Calcium in PDB 6r7u: Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A

The structure of Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7u 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)	44.97 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.780, 79.210, 75.500, 90.00, 106.80, 90.00
R / Rfree (%)	18.6 / 22

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

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A (pdb code 6r7u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Selenomethionine Variant of 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 Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.7 occ:1.00 O A:TRP236 2.3 13.1 1.0 O A:SER242 2.3 15.2 1.0 O A:GLY256 2.3 14.8 1.0 O A:HOH502 2.3 12.7 1.0 O A:GLN255 2.4 12.3 1.0 OD1 A:ASP239 2.4 12.2 1.0 OD2 A:ASP239 2.4 11.8 1.0 CG A:ASP239 2.7 11.8 1.0 C A:GLY256 3.3 13.6 1.0 C A:TRP236 3.5 14.4 1.0 C A:GLN255 3.5 14.0 1.0 C A:SER242 3.5 16.9 1.0 CA A:GLY256 3.6 13.7 1.0 N A:GLY256 4.0 14.3 1.0 CA A:TRP236 4.2 11.7 1.0 N A:SER242 4.2 16.1 1.0 CB A:TRP236 4.2 11.1 1.0 CB A:ASP239 4.3 15.4 1.0 C A:GLY241 4.4 18.6 1.0 CA A:CYS243 4.4 17.2 1.0 N A:CYS243 4.4 15.9 1.0 O A:HOH571 4.4 17.0 1.0 CA A:SER242 4.4 14.6 1.0 N A:GLY257 4.5 11.8 1.0 N A:GLY237 4.5 11.3 1.0 OD1 A:ASN254 4.6 20.8 1.0 CD1 A:TRP236 4.6 13.8 1.0 OG A:SER242 4.6 23.5 1.0 O A:GLY245 4.7 15.3 1.0 O A:GLY241 4.7 17.1 1.0 CA A:GLY237 4.7 10.9 1.0 C A:CYS243 4.8 18.1 1.0 CA A:GLN255 4.8 10.2 1.0 N A:GLY245 4.8 12.7 1.0 CA A:GLY241 4.8 14.5 1.0 CG A:TRP236 4.8 10.9 1.0 N A:GLY241 4.9 17.3 1.0 SG A:CYS271 4.9 22.2 1.0 N A:GLN255 4.9 10.9 1.0 N A:SER244 4.9 14.4 1.0 N A:ASP239 5.0 15.2 1.0

Calcium binding site 2 out of 4 in the Selenomethionine Variant of 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 Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:11.8 occ:1.00 OD1 A:ASP247 2.3 12.2 1.0 O A:HOH594 2.3 12.0 1.0 O A:ILE249 2.5 12.5 1.0 O A:THR252 2.5 12.2 1.0 O2 A:GOL406 2.5 11.2 0.8 OG1 A:THR252 2.5 12.8 1.0 O1 A:GOL406 2.5 13.8 0.8 O3 A:GOL406 2.5 10.0 0.8 C2 A:GOL406 3.1 19.5 0.8 C1 A:GOL406 3.1 19.1 0.8 C3 A:GOL406 3.3 18.9 0.8 CG A:ASP247 3.3 14.8 1.0 C A:THR252 3.5 14.2 1.0 C A:ILE249 3.6 16.1 1.0 CB A:THR252 3.6 13.2 1.0 OD2 A:ASP247 3.8 13.9 1.0 CA A:THR252 4.0 9.6 1.0 N A:ILE249 4.1 12.3 1.0 N A:THR252 4.1 13.2 1.0 O A:HOH501 4.1 21.2 1.0 CA A:ILE249 4.3 11.1 1.0 C A:PRO253 4.4 10.9 1.0 O A:PRO253 4.4 11.8 1.0 CB A:ILE249 4.5 14.8 1.0 N A:ASP247 4.5 11.1 1.0 O A:HOH571 4.6 17.0 1.0 N A:PRO253 4.6 12.8 1.0 CB A:ASP247 4.6 12.7 1.0 N A:ASN254 4.6 11.4 1.0 N A:ALA250 4.6 12.9 1.0 O A:ALA250 4.7 14.8 1.0 C A:ALA250 4.8 15.7 1.0 CA A:ALA250 4.8 11.6 1.0 O A:ILE235 4.8 10.7 1.0 CG2 A:THR252 4.9 12.1 1.0 OG1 A:THR246 4.9 14.4 1.0 CA A:PRO253 4.9 12.3 1.0 CA A:ASN254 4.9 11.1 1.0 N A:ASN248 4.9 11.7 1.0 CA A:ASP247 5.0 10.0 1.0

Calcium binding site 3 out of 4 in the Selenomethionine Variant of 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 3 of Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:16.4 occ:1.00 O B:TRP236 2.3 17.6 1.0 O B:SER242 2.3 18.1 1.0 O B:GLY256 2.4 17.1 1.0 O B:GLN255 2.4 16.9 1.0 OD2 B:ASP239 2.4 18.3 1.0 O B:HOH505 2.4 15.6 1.0 OD1 B:ASP239 2.5 16.1 1.0 CG B:ASP239 2.8 15.0 1.0 C B:GLY256 3.3 17.9 1.0 C B:TRP236 3.5 17.6 1.0 C B:GLN255 3.5 18.5 1.0 C B:SER242 3.5 22.3 1.0 CA B:GLY256 3.6 17.8 1.0 N B:GLY256 4.0 17.5 1.0 N B:SER242 4.1 18.0 1.0 CA B:TRP236 4.2 13.3 1.0 CB B:TRP236 4.2 13.2 1.0 CB B:ASP239 4.3 19.9 1.0 C B:GLY241 4.3 22.9 1.0 N B:CYS243 4.4 21.3 1.0 CA B:CYS243 4.4 22.6 1.0 CA B:SER242 4.4 19.0 1.0 O B:HOH554 4.4 20.4 1.0 N B:GLY237 4.5 13.7 1.0 N B:GLY257 4.5 14.3 1.0 CD1 B:TRP236 4.6 16.4 1.0 O B:GLY245 4.6 20.0 1.0 OD1 B:ASN254 4.6 21.2 1.0 N B:GLY245 4.7 20.2 1.0 O B:GLY241 4.7 22.7 1.0 CA B:GLN255 4.7 16.1 1.0 CA B:GLY237 4.7 14.9 1.0 C B:CYS243 4.7 26.3 1.0 OG B:SER242 4.8 34.9 1.0 CA B:GLY241 4.8 21.9 1.0 CG B:TRP236 4.8 13.9 1.0 SG B:CYS271 4.8 28.2 1.0 N B:GLN255 4.9 15.0 1.0 N B:GLY241 4.9 22.8 1.0 CA B:GLY245 5.0 18.2 1.0 N B:SER244 5.0 23.7 1.0

Calcium binding site 4 out of 4 in the Selenomethionine Variant of 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 4 of Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:16.5 occ:1.00 OD1 B:ASP247 2.3 14.4 1.0 O B:HOH555 2.4 23.8 1.0 O B:ILE249 2.4 15.5 1.0 O B:HOH542 2.5 12.8 1.0 O B:THR252 2.5 15.7 1.0 OG1 B:THR252 2.5 11.5 1.0 O B:HOH549 2.5 18.0 1.0 O B:HOH677 2.6 19.1 1.0 CG B:ASP247 3.4 15.6 1.0 C B:THR252 3.5 17.5 1.0 C B:ILE249 3.6 18.7 1.0 CB B:THR252 3.7 16.4 1.0 OD2 B:ASP247 3.8 14.9 1.0 CA B:THR252 3.9 13.2 1.0 N B:ILE249 4.1 15.0 1.0 N B:THR252 4.1 15.4 1.0 CA B:ILE249 4.3 14.0 1.0 O B:PRO253 4.5 12.7 1.0 C B:PRO253 4.5 17.0 1.0 CB B:ILE249 4.5 16.3 1.0 N B:ASP247 4.6 12.9 1.0 N B:ALA250 4.6 17.6 1.0 N B:PRO253 4.6 16.5 1.0 CB B:ASP247 4.6 12.5 1.0 O B:HOH554 4.7 20.4 1.0 OG1 B:THR246 4.7 18.4 1.0 CA B:ALA250 4.8 18.3 1.0 N B:ASN254 4.8 14.1 1.0 C B:ALA250 4.8 19.8 1.0 O B:HOH691 4.8 32.5 1.0 O B:ILE235 4.9 15.5 1.0 CG2 B:THR252 4.9 18.4 1.0 N B:ASN248 5.0 14.5 1.0 CA B:PRO253 5.0 15.8 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 V. 7 18 2020.
ISSN: ESSN 2052-2525
PubMed: 31949901
DOI: 10.1107/S2052252519013848