASP191 4.2 21.1 1.0 C E:PRO184 4.2 26.0 1.0 N E:PRO184 4.3 24.3 1.0 CB E:ASP185 4.4 21.2 1.0 CB E:ASN183 4.4 25.2 1.0 CG E:ASP191 4.5 22.3 1.0 O E:HOH980 4.6 49.0 1.0 CA E:ASN183 4.7 18.0 1.0 CA E:ASP185 4.9 10.8 1.0 O E:PRO184 4.9 23.9 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:14.7 occ:1.00 O E:GLN61 2.3 14.6 1.0 O E:HOH909 2.3 16.5 1.0 O E:HOH908 2.3 19.7 1.0 OD1 E:ASP59 2.4 16.5 1.0 OD1 E:ASP57 2.4 15.6 1.0 O E:HOH963 2.5 14.9 1.0 OD2 E:ASP57 2.6 15.9 1.0 CG E:ASP57 2.8 17.1 1.0 CG E:ASP59 3.3 23.3 1.0 C E:GLN61 3.5 27.4 1.0 OD2 E:ASP59 3.7 22.7 1.0 O E:HOH988 3.8 31.7 1.0 N E:GLN61 4.0 13.0 1.0 CA E:GLN61 4.2 14.8 1.0 N E:ASP59 4.3 13.6 1.0 CB E:ASP57 4.3 9.7 1.0 O E:HOH1041 4.4 43.7 1.0 CB E:GLN61 4.4 13.7 1.0 N E:PHE62 4.5 12.5 1.0 O E:HOH999 4.5 17.9 1.0 O E:HOH933 4.6 13.3 1.0 CA E:PHE62 4.6 13.2 1.0 CB E:ASP59 4.6 12.3 1.0 OD2 E:ASP67 4.6 15.2 1.0 N E:ALA58 4.7 12.8 1.0 N E:ASN60 4.7 15.9 1.0 CA E:ASP59 4.8 11.9 1.0 O E:HOH1056 4.8 64.8 1.0 C E:ASP59 4.9 19.1 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:18.8 occ:1.00 O E:HOH907 2.2 30.4 1.0 O E:ILE197 2.2 29.9 1.0 OD1 E:ASP200 2.2 21.6 1.0 OG1 E:THR194 2.3 20.2 1.0 O E:THR194 2.3 20.8 1.0 O E:TYR193 2.4 14.7 1.0 O E:HOH931 2.5 15.9 1.0 C E:THR194 3.1 25.6 1.0 CG E:ASP200 3.3 14.9 1.0 C E:TYR193 3.4 17.6 1.0 C E:ILE197 3.4 39.1 1.0 CB E:THR194 3.4 18.0 1.0 CA E:THR194 3.6 17.7 1.0 OD2 E:ASP200 3.7 23.8 1.0 N E:THR194 3.9 16.1 1.0 N E:PRO195 4.1 22.7 1.0 CA E:ILE197 4.1 24.2 1.0 N E:ILE197 4.1 37.8 1.0 CB E:ILE197 4.1 38.2 1.0 N E:SER198 4.4 32.1 1.0 O E:ASP200 4.4 19.1 1.0 CA E:PRO195 4.5 20.9 1.0 CA E:SER198 4.6 30.6 1.0 N E:ASP200 4.6 21.7 1.0 CA E:TYR193 4.6 15.1 1.0 O E:GLU190 4.6 16.4 1.0 CG2 E:THR194 4.6 16.8 1.0 CB E:ASP200 4.6 15.9 1.0 CD2 E:TYR193 4.7 21.2 1.0 O E:HOH982 4.7 48.0 1.0 CB E:TYR193 4.7 19.4 1.0 C E:PRO195 4.8 39.5 1.0 C E:ASP200 4.8 13.7 1.0 C E:SER198 4.9 38.5 1.0 CG2 E:ILE197 4.9 24.6 1.0 CA E:ASP200 4.9 17.1 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