Calcium in PDB 6r7v: Tannerella Forsythia Promirolysin Mutant E225A

The structure of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v was solved by A.Rodriguez-Banqueri, T.Guevara, M.Ksiazek, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.34 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.330, 67.250, 79.640, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.8

The structure of Tannerella Forsythia Promirolysin Mutant E225A also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Tannerella Forsythia Promirolysin Mutant E225A (pdb code 6r7v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.2 occ:1.00 O A:TRP236 2.3 17.9 1.0 O A:SER242 2.3 20.7 1.0 OD2 A:ASP239 2.4 20.9 1.0 O A:GLY256 2.4 19.2 1.0 O A:HOH562 2.4 19.3 1.0 O A:GLN255 2.4 20.0 1.0 OD1 A:ASP239 2.4 19.0 1.0 CG A:ASP239 2.7 18.8 1.0 C A:GLY256 3.3 20.1 1.0 C A:SER242 3.4 23.8 1.0 C A:TRP236 3.5 18.9 1.0 C A:GLN255 3.5 20.0 1.0 CA A:GLY256 3.6 17.9 1.0 N A:GLY256 4.0 18.9 1.0 N A:SER242 4.2 22.8 1.0 CA A:TRP236 4.2 16.4 1.0 CB A:TRP236 4.2 15.6 1.0 CB A:ASP239 4.3 19.4 1.0 CA A:CYS243 4.3 24.8 1.0 N A:CYS243 4.3 25.0 1.0 C A:GLY241 4.3 23.8 1.0 O A:HOH637 4.4 22.3 1.0 CA A:SER242 4.4 23.2 1.0 N A:GLY237 4.5 17.4 1.0 N A:GLY257 4.6 19.1 1.0 CD1 A:TRP236 4.6 18.5 1.0 O A:GLY245 4.7 23.6 1.0 CA A:GLY237 4.7 17.9 1.0 OD1 A:ASN254 4.7 35.0 1.0 O A:GLY241 4.7 23.2 1.0 CA A:GLN255 4.8 18.2 1.0 N A:GLY245 4.8 22.2 1.0 C A:CYS243 4.8 31.6 1.0 CA A:GLY241 4.8 20.4 1.0 OG A:SER242 4.8 31.8 1.0 SG A:CYS271 4.8 29.2 1.0 CG A:TRP236 4.8 15.5 1.0 N A:GLY241 4.9 21.0 1.0 N A:GLN255 4.9 19.6 1.0 N A:SER244 4.9 26.7 1.0 N A:ASP239 4.9 17.6 1.0

Calcium binding site 2 out of 2 in the Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.8 occ:0.97 O A:HOH642 2.4 28.7 1.0 OD1 A:ASP247 2.4 18.0 1.0 O A:ILE249 2.4 18.1 1.0 O A:THR252 2.5 16.8 1.0 O A:HOH594 2.5 17.7 1.0 OG1 A:THR252 2.5 16.8 1.0 O A:HOH601 2.6 21.3 1.0 O A:HOH722 2.6 22.2 1.0 CG A:ASP247 3.4 17.6 1.0 C A:THR252 3.5 18.6 1.0 C A:ILE249 3.6 18.8 1.0 CB A:THR252 3.6 16.5 1.0 OD2 A:ASP247 3.8 16.0 1.0 CA A:THR252 3.9 14.8 1.0 N A:THR252 4.1 16.7 1.0 N A:ILE249 4.1 17.9 1.0 CA A:ILE249 4.2 15.5 1.0 O A:PRO253 4.4 19.6 1.0 CB A:ILE249 4.4 16.8 1.0 C A:PRO253 4.5 21.1 1.0 O A:HOH672 4.5 30.2 0.5 N A:ASP247 4.6 17.8 1.0 N A:PRO253 4.6 18.3 1.0 N A:ALA250 4.6 17.7 1.0 N A:ASN254 4.7 19.7 1.0 CB A:ASP247 4.7 17.2 1.0 O A:HOH637 4.7 22.3 1.0 CA A:ALA250 4.8 19.1 1.0 OG1 A:THR246 4.8 23.0 1.0 C A:ALA250 4.8 23.1 1.0 O A:ALA250 4.9 24.1 1.0 O A:ILE235 4.9 17.9 1.0 CG2 A:THR252 4.9 15.3 1.0 CA A:ASN254 5.0 20.0 1.0 O A:HOH740 5.0 32.4 1.0

T.Guevara, A.Rodriguez-Banqueri, M.Ksiazek, J.Potempa, F.X.Gomis-Ruth. Structure-Based Mechanism of Cysteine-Switch Latency and of Catalysis By Pappalysin-Family Metallopeptidases Iucrj 2019.
ISSN: ESSN 2052-2525