Calcium in PDB 7bb9: Crystal Structure of Lugdulysin E242Q Y315F Mutant

The structure of Crystal Structure of Lugdulysin E242Q Y315F Mutant, PDB code: 7bb9 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)	42.08 / 1.97
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.25, 96.25, 84.17, 90, 90, 90
R / Rfree (%)	19 / 24

The structure of Crystal Structure of Lugdulysin E242Q Y315F Mutant also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Lugdulysin E242Q Y315F Mutant (pdb code 7bb9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Lugdulysin E242Q Y315F Mutant, PDB code: 7bb9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Lugdulysin E242Q Y315F Mutant


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 E242Q Y315F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:20.1 occ:1.00 OD1 A:ASP182 2.3 21.6 1.0 O A:ILE183 2.3 13.7 1.0 O A:TYR220 2.4 14.7 1.0 OD1 A:ASP218 2.4 17.1 1.0 O A:HOH655 2.4 17.1 1.0 O A:HOH657 2.6 16.9 1.0 CG A:ASP218 3.2 19.6 1.0 OD2 A:ASP218 3.4 20.1 1.0 C A:ILE183 3.4 16.5 1.0 N A:ILE183 3.5 16.9 1.0 C A:TYR220 3.5 21.1 1.0 CG A:ASP182 3.6 23.6 1.0 CA A:ILE183 3.9 11.9 1.0 C A:ASP182 3.9 20.4 1.0 CD A:PRO221 4.0 13.3 1.0 N A:PRO221 4.2 17.2 1.0 CB A:ILE183 4.2 19.4 1.0 CA A:ASP182 4.2 17.6 1.0 OD2 A:ASP185 4.3 22.0 1.0 OD2 A:ASP182 4.4 24.8 1.0 OD1 A:ASP185 4.4 19.3 1.0 CB A:ASP182 4.5 21.3 1.0 CB A:ASP218 4.5 15.5 1.0 CG A:ASP185 4.6 18.9 1.0 N A:LYS184 4.6 13.7 1.0 O A:ASP182 4.6 27.4 1.0 CA A:TYR220 4.6 22.0 1.0 N A:TYR220 4.6 17.2 1.0 O A:HOH813 4.7 31.0 1.0 O A:ILE194 4.8 17.5 1.0 O A:HOH797 4.8 32.9 1.0 CA A:LYS184 5.0 18.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Lugdulysin E242Q Y315F Mutant


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 E242Q Y315F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:20.3 occ:1.00 OE1 A:GLU213 2.3 16.3 1.0 OD1 A:ASP169 2.4 17.0 1.0 OD1 A:ASP171 2.4 28.9 1.0 O A:LYS175 2.4 22.1 1.0 OD1 A:ASN173 2.4 24.0 1.0 O A:HOH698 2.5 16.4 1.0 O A:HOH659 2.5 18.6 1.0 CG A:ASP171 3.4 24.0 1.0 CD A:GLU213 3.5 15.0 1.0 CG A:ASP169 3.5 19.8 1.0 CG A:ASN173 3.5 24.9 1.0 C A:LYS175 3.6 21.4 1.0 OD2 A:ASP171 3.7 22.6 1.0 N A:LYS175 3.8 21.5 1.0 CA A:ASP169 3.9 20.4 1.0 CB A:GLU213 4.2 13.4 1.0 CG A:GLU213 4.2 16.9 1.0 ND2 A:ASN173 4.2 22.5 1.0 CB A:ASP169 4.2 18.1 1.0 N A:ASN173 4.3 18.2 1.0 CA A:LYS175 4.3 26.3 1.0 N A:GLY174 4.4 27.2 1.0 O A:HOH743 4.4 24.3 1.0 OE2 A:GLU213 4.4 22.5 1.0 OD2 A:ASP169 4.4 18.3 1.0 C A:ASP169 4.5 21.8 1.0 N A:GLU213 4.5 17.9 1.0 O A:SER168 4.5 17.2 1.0 N A:ASP171 4.6 17.1 1.0 N A:VAL176 4.6 17.8 1.0 CB A:ASN173 4.6 20.5 1.0 C A:ASN173 4.7 27.1 1.0 C A:GLY174 4.7 23.7 1.0 CA A:ASN173 4.7 26.0 1.0 CB A:ASP171 4.7 17.8 1.0 N A:VAL170 4.7 21.4 1.0 N A:ASN172 4.8 27.4 1.0 CA A:VAL176 4.8 16.6 1.0 O A:HOH773 4.8 39.8 1.0 CA A:GLY174 5.0 23.0 1.0 CA A:GLU213 5.0 19.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Lugdulysin E242Q Y315F Mutant


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 E242Q Y315F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:23.4 occ:1.00 O A:ASP342 2.2 24.5 1.0 OD1 A:ASN252 2.2 25.5 1.0 O A:ILE340 2.3 25.0 1.0 O A:HOH636 2.4 24.7 1.0 OE1 A:GLU256 2.4 30.8 1.0 O A:HOH766 2.5 20.0 1.0 OE2 A:GLU256 2.6 30.4 1.0 CD A:GLU256 2.8 30.7 1.0 C A:ASP342 3.3 25.3 1.0 CG A:ASN252 3.4 19.6 1.0 C A:ILE340 3.5 20.4 1.0 N A:ASP342 3.9 18.9 1.0 C A:ASN341 4.0 25.5 1.0 ND2 A:ASN252 4.1 17.2 1.0 CA A:PRO343 4.2 25.5 1.0 CA A:ASP342 4.2 24.0 1.0 N A:PRO343 4.2 22.3 1.0 O A:ASN341 4.3 25.9 1.0 O A:LEU339 4.3 18.1 1.0 CG A:GLU256 4.3 17.9 1.0 N A:ASN341 4.4 24.9 1.0 CA A:ILE340 4.4 21.1 1.0 CA A:ASN341 4.4 28.0 1.0 O A:HOH758 4.6 27.7 1.0 CB A:ASN252 4.6 15.2 1.0 O A:GLY344 4.7 30.7 1.0 C A:PRO343 4.7 24.9 1.0 CA A:ASN252 4.8 16.8 1.0 CB A:ASP342 4.9 16.4 1.0

M.Ruff, G.Prevost, K.Prola, N.Levy. Crystal Structure of Lugdulysin E242Q Y315F Mutant To Be Published.