Zinc in PDB 7bb8: Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase

The structure of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase, PDB code: 7bb8 was solved by M.Ruff, G.Prevost, K.Prola, N.Levy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.77 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.59, 68.19, 122.96, 90, 134.19, 90
R / Rfree (%)	15.6 / 17.6

The structure of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase (pdb code 7bb8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase, PDB code: 7bb8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:23.0 occ:1.00 OE1 A:GLU268 2.0 21.3 1.0 NE2 A:HIS241 2.0 21.5 1.0 NE2 A:HIS245 2.0 19.8 1.0 O1 A:CAC505 2.0 18.7 0.6 CD A:GLU268 2.8 21.2 1.0 CE1 A:HIS245 2.9 20.4 1.0 O2 A:CAC505 3.0 22.9 0.6 CD2 A:HIS241 3.0 21.1 1.0 OE2 A:GLU268 3.0 24.9 1.0 CE1 A:HIS241 3.0 21.0 1.0 AS A:CAC505 3.0 28.4 0.6 CD2 A:HIS245 3.1 21.2 1.0 HE1 A:HIS245 3.1 24.7 1.0 HD2 A:HIS241 3.1 25.5 1.0 HE1 A:HIS241 3.2 25.4 1.0 HD2 A:HIS245 3.3 25.5 1.0 HH A:TYR315 3.4 31.9 1.0 HE1 A:TYR315 3.4 25.6 1.0 H22 A:CAC505 3.9 35.8 0.6 HA A:GLU268 3.9 21.7 1.0 HB2 A:SER271 4.0 24.9 1.0 ND1 A:HIS245 4.1 20.3 1.0 ND1 A:HIS241 4.1 22.8 1.0 CG A:HIS241 4.1 23.7 1.0 C2 A:CAC505 4.1 29.7 0.6 CG A:HIS245 4.2 21.2 1.0 HB3 A:SER271 4.2 24.9 1.0 OH A:TYR315 4.2 26.5 1.0 CE1 A:TYR315 4.3 21.2 1.0 CG A:GLU268 4.3 24.2 1.0 O A:HOH875 4.3 45.3 1.0 OG A:SER271 4.4 20.9 1.0 CB A:SER271 4.4 20.6 1.0 O A:HOH696 4.4 24.2 1.0 HB3 A:GLU268 4.5 24.5 1.0 H21 A:CAC505 4.6 35.8 0.6 C1 A:CAC505 4.6 22.9 0.6 H11 A:CAC505 4.6 27.6 0.6 CA A:GLU268 4.7 18.0 1.0 CB A:GLU268 4.7 20.3 1.0 CZ A:TYR315 4.8 29.9 1.0 HG2 A:GLU268 4.8 29.1 1.0 HG3 A:GLU268 4.8 29.1 1.0 HG A:SER271 4.8 25.2 1.0 HD1 A:HIS245 4.8 24.5 1.0 OE2 A:GLU242 4.8 30.2 1.0 H23 A:CAC505 4.9 35.8 0.6 HD1 A:HIS241 4.9 27.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.6 occ:1.00 OXT B:ACT505 2.0 34.9 1.0 OE1 B:GLU268 2.0 22.0 1.0 NE2 B:HIS245 2.0 22.3 1.0 NE2 B:HIS241 2.0 25.9 1.0 C B:ACT505 2.3 35.8 1.0 H1 B:ACT505 2.4 36.9 1.0 CD B:GLU268 2.7 21.1 1.0 CH3 B:ACT505 2.8 30.6 1.0 OE2 B:GLU268 2.9 23.8 1.0 CE1 B:HIS245 3.0 23.5 1.0 CD2 B:HIS241 3.0 21.7 1.0 CD2 B:HIS245 3.0 23.2 1.0 CE1 B:HIS241 3.1 24.1 1.0 HE1 B:HIS245 3.1 28.3 1.0 H3 B:ACT505 3.1 36.9 1.0 HD2 B:HIS241 3.2 26.2 1.0 O B:ACT505 3.2 35.4 1.0 HD2 B:HIS245 3.3 28.0 1.0 HE1 B:HIS241 3.3 29.0 1.0 HH B:TYR315 3.5 38.3 1.0 HE1 B:TYR315 3.5 35.1 1.0 H2 B:ACT505 3.6 36.9 1.0 OE2 B:GLU242 3.8 31.9 1.0 HA B:GLU268 3.9 20.8 1.0 HB2 B:SER271 4.0 23.0 1.0 ND1 B:HIS245 4.1 21.8 1.0 ND1 B:HIS241 4.2 23.7 1.0 CG B:HIS241 4.2 22.0 1.0 CG B:HIS245 4.2 23.0 1.0 HB3 B:SER271 4.2 23.0 1.0 CG B:GLU268 4.2 21.9 1.0 OH B:TYR315 4.3 31.8 1.0 OG B:SER271 4.3 20.0 1.0 CB B:SER271 4.4 19.1 1.0 CE1 B:TYR315 4.4 29.1 1.0 HB3 B:GLU268 4.6 23.1 1.0 CA B:GLU268 4.7 17.2 1.0 HG3 B:GLU268 4.7 26.4 1.0 HG2 B:GLU268 4.7 26.4 1.0 CD B:GLU242 4.7 33.4 1.0 CB B:GLU268 4.7 19.1 1.0 HG B:SER271 4.8 24.2 1.0 O B:HOH607 4.8 42.6 1.0 HD1 B:HIS245 4.9 26.3 1.0 CZ B:TYR315 4.9 28.8 1.0 O B:HOH613 4.9 41.1 1.0 HD1 B:HIS241 4.9 28.6 1.0 O B:HOH934 5.0 50.9 1.0 OE1 B:GLU242 5.0 29.3 1.0

M.Ruff, G.Prevost, K.Prola, N.Levy. Crystal Structure of Staphylococcus Lugdunensis Protease, Lugdulysin To Be Published.