Calcium 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:

Zinc	(Zn)	2 atoms
Arsenic	(As)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase, PDB code: 7bb8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca502 b:22.6 occ:0.62 O A:HOH783 2.3 35.9 1.0 OE2 A:GLU256 2.4 31.3 1.0 OD1 A:ASN252 2.4 26.4 1.0 O A:ASP342 2.4 26.4 1.0 O A:ILE340 2.4 23.4 1.0 O A:HOH676 2.5 27.9 1.0 OE1 A:GLU256 2.8 39.2 1.0 CD A:GLU256 2.9 31.0 1.0 CG A:ASN252 3.4 25.6 1.0 C A:ASP342 3.5 27.4 1.0 HD21 A:ASN252 3.5 32.6 1.0 C A:ILE340 3.5 23.1 1.0 HG3 A:GLU251 3.7 33.9 1.0 HA A:ASN341 3.8 31.0 1.0 HA A:PRO343 3.9 32.7 1.0 ND2 A:ASN252 3.9 27.1 1.0 N A:ASP342 3.9 25.2 1.0 C A:ASN341 3.9 25.3 1.0 H A:ASP342 4.0 30.4 1.0 O A:HOH603 4.2 34.3 1.0 HG2 A:GLU251 4.2 33.9 1.0 CA A:ASN341 4.2 25.7 1.0 O A:LEU339 4.2 24.8 1.0 HA A:ILE340 4.3 26.4 1.0 N A:ASN341 4.3 23.9 1.0 CA A:ASP342 4.3 24.5 1.0 HA A:ASN252 4.3 27.1 1.0 O A:ASN341 4.3 26.1 1.0 HB3 A:ASP342 4.4 31.8 1.0 CG A:GLU256 4.4 32.0 1.0 CG A:GLU251 4.4 28.1 1.0 O A:GLY344 4.4 26.6 1.0 N A:PRO343 4.4 25.9 1.0 CA A:PRO343 4.5 27.1 1.0 CA A:ILE340 4.5 21.9 1.0 O A:HOH851 4.6 37.3 1.0 OE2 A:GLU251 4.6 33.7 1.0 HG3 A:GLU256 4.6 38.6 1.0 HD22 A:ASN252 4.7 32.6 1.0 CB A:ASN252 4.7 23.4 1.0 C A:PRO343 4.8 27.1 1.0 HG23 A:ILE340 4.8 29.7 1.0 O A:HOH657 4.8 30.8 1.0 HG2 A:GLU256 4.8 38.6 1.0 CB A:ASP342 4.9 26.4 1.0 CA A:ASN252 5.0 22.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca503 b:21.0 occ:0.89 OE2 A:GLU213 2.3 23.9 1.0 O A:LYS175 2.4 21.5 1.0 OD1 A:ASP171 2.4 23.4 1.0 OD1 A:ASN173 2.4 22.3 1.0 OD1 A:ASP169 2.4 22.2 1.0 O A:HOH680 2.5 23.0 1.0 O A:HOH655 2.5 22.8 1.0 H A:LYS175 3.1 26.6 1.0 HA A:ASP169 3.2 26.1 1.0 HB2 A:GLU213 3.4 24.5 1.0 CG A:ASP171 3.4 24.8 1.0 CG A:ASN173 3.5 24.6 1.0 CG A:ASP169 3.5 25.0 1.0 CD A:GLU213 3.5 24.5 1.0 H A:ASN173 3.5 28.0 1.0 C A:LYS175 3.5 23.1 1.0 H A:GLU213 3.7 28.7 1.0 OD2 A:ASP171 3.7 26.4 1.0 HD21 A:ASN173 3.8 38.4 1.0 N A:LYS175 3.8 22.0 1.0 H A:ASP171 3.9 25.7 1.0 HA A:VAL176 4.0 26.1 1.0 CA A:ASP169 4.0 21.7 1.0 ND2 A:ASN173 4.0 31.9 1.0 H A:GLY174 4.0 26.8 1.0 CB A:GLU213 4.2 20.3 1.0 CG A:GLU213 4.2 23.6 1.0 HG2 A:GLU213 4.2 28.5 1.0 CB A:ASP169 4.3 23.6 1.0 CA A:LYS175 4.3 24.6 1.0 N A:ASN173 4.4 23.2 1.0 N A:GLY174 4.4 22.2 1.0 OD2 A:ASP169 4.4 23.7 1.0 OE1 A:GLU213 4.4 24.4 1.0 N A:GLU213 4.5 23.8 1.0 HB2 A:ASP169 4.5 28.4 1.0 HG12 A:VAL176 4.5 37.9 1.0 C A:ASP169 4.5 23.1 1.0 O A:SER168 4.5 22.1 1.0 N A:VAL176 4.6 21.8 1.0 O A:HOH761 4.6 30.6 1.0 H A:VAL170 4.6 26.9 1.0 H A:ASN172 4.6 24.6 1.0 CB A:ASN173 4.6 23.7 1.0 N A:ASP171 4.7 21.3 1.0 C A:GLY174 4.7 24.4 1.0 C A:ASN173 4.8 24.2 1.0 CB A:ASP171 4.8 23.0 1.0 CA A:VAL176 4.8 21.7 1.0 N A:VAL170 4.8 22.3 1.0 O A:HOH905 4.8 32.0 1.0 CA A:ASN173 4.8 24.4 1.0 HB3 A:GLU213 4.8 24.5 1.0 N A:ASN172 4.9 20.4 1.0 HD22 A:ASN173 4.9 38.4 1.0 HB2 A:LYS175 4.9 29.9 1.0 HB2 A:SER212 4.9 31.9 1.0 HA A:SER212 4.9 25.7 1.0 HB3 A:ASN173 4.9 28.6 1.0 CA A:GLU213 5.0 21.7 1.0 HA A:LYS175 5.0 29.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:21.6 occ:0.91 O A:TYR220 2.3 22.8 1.0 OD1 A:ASP218 2.3 22.1 1.0 OD1 A:ASP182 2.3 22.8 1.0 O A:ILE183 2.4 22.7 1.0 O A:HOH635 2.4 22.3 1.0 O A:HOH660 2.4 23.7 1.0 CG A:ASP218 3.2 21.9 1.0 H A:ILE183 3.3 25.0 1.0 N A:ILE183 3.4 20.7 1.0 C A:ILE183 3.4 22.8 1.0 C A:TYR220 3.5 21.3 1.0 OD2 A:ASP218 3.5 25.0 1.0 CG A:ASP182 3.5 28.0 1.0 HB A:ILE183 3.6 26.9 1.0 HA A:ASP182 3.6 27.2 1.0 HD3 A:PRO221 3.6 30.9 1.0 HD2 A:PRO221 3.7 30.9 1.0 C A:ASP182 3.8 22.4 1.0 CA A:ILE183 3.8 20.1 1.0 CD A:PRO221 4.0 25.7 1.0 H A:TYR220 4.0 30.9 1.0 CA A:ASP182 4.1 22.5 1.0 HD1 A:TYR220 4.2 37.7 1.0 N A:PRO221 4.2 23.0 1.0 CB A:ILE183 4.2 22.3 1.0 OD2 A:ASP182 4.3 24.0 1.0 OD2 A:ASP185 4.4 25.9 1.0 CB A:ASP182 4.4 24.2 1.0 HB3 A:TYR220 4.4 31.1 1.0 N A:TYR220 4.5 25.6 1.0 OD1 A:ASP185 4.5 26.5 1.0 CB A:ASP218 4.5 20.6 1.0 O A:ASP182 4.5 23.1 1.0 CA A:TYR220 4.5 23.8 1.0 HB2 A:ASP218 4.5 24.9 1.0 N A:LYS184 4.6 24.6 1.0 HA A:LYS184 4.6 26.3 1.0 CG A:ASP185 4.7 22.9 1.0 HB2 A:TYR193 4.7 27.2 1.0 O A:HOH781 4.7 27.7 1.0 HG22 A:ILE183 4.7 30.3 1.0 H A:THR219 4.7 25.7 1.0 HA A:ILE183 4.8 24.3 1.0 O A:ILE194 4.8 24.5 1.0 O A:HOH626 4.8 29.3 1.0 CB A:TYR220 4.9 25.8 1.0 CD1 A:TYR220 5.0 31.3 1.0 H A:ASP185 5.0 29.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:22.8 occ:0.96 OE2 B:GLU213 2.3 24.4 1.0 O B:LYS175 2.4 22.9 1.0 O B:HOH693 2.4 25.4 1.0 OD1 B:ASP169 2.4 23.8 1.0 OD1 B:ASP171 2.4 23.1 1.0 OD1 B:ASN173 2.4 24.0 1.0 O B:HOH750 2.4 24.4 1.0 HA B:ASP169 3.1 26.8 1.0 H B:LYS175 3.2 28.2 1.0 HB2 B:GLU213 3.4 27.9 1.0 CG B:ASP171 3.5 26.9 1.0 CG B:ASP169 3.5 27.0 1.0 CG B:ASN173 3.5 28.9 1.0 CD B:GLU213 3.5 23.4 1.0 C B:LYS175 3.6 25.2 1.0 H B:ASN173 3.6 28.4 1.0 H B:GLU213 3.7 30.0 1.0 OD2 B:ASP171 3.8 25.9 1.0 HD21 B:ASN173 3.8 46.5 1.0 H B:ASP171 3.9 27.7 1.0 N B:LYS175 3.9 23.4 1.0 CA B:ASP169 4.0 22.2 1.0 HA B:VAL176 4.0 28.1 1.0 H B:GLY174 4.1 32.2 1.0 ND2 B:ASN173 4.1 38.6 1.0 CB B:ASP169 4.2 24.8 1.0 CB B:GLU213 4.2 23.2 1.0 CG B:GLU213 4.3 22.6 1.0 HG2 B:GLU213 4.3 27.3 1.0 CA B:LYS175 4.4 24.8 1.0 OD2 B:ASP169 4.4 25.7 1.0 N B:ASN173 4.4 23.5 1.0 N B:GLY174 4.4 26.7 1.0 OE1 B:GLU213 4.5 25.9 1.0 HB2 B:ASP169 4.5 29.9 1.0 H B:ASN172 4.5 32.1 1.0 C B:ASP169 4.5 21.4 1.0 HG12 B:VAL176 4.5 39.3 1.0 N B:GLU213 4.5 24.9 1.0 O B:SER168 4.6 23.3 1.0 H B:VAL170 4.6 29.9 1.0 N B:VAL176 4.6 24.8 1.0 O B:HOH711 4.6 33.1 1.0 N B:ASP171 4.6 23.0 1.0 CB B:ASN173 4.7 26.6 1.0 O B:HOH919 4.7 32.0 1.0 N B:VAL170 4.8 24.8 1.0 CA B:VAL176 4.8 23.3 1.0 C B:ASN173 4.8 24.4 1.0 CB B:ASP171 4.8 25.6 1.0 C B:GLY174 4.8 31.8 1.0 N B:ASN172 4.8 26.6 1.0 CA B:ASN173 4.9 24.2 1.0 HB2 B:LYS175 4.9 32.4 1.0 HA B:SER212 4.9 26.3 1.0 HB3 B:GLU213 4.9 27.9 1.0 HB2 B:SER212 4.9 27.9 1.0 HD22 B:ASN173 4.9 46.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:23.1 occ:0.64 O B:ASP342 2.3 25.7 1.0 OD1 B:ASN252 2.4 29.7 1.0 OE2 B:GLU256 2.4 30.5 1.0 O B:ILE340 2.4 25.1 1.0 O B:HOH733 2.4 30.6 1.0 O B:HOH707 2.5 27.7 1.0 OE1 B:GLU256 2.9 40.1 1.0 CD B:GLU256 3.0 30.3 1.0 CG B:ASN252 3.4 26.6 1.0 HD21 B:ASN252 3.5 32.9 1.0 C B:ASP342 3.5 26.2 1.0 C B:ILE340 3.5 22.7 1.0 HG3 B:GLU251 3.7 33.1 1.0 HA B:PRO343 3.8 34.8 1.0 HA B:ASN341 3.8 26.7 1.0 ND2 B:ASN252 3.8 27.3 1.0 C B:ASN341 3.9 25.8 1.0 N B:ASP342 3.9 23.8 1.0 HG2 B:GLU251 4.1 33.1 1.0 H B:ASP342 4.1 28.7 1.0 CA B:ASN341 4.2 22.2 1.0 O B:HOH618 4.2 42.6 1.0 O B:ASN341 4.2 24.8 1.0 N B:ASN341 4.2 22.4 1.0 HA B:ILE340 4.2 26.8 1.0 CA B:ASP342 4.3 25.8 1.0 O B:LEU339 4.3 23.6 1.0 CG B:GLU251 4.4 27.5 1.0 HA B:ASN252 4.4 29.1 1.0 HB3 B:ASP342 4.4 29.3 1.0 N B:PRO343 4.4 24.8 1.0 CA B:PRO343 4.4 28.8 1.0 O B:GLY344 4.4 28.7 1.0 CG B:GLU256 4.5 30.6 1.0 O B:HOH926 4.5 37.5 1.0 OE2 B:GLU251 4.5 33.8 1.0 CA B:ILE340 4.5 22.2 1.0 HG3 B:GLU256 4.7 36.9 1.0 HD22 B:ASN252 4.7 32.9 1.0 CB B:ASN252 4.7 21.8 1.0 C B:PRO343 4.8 26.9 1.0 CB B:ASP342 4.9 24.3 1.0 HG2 B:GLU256 4.9 36.9 1.0 HG23 B:ILE340 5.0 30.8 1.0 CD B:GLU251 5.0 32.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Lugdulysin, A Staphylococcus Lugdunensis M30 Zinc Metallopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:29.9 occ:1.00 OD1 B:ASP182 2.2 29.7 1.0 OD1 B:ASP218 2.3 25.5 1.0 O B:TYR220 2.3 25.9 1.0 O B:ILE183 2.4 32.4 1.0 O B:HOH660 2.4 31.4 1.0 O B:HOH638 2.5 31.4 1.0 CG B:ASP218 3.2 22.1 1.0 H B:ILE183 3.3 33.8 1.0 N B:ILE183 3.4 28.1 1.0 C B:ILE183 3.4 34.7 1.0 C B:TYR220 3.5 25.0 1.0 OD2 B:ASP218 3.5 29.8 1.0 CG B:ASP182 3.5 28.4 1.0 HB B:ILE183 3.5 34.8 1.0 HD2 B:PRO221 3.6 39.4 1.0 HA B:ASP182 3.6 34.4 1.0 C B:ASP182 3.8 24.3 1.0 HD3 B:PRO221 3.8 39.4 1.0 CA B:ILE183 3.9 27.8 1.0 H B:TYR220 4.0 36.9 1.0 CD B:PRO221 4.0 32.7 1.0 CA B:ASP182 4.1 28.6 1.0 CB B:ILE183 4.2 28.9 1.0 N B:PRO221 4.2 29.1 1.0 HD2 B:TYR220 4.3 36.8 1.0 OD2 B:ASP182 4.3 31.2 1.0 O B:HOH944 4.4 38.2 1.0 CB B:ASP182 4.4 27.8 1.0 OD2 B:ASP185 4.4 38.5 1.0 OD1 B:ASP185 4.5 37.4 1.0 N B:TYR220 4.5 30.6 1.0 HB3 B:TYR220 4.5 37.3 1.0 CB B:ASP218 4.5 27.9 1.0 CA B:TYR220 4.5 29.4 1.0 O B:ASP182 4.5 27.0 1.0 HB2 B:ASP218 4.5 33.6 1.0 O B:HOH782 4.6 39.7 1.0 N B:LYS184 4.6 29.7 1.0 HA B:LYS184 4.6 42.8 1.0 CG B:ASP185 4.7 30.9 1.0 H B:THR219 4.7 29.3 1.0 HG22 B:ILE183 4.8 41.0 1.0 HA B:ILE183 4.8 33.4 1.0 HB2 B:TYR193 4.8 38.0 1.0 O B:HOH635 4.8 37.5 1.0 H B:ASP185 4.9 48.1 1.0 CB B:TYR220 5.0 31.0 1.0 HA B:ASP218 5.0 33.5 1.0

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