Zinc in PDB 1b3d: Stromelysin-1

All present enzymatic activity of Stromelysin-1:
3.4.24.17;

The structure of Stromelysin-1, PDB code: 1b3d was solved by L.Chen, T.J.Rydel, C.M.Dunaway, S.Pikul, K.M.Dunham, F.Gu, B.L.Barnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.900, 78.800, 105.400, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 26.3

The structure of Stromelysin-1 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Stromelysin-1 (pdb code 1b3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Stromelysin-1, PDB code: 1b3d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Stromelysin-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Stromelysin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.7 occ:1.00 O B:THR255 2.0 10.1 1.0 NE2 A:HIS201 2.0 2.0 1.0 NE2 A:HIS205 2.1 8.5 1.0 NE2 A:HIS211 2.2 10.9 1.0 C B:THR255 2.7 7.0 1.0 OXT B:THR255 2.7 7.4 1.0 CD2 A:HIS201 2.9 2.0 1.0 CE1 A:HIS205 3.0 2.1 1.0 CE1 A:HIS201 3.1 2.0 1.0 CE1 A:HIS211 3.1 8.8 1.0 CD2 A:HIS211 3.2 8.6 1.0 CD2 A:HIS205 3.2 8.4 1.0 O A:HOH339 3.9 22.8 1.0 CG A:HIS201 4.1 2.0 1.0 CA B:THR255 4.1 10.2 1.0 ND1 A:HIS201 4.1 2.9 1.0 ND1 A:HIS205 4.2 5.9 1.0 ND1 A:HIS211 4.2 9.8 1.0 CG A:HIS211 4.3 6.0 1.0 CG A:HIS205 4.3 6.8 1.0 N B:THR255 4.4 13.0 1.0 CG B:GLU254 4.4 17.8 1.0 C B:GLU254 4.5 12.3 1.0 O B:GLU254 4.6 14.0 1.0 OG1 B:THR255 4.9 13.8 1.0 OE2 A:GLU202 4.9 11.2 1.0 CB B:GLU254 4.9 11.6 1.0

Zinc binding site 2 out of 4 in the Stromelysin-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Stromelysin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.7 occ:1.00 OD2 A:ASP153 2.0 6.8 1.0 ND1 A:HIS179 2.1 2.0 1.0 NE2 A:HIS151 2.2 5.6 1.0 NE2 A:HIS166 2.2 2.0 1.0 CG A:ASP153 2.8 4.3 1.0 CD2 A:HIS151 2.9 3.9 1.0 OD1 A:ASP153 2.9 7.6 1.0 CE1 A:HIS179 3.0 2.0 1.0 CE1 A:HIS166 3.1 2.1 1.0 CG A:HIS179 3.1 2.0 1.0 CD2 A:HIS166 3.3 2.7 1.0 CE1 A:HIS151 3.3 2.0 1.0 CB A:HIS179 3.6 3.6 1.0 NE2 A:HIS179 4.1 2.4 1.0 CG A:HIS151 4.1 8.6 1.0 CD2 A:HIS179 4.2 2.0 1.0 O A:TYR155 4.2 11.0 1.0 ND1 A:HIS151 4.3 5.4 1.0 ND1 A:HIS166 4.3 4.1 1.0 OH A:TYR168 4.3 4.0 1.0 CB A:ASP153 4.3 9.8 1.0 CG A:HIS166 4.4 2.0 1.0 CE1 A:TYR168 4.5 2.0 1.0 O A:HOH313 4.8 9.2 1.0 CZ A:PHE157 4.9 2.8 1.0 CZ A:TYR168 4.9 6.2 1.0 CE2 A:PHE157 5.0 3.3 1.0

Zinc binding site 3 out of 4 in the Stromelysin-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Stromelysin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.9 occ:1.00 OA B:S27401 1.9 20.7 1.0 OB B:S27401 2.0 28.0 1.0 NE2 B:HIS201 2.2 3.3 1.0 NE2 B:HIS211 2.2 11.6 1.0 NE2 B:HIS205 2.3 2.5 1.0 NA B:S27401 2.7 18.1 1.0 C B:S27401 2.7 21.7 1.0 CD2 B:HIS201 2.8 2.0 1.0 CD2 B:HIS205 3.1 6.2 1.0 CD2 B:HIS211 3.1 11.1 1.0 CE1 B:HIS211 3.2 14.5 1.0 CE1 B:HIS205 3.4 3.4 1.0 CE1 B:HIS201 3.4 2.0 1.0 CG B:HIS201 4.1 2.0 1.0 OE2 B:GLU202 4.2 12.8 1.0 C18 B:S27401 4.2 19.0 1.0 CG B:HIS211 4.2 8.0 1.0 ND1 B:HIS211 4.3 11.6 1.0 CG B:HIS205 4.3 7.5 1.0 ND1 B:HIS201 4.3 2.3 1.0 ND1 B:HIS205 4.4 6.3 1.0 C7 B:S27401 4.7 16.5 1.0 C1 B:S27401 4.7 12.8 1.0 C2 B:S27401 4.7 10.9 1.0 OE1 B:GLU202 4.8 11.7 1.0 C8 B:S27401 4.8 13.6 1.0 CD B:GLU202 4.9 10.8 1.0 O B:HOH422 5.0 22.9 1.0

Zinc binding site 4 out of 4 in the Stromelysin-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Stromelysin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:11.1 occ:1.00 OD2 B:ASP153 1.9 6.8 1.0 ND1 B:HIS179 2.0 4.2 1.0 NE2 B:HIS166 2.1 5.5 1.0 NE2 B:HIS151 2.2 5.1 1.0 CE1 B:HIS179 2.8 2.4 1.0 CG B:ASP153 2.8 5.8 1.0 CE1 B:HIS166 3.0 6.5 1.0 CG B:HIS179 3.0 2.8 1.0 CD2 B:HIS166 3.1 5.3 1.0 CD2 B:HIS151 3.2 7.4 1.0 OD1 B:ASP153 3.2 6.1 1.0 CE1 B:HIS151 3.2 5.4 1.0 CB B:HIS179 3.5 2.0 1.0 NE2 B:HIS179 4.0 2.0 1.0 CD2 B:HIS179 4.1 2.0 1.0 CB B:ASP153 4.1 3.0 1.0 OH B:TYR168 4.1 9.9 1.0 ND1 B:HIS166 4.1 5.8 1.0 O B:TYR155 4.2 8.9 1.0 CG B:HIS166 4.2 4.6 1.0 ND1 B:HIS151 4.3 4.4 1.0 CG B:HIS151 4.3 7.0 1.0 CE1 B:TYR168 4.6 6.1 1.0 CE2 B:PHE157 4.6 2.0 1.0 CZ B:PHE157 4.7 2.0 1.0 CZ B:TYR168 4.9 9.0 1.0 CA B:HIS179 5.0 5.7 1.0

L.Chen, T.J.Rydel, F.Gu, C.M.Dunaway, S.Pikul, K.M.Dunham, B.L.Barnett. Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution: Inhibitor-Induced Conformational Changes. J.Mol.Biol. V. 293 545 1999.
ISSN: ISSN 0022-2836
PubMed: 10543949
DOI: 10.1006/JMBI.1999.3147