Cadmium in PDB 1lne: 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: 1lne 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 (°)	93.888, 93.888, 131.164, 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:

Calcium

(Ca)

2 atoms

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

Cadmium 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 Cadmium with other atoms in the Cd 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:Cd900 b:10.9 occ:1.00 OE2 E:GLU166 2.1 16.5 1.0 NE2 E:HIS142 2.2 14.6 1.0 NE2 E:HIS146 2.2 5.9 1.0 O E:HOH1059 2.3 22.8 1.0 O E:HOH907 2.4 39.4 1.0 OE2 E:GLU143 2.6 11.1 0.6 CD E:GLU166 2.9 11.0 1.0 OE1 E:GLU166 3.0 16.4 1.0 CE1 E:HIS146 3.1 10.6 1.0 CD2 E:HIS142 3.1 18.8 1.0 CD2 E:HIS146 3.2 14.7 1.0 CE1 E:HIS142 3.2 22.5 1.0 CD E:GLU143 3.6 78.8 0.6 OH E:TYR157 3.9 23.1 1.0 CA E:VAL1321 3.9 83.0 1.0 OE1 E:GLU143 4.0 14.9 0.6 OE1 E:GLU143 4.1 3.4 0.5 N E:VAL1321 4.1 31.0 1.0 NE2 E:HIS231 4.3 16.6 1.0 O E:HOH1058 4.3 27.6 1.0 ND1 E:HIS146 4.3 14.1 1.0 CG E:HIS146 4.3 8.9 1.0 CG E:HIS142 4.3 16.5 1.0 CG E:GLU166 4.4 8.5 1.0 ND1 E:HIS142 4.4 9.7 1.0 C E:VAL1321 4.4 83.1 1.0 O E:VAL1321 4.5 38.8 1.0 OE2 E:GLU143 4.7 18.6 0.5 CD E:GLU143 4.7 5.5 0.5 CB E:SER169 4.9 9.7 1.0 CZ E:TYR157 4.9 18.8 1.0 CD2 E:HIS231 5.0 16.4 1.0

Cadmium 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 Cadmium with other atoms in the Cd 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:Cd902 b:19.3 occ:1.00 OE2 E:GLU190 2.3 8.7 1.0 OD2 E:ASP185 2.3 15.1 1.0 O E:HOH981 2.3 18.0 1.0 O E:HOH931 2.4 11.8 1.0 O E:ASN183 2.4 17.4 1.0 OE2 E:GLU177 2.5 12.8 1.0 CG E:ASP185 3.2 16.8 1.0 CD E:GLU177 3.3 18.8 1.0 CD E:GLU190 3.3 3.0 1.0 C E:ASN183 3.6 17.5 1.0 OD1 E:ASP185 3.7 10.3 1.0 CG E:GLU190 3.7 4.2 1.0 CA E:CA901 3.8 22.3 1.0 OE1 E:GLU177 3.8 11.8 1.0 O E:LYS182 3.8 28.4 1.0 OD2 E:ASP191 4.1 12.7 1.0 OD1 E:ASP191 4.1 20.6 1.0 N E:ASP185 4.2 12.7 1.0 CA E:PRO184 4.2 13.2 1.0 CB E:ASN183 4.3 15.2 1.0 C E:PRO184 4.3 27.3 1.0 OE1 E:GLU190 4.3 9.0 1.0 CG E:GLU177 4.3 9.0 1.0 N E:PRO184 4.3 24.3 1.0 CG E:ASP191 4.4 17.4 1.0 CB E:ASP185 4.5 13.4 1.0 CA E:ASN183 4.6 12.8 1.0 O E:HOH979 4.6 39.2 1.0 CA E:ASP185 4.9 3.1 1.0 C E:LYS182 4.9 21.5 1.0 O E:PRO184 4.9 20.0 1.0

Cadmium 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 Cadmium with other atoms in the Cd 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:Cd903 b:14.0 occ:1.00 O E:HOH910 2.0 19.9 1.0 OD1 E:ASP57 2.1 11.7 1.0 O E:GLN61 2.3 14.9 1.0 O E:HOH908 2.3 14.0 1.0 OD1 E:ASP59 2.3 18.6 1.0 O E:HOH911 2.4 11.7 1.0 OD2 E:ASP57 2.7 17.7 1.0 CG E:ASP57 2.8 10.1 1.0 CG E:ASP59 3.2 15.5 1.0 C E:GLN61 3.4 17.1 1.0 OD2 E:ASP59 3.6 18.8 1.0 O E:HOH988 3.9 30.7 1.0 N E:GLN61 3.9 11.5 1.0 CA E:GLN61 4.1 6.9 1.0 O E:HOH1038 4.2 40.3 1.0 N E:ASP59 4.2 14.1 1.0 CB E:ASP57 4.3 6.5 1.0 CB E:GLN61 4.3 11.2 1.0 O E:HOH999 4.3 20.2 1.0 O E:HOH934 4.5 14.9 1.0 N E:PHE62 4.5 5.7 1.0 OD2 E:ASP67 4.6 12.4 1.0 CB E:ASP59 4.6 11.4 1.0 N E:ALA58 4.6 10.6 1.0 O E:HOH1053 4.6 54.8 1.0 CA E:PHE62 4.7 8.4 1.0 N E:ASN60 4.7 14.1 1.0 CA E:ASP59 4.8 12.5 1.0 C E:ASP59 4.9 16.2 1.0

Cadmium 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 Cadmium with other atoms in the Cd 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:Cd905 b:31.3 occ:1.00 O E:HOH1055 2.5 27.4 1.0 OD1 E:ASP213 2.5 13.8 1.0 OD2 E:ASP213 2.6 15.8 1.0 O E:HOH1056 2.6 5.5 1.0 O E:HIS231 2.7 12.2 1.0 O E:HOH1057 2.8 42.2 1.0 CG E:ASP213 2.9 10.9 1.0 C E:HIS231 3.7 9.7 1.0 CA E:ILE232 4.3 15.0 1.0 O E:HOH954 4.3 17.2 1.0 CG E:ARG203 4.3 19.8 1.0 CB E:ASP213 4.4 10.7 1.0 N E:ILE232 4.4 10.4 1.0 CB E:HIS231 4.4 7.9 1.0 CD E:ARG203 4.5 14.7 1.0 CG1 E:ILE232 4.7 22.5 1.0 CA E:HIS231 4.7 10.0 1.0 O E:TYR211 4.9 28.5 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