Calcium in PDB 8ehe: Structure of Tannerella Forsythia Potempin C in Complex with Mirolase

The structure of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase, PDB code: 8ehe was solved by F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.87 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.65, 113.36, 50.2, 90, 112.69, 90
R / Rfree (%)	13.9 / 14.8

The structure of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase (pdb code 8ehe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase, PDB code: 8ehe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:11.1 occ:0.63 O A:HOH1035 2.3 14.6 0.5 OD2 A:ASP441 2.3 10.0 1.0 O A:SER439 2.4 10.7 1.0 O A:HOH779 2.4 12.3 1.0 O A:VAL418 2.4 10.2 1.0 OG1 A:THR420 2.4 10.6 1.0 O A:HOH1035 2.6 14.7 0.5 HB A:THR420 3.1 11.5 1.0 HB2 A:SER439 3.2 12.3 1.0 H A:THR420 3.2 8.6 1.0 CB A:THR420 3.3 9.9 1.0 CG A:ASP441 3.4 9.9 1.0 O A:HOH885 3.5 18.5 1.0 C A:SER439 3.5 10.5 1.0 C A:VAL418 3.6 9.5 1.0 N A:THR420 3.7 8.3 1.0 HA A:ILE419 3.8 8.3 1.0 OD1 A:ASP441 3.9 10.5 1.0 HA A:SER439 3.9 10.3 1.0 O A:GLY413 4.0 13.5 1.0 CB A:SER439 4.1 12.9 1.0 HG12 A:VAL418 4.1 10.4 1.0 O A:HOH880 4.1 14.5 0.5 CA A:SER439 4.1 9.9 1.0 HB A:VAL418 4.2 11.2 1.0 CA A:THR420 4.2 8.5 1.0 O A:HOH870 4.2 30.9 1.0 HG21 A:THR420 4.3 10.7 1.0 CA A:ILE419 4.4 8.7 1.0 N A:ILE419 4.4 8.9 1.0 C A:ILE419 4.4 8.8 1.0 O A:HOH1212 4.4 23.1 0.5 CG2 A:THR420 4.5 10.7 1.0 CA A:VAL418 4.5 9.1 1.0 O A:HOH880 4.6 11.7 0.5 H A:VAL418 4.6 10.2 1.0 N A:MET440 4.6 9.9 1.0 C A:MET440 4.6 9.3 1.0 N A:VAL418 4.6 10.1 1.0 CB A:ASP441 4.7 9.0 1.0 HA A:MET440 4.7 6.5 1.0 O A:VAL415 4.7 11.2 1.0 HB2 A:ASP441 4.7 8.0 1.0 N A:ASP441 4.7 8.8 1.0 OG A:SER439 4.7 15.8 1.0 H A:GLY417 4.7 11.2 1.0 CB A:VAL418 4.7 10.6 1.0 H A:ASP441 4.8 9.0 1.0 HA A:THR420 4.8 7.4 1.0 HB3 A:SER439 4.9 12.4 1.0 CA A:MET440 4.9 8.8 1.0 CG1 A:VAL418 4.9 9.8 1.0 O A:MET440 4.9 9.5 1.0 HG23 A:THR420 5.0 7.5 1.0 HA A:ASN414 5.0 12.2 1.0

Calcium binding site 2 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:7.9 occ:1.00 O A:ARG458 2.3 7.9 1.0 O A:PHE462 2.3 8.5 1.0 OD2 A:ASP457 2.3 8.2 1.0 O A:ASN465 2.3 8.8 1.0 O A:THR467 2.3 8.7 1.0 O A:GLY460 2.3 8.6 1.0 H A:ASN465 3.4 9.7 1.0 CG A:ASP457 3.5 7.8 1.0 C A:GLY460 3.5 9.0 1.0 C A:ARG458 3.5 7.9 1.0 C A:ASN465 3.5 9.4 1.0 C A:THR467 3.6 9.0 1.0 C A:PHE462 3.6 8.7 1.0 HB3 A:ASP457 3.6 8.0 1.0 HA3 A:GLY463 3.7 7.0 1.0 HA A:ASN466 3.7 9.5 1.0 HA A:ASN468 3.8 7.1 1.0 H A:THR467 3.9 9.3 1.0 N A:THR467 3.9 8.9 1.0 N A:GLY460 3.9 8.5 1.0 H A:GLY460 4.0 7.7 1.0 C A:MET459 4.1 8.7 1.0 C A:ASN466 4.1 10.4 1.0 CB A:ASP457 4.1 8.0 1.0 HB2 A:ARG458 4.1 7.6 1.0 C A:ASN461 4.2 9.4 1.0 N A:PHE462 4.2 9.0 1.0 N A:ASN465 4.2 8.7 1.0 CA A:ASN466 4.3 9.1 1.0 N A:ARG458 4.3 7.7 1.0 CA A:GLY460 4.3 8.8 1.0 N A:ASN466 4.3 8.7 1.0 OD1 A:ASN465 4.4 10.2 1.0 CA A:THR467 4.4 8.9 1.0 CA A:ARG458 4.4 7.9 1.0 O A:MET459 4.4 9.3 1.0 CA A:GLY463 4.4 8.0 1.0 HA A:ASN461 4.4 9.3 1.0 OD1 A:ASP457 4.4 8.4 1.0 N A:GLY463 4.4 8.4 1.0 H A:PHE462 4.5 9.3 0.3 C A:ASP457 4.5 7.9 1.0 HA A:MET459 4.5 8.2 1.0 CA A:PHE462 4.5 8.5 0.7 O A:ASN461 4.5 10.3 1.0 N A:MET459 4.5 7.6 1.0 N A:ASN461 4.5 9.0 1.0 CA A:ASN465 4.5 8.8 1.0 N A:ASN468 4.5 8.2 1.0 H A:ARG458 4.5 9.0 1.0 CA A:PHE462 4.6 8.4 0.3 H A:PHE462 4.6 9.5 0.7 HB2 A:PHE462 4.6 10.3 0.7 CA A:MET459 4.6 7.5 1.0 H A:TYR464 4.6 9.6 1.0 CA A:ASN461 4.6 9.2 1.0 CA A:ASN468 4.6 7.9 1.0 O A:ASN466 4.7 11.6 1.0 O A:ASP457 4.7 7.7 1.0 C A:GLY463 4.7 8.6 1.0 CB A:ARG458 4.8 8.1 1.0 N A:TYR464 4.8 8.3 1.0 HA2 A:GLY460 4.8 9.7 1.0 CG A:ASN465 4.9 9.6 1.0 CA A:ASP457 5.0 7.2 1.0 HA A:THR467 5.0 9.0 1.0 HB2 A:ASP457 5.0 7.3 1.0

Calcium binding site 3 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:10.6 occ:1.00 OD2 A:ASP519 2.3 11.2 1.0 O A:SER515 2.3 13.1 1.0 O A:LEU513 2.3 11.3 1.0 O A:GLY517 2.3 11.4 1.0 O A:HOH884 2.3 10.4 1.0 OD1 A:ASP512 2.4 11.6 1.0 H A:LEU513 3.4 10.5 1.0 CG A:ASP519 3.5 10.9 1.0 C A:SER515 3.5 14.3 1.0 C A:LEU513 3.5 11.6 1.0 CG A:ASP512 3.5 11.6 1.0 C A:GLY517 3.5 12.0 1.0 HB3 A:ASP519 3.7 12.2 1.0 HB2 A:TYR522 3.9 9.7 1.0 N A:LEU513 3.9 10.0 1.0 N A:GLY517 3.9 12.0 1.0 H A:GLY517 4.0 12.0 1.0 N A:SER515 4.1 13.2 1.0 OD2 A:ASP512 4.1 12.7 1.0 H A:ASP519 4.1 10.2 1.0 HA A:ALA516 4.1 13.7 1.0 C A:GLY514 4.1 14.5 1.0 CB A:ASP519 4.2 11.7 1.0 C A:ALA516 4.2 13.3 1.0 HA A:PHE518 4.2 9.6 1.0 O A:HOH794 4.2 12.9 1.0 HA A:ASP512 4.2 9.1 1.0 N A:ASP519 4.2 9.8 1.0 H A:SER515 4.3 12.9 0.5 HA3 A:GLY514 4.3 13.2 1.0 H A:SER515 4.3 12.8 0.6 CA A:GLY517 4.3 11.7 1.0 HB2 A:SER515 4.4 15.3 0.6 CA A:SER515 4.4 13.3 0.6 O A:GLY523 4.4 9.6 1.0 CA A:LEU513 4.4 10.1 1.0 C A:PHE518 4.4 10.9 1.0 CA A:SER515 4.4 13.2 0.5 N A:ALA516 4.4 13.3 1.0 N A:GLY514 4.4 12.3 1.0 OD1 A:ASP519 4.5 11.1 1.0 O A:GLY514 4.5 14.4 1.0 CA A:ALA516 4.5 13.7 1.0 N A:PHE518 4.5 11.1 1.0 CA A:GLY514 4.5 12.7 1.0 HD2 A:TYR522 4.5 11.7 1.0 OG A:SER515 4.6 18.5 0.5 CA A:PHE518 4.6 10.6 1.0 O A:HOH933 4.6 40.5 1.0 CB A:ASP512 4.6 10.5 1.0 C A:ASP512 4.7 11.5 1.0 CA A:ASP512 4.7 9.3 1.0 O A:ALA516 4.7 13.4 1.0 O A:HOH793 4.8 15.1 0.5 CA A:ASP519 4.8 10.2 1.0 HA2 A:GLY517 4.9 13.2 1.0 HG A:SER515 4.9 18.4 0.5 CB A:TYR522 4.9 9.5 1.0 CB A:SER515 4.9 15.7 0.6 O A:PHE518 4.9 11.4 1.0

Calcium binding site 4 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:8.2 occ:1.00 O A:MET298 2.3 9.2 1.0 OD2 A:ASP187 2.3 8.9 1.0 O A:ILE300 2.3 8.6 1.0 OD1 A:ASP239 2.4 9.2 1.0 O A:ASN294 2.4 8.8 1.0 OD1 A:ASN296 2.4 8.6 1.0 OD2 A:ASP239 2.5 8.5 1.0 CG A:ASP239 2.8 8.3 1.0 H A:ASN296 3.2 8.8 1.0 CG A:ASN296 3.4 9.1 1.0 C A:ILE300 3.5 8.4 1.0 C A:MET298 3.5 9.0 1.0 CG A:ASP187 3.5 8.4 1.0 H A:ILE300 3.5 8.2 1.0 H A:MET298 3.5 8.8 1.0 C A:ASN294 3.6 9.0 1.0 HD21 A:ASN296 3.6 12.2 1.0 HB3 A:ASP187 3.6 8.4 1.0 HB2 A:ASN294 3.6 8.6 0.4 N A:ILE300 3.7 8.3 1.0 HA A:HIS295 3.8 8.4 1.0 HB1 A:ALA293 3.9 8.3 1.0 ND2 A:ASN296 3.9 9.7 1.0 N A:ASN296 4.0 8.4 1.0 HA3 A:GLY299 4.0 7.9 1.0 C A:GLY299 4.0 9.1 1.0 HB2 A:MET298 4.1 10.2 1.0 HA A:ARG301 4.1 7.1 1.0 CB A:ASP187 4.1 8.8 1.0 CA A:ILE300 4.2 7.9 1.0 CB A:ASP239 4.3 9.1 1.0 HB2 A:ASN294 4.3 8.2 0.6 CA A:GLY299 4.3 8.8 1.0 N A:MET298 4.3 9.2 1.0 N A:GLY299 4.4 8.9 1.0 HG13 A:ILE300 4.4 9.4 1.0 CA A:MET298 4.4 9.3 1.0 CA A:ASN294 4.4 7.7 0.4 N A:HIS295 4.5 8.4 1.0 CB A:ASN294 4.5 9.1 0.4 N A:ASN294 4.5 7.8 1.0 CA A:HIS295 4.5 8.2 1.0 N A:ARG301 4.5 8.5 1.0 CA A:ASN294 4.5 7.9 0.6 OD1 A:ASP187 4.5 9.1 1.0 O A:GLY299 4.6 9.2 1.0 CB A:ASN296 4.6 9.4 1.0 HA A:ASP187 4.6 8.7 1.0 H A:ASN294 4.6 8.3 0.6 H A:ASN294 4.6 8.2 0.4 HA A:ASP239 4.6 8.9 1.0 CA A:ASN296 4.7 8.9 1.0 C A:HIS295 4.7 9.7 1.0 HG2 A:ARG301 4.7 8.5 1.0 CB A:MET298 4.7 10.9 1.0 HB2 A:ASP239 4.7 10.1 1.0 C A:ASN296 4.8 9.2 1.0 HA A:ILE300 4.8 8.0 1.0 HB3 A:ASP239 4.8 8.0 1.0 CA A:ARG301 4.8 7.8 1.0 HD22 A:ASN296 4.8 9.4 1.0 O A:ASN296 4.8 10.2 1.0 CB A:ALA293 4.9 7.8 1.0 C A:ALA293 4.9 7.8 1.0 CB A:ASN294 4.9 9.1 0.6 HB3 A:ASN294 4.9 8.9 0.4 HB3 A:ASN296 4.9 8.6 1.0 HD2 A:PRO188 5.0 8.8 1.0 HB2 A:ASP187 5.0 9.7 1.0 HB3 A:MET298 5.0 10.8 1.0

Calcium binding site 5 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:10.5 occ:0.87 OD1 A:ASN207 2.2 13.5 1.0 OD1 A:ASN211 2.4 11.8 1.0 O A:HOH774 2.4 11.9 1.0 O A:HOH852 2.4 13.4 1.0 OD1 A:ASP209 2.4 9.9 1.0 O A:HOH1038 2.4 18.4 1.0 OD2 A:ASP209 2.6 10.4 1.0 CG A:ASP209 2.9 9.4 1.0 HA A:ASN211 3.3 9.5 1.0 HA A:ASN207 3.3 11.1 1.0 CG A:ASN207 3.5 14.5 1.0 CG A:ASN211 3.5 12.6 1.0 H A:ASN211 3.7 10.7 1.0 HA A:ASN197 4.1 7.8 1.0 CA A:ASN211 4.1 9.1 1.0 H A:ASN198 4.1 9.2 1.0 CA A:ASN207 4.2 10.1 1.0 OE1 A:GLU214 4.2 11.1 1.0 OD1 A:ASN197 4.3 12.2 1.0 O A:HOH1107 4.3 32.3 1.0 OE2 A:GLU214 4.3 13.5 1.0 CB A:ASN207 4.3 10.9 1.0 N A:ASN211 4.3 9.2 1.0 HH22 A:ARG511 4.3 16.2 1.0 HD21 A:ASN207 4.3 13.5 1.0 O A:HOH1057 4.4 17.1 1.0 CB A:ASP209 4.4 9.8 1.0 ND2 A:ASN207 4.4 13.5 1.0 CB A:ASN211 4.4 10.8 1.0 HD21 A:ASN211 4.4 13.1 1.0 ND2 A:ASN211 4.5 12.0 1.0 O A:ASN207 4.5 10.8 1.0 CD A:GLU214 4.6 13.3 1.0 HB2 A:ASN207 4.6 11.6 1.0 O A:HOH803 4.7 20.5 1.0 O A:HOH998 4.7 16.2 1.0 HB2 A:ASP209 4.7 10.6 1.0 C A:ASN207 4.8 10.7 1.0 HB3 A:ASP209 4.8 10.8 1.0 HB3 A:ASN211 4.8 10.5 1.0 H A:ASP209 4.9 8.4 1.0 HH21 A:ARG511 5.0 15.5 1.0

Calcium binding site 6 out of 6 in the Structure of Tannerella Forsythia Potempin C in Complex with Mirolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Tannerella Forsythia Potempin C in Complex with Mirolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:10.2 occ:1.00 O A:TYR273 2.3 11.0 1.0 OD2 A:ASP278 2.3 11.0 1.0 O A:THR271 2.4 11.3 1.0 OD1 A:ASP276 2.4 10.8 1.0 O A:HOH833 2.4 10.4 1.0 OG B:SER68 2.4 11.3 1.0 OG1 A:THR271 2.4 11.1 1.0 H A:THR271 3.1 10.1 1.0 CG A:ASP278 3.3 11.7 1.0 C A:THR271 3.3 12.3 1.0 CG A:ASP276 3.5 10.8 1.0 HA B:SER68 3.5 14.2 1.0 C A:TYR273 3.5 11.4 1.0 CB B:SER68 3.5 14.3 1.0 HB3 B:SER68 3.6 16.0 1.0 CB A:THR271 3.7 10.6 1.0 HA A:PRO274 3.8 10.0 1.0 H A:ASP276 3.8 10.7 1.0 CA A:THR271 3.8 10.8 1.0 N A:THR271 3.8 11.2 1.0 OD2 A:ASP276 3.8 11.3 1.0 HB3 A:ASP278 3.9 9.5 1.0 OD1 A:ASP278 4.0 15.9 1.0 CA B:SER68 4.0 13.5 1.0 N A:TYR273 4.1 12.7 1.0 HB3 A:TYR273 4.1 12.9 1.0 HB A:THR271 4.2 8.6 1.0 CB A:ASP278 4.2 10.7 1.0 C A:PRO272 4.3 14.3 1.0 CA A:TYR273 4.3 12.1 1.0 CA A:PRO274 4.4 10.7 1.0 N A:PRO272 4.4 11.9 1.0 HB2 B:SER68 4.4 14.7 1.0 H A:TYR273 4.4 11.0 1.0 O B:HOH357 4.4 14.3 1.0 N A:PRO274 4.4 11.2 1.0 H B:SER68 4.4 12.3 1.0 O A:ASP276 4.5 11.1 1.0 C A:PRO274 4.5 11.1 1.0 HD2 A:TYR273 4.5 15.5 1.0 O A:PRO272 4.5 14.2 1.0 N B:SER68 4.6 12.5 1.0 HG23 A:THR271 4.7 11.2 1.0 H A:ASP278 4.7 10.5 1.0 N A:ASP276 4.7 9.8 1.0 CA A:PRO272 4.7 12.1 1.0 HA A:PRO272 4.7 12.3 1.0 CB A:ASP276 4.8 10.4 1.0 CG2 A:THR271 4.8 11.2 1.0 HB2 A:ASP278 4.8 10.3 1.0 CB A:TYR273 4.8 13.8 1.0 O A:PRO274 4.8 10.9 1.0 O A:HOH701 4.8 25.0 1.0 HA A:THR271 4.9 10.8 1.0

M.Ksiazek, T.Goulas, D.Mizgalska, A.Rodriguez-Banqueri, U.Eckhard, F.Veillard, I.Waligorska, M.Benedyk-Machaczka, A.M.Sochaj-Gregorczyk, M.Madej, I.B.Thogersen, J.J.Enghild, A.Cuppari, J.L.Arolas, I.De Diego, M.Lopez-Pelegrin, I.Garcia-Ferrer, T.Guevara, V.Dive, M.L.Zani, T.Moreau, J.Potempa, F.X.Gomis-Ruth. A Unique Network of Attack, Defence and Competence on the Outer Membrane of the Periodontitis Pathogen Tannerella Forsythia Chem Sci 2022.
ISSN: ESSN 2041-6539