Zinc in PDB 8b2q: Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin.

The structure of Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin., PDB code: 8b2q was solved by J.Potempa, M.Ksiazek, T.Goulas, A.Cuppari, A.Rodriguez-Banqueri, J.L.Arolas, M.Lopez-Pelegrin, I.Garcia-Ferrer, T.Guevara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.07 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.24, 62.94, 108.68, 90, 90, 90
R / Rfree (%)	15.4 / 17.1

The structure of Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin. also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin. (pdb code 8b2q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin., PDB code: 8b2q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.4 occ:1.00 NE2 A:HIS165 2.0 11.1 1.0 NE2 A:HIS155 2.1 11.2 1.0 NE2 A:HIS159 2.1 10.1 1.0 OD1 I:ASP64 2.2 13.1 1.0 OD2 I:ASP64 2.3 13.2 1.0 CG I:ASP64 2.6 10.8 1.0 CE1 A:HIS165 3.0 11.8 1.0 CE1 A:HIS159 3.0 11.4 1.0 CD2 A:HIS155 3.0 10.8 1.0 CE1 A:HIS155 3.0 10.5 1.0 CD2 A:HIS165 3.1 11.6 1.0 CD2 A:HIS159 3.1 11.3 1.0 HE1 A:HIS165 3.2 11.2 1.0 HE1 A:HIS159 3.2 11.4 1.0 HE1 A:HIS155 3.3 12.3 1.0 HD2 A:HIS155 3.3 10.3 1.0 HD2 A:HIS165 3.3 9.0 1.0 HD2 A:HIS159 3.4 12.8 1.0 HB2 I:TYR63 3.4 14.0 1.0 O A:HOH441 3.6 13.9 1.0 CB I:ASP64 4.1 11.7 1.0 ND1 A:HIS165 4.1 12.1 1.0 CG A:HIS165 4.2 11.4 1.0 CG A:HIS155 4.2 10.5 1.0 HA3 I:GLY103 4.2 13.3 1.0 ND1 A:HIS155 4.2 10.3 1.0 ND1 A:HIS159 4.2 10.9 1.0 CG A:HIS159 4.2 10.9 1.0 HE3 A:MET173 4.2 15.8 1.0 HA A:PRO175 4.2 15.2 1.0 H I:ASP64 4.3 13.2 1.0 HE1 A:MET173 4.3 10.8 1.0 CB I:TYR63 4.4 12.5 1.0 HD1 I:TYR63 4.5 14.5 1.0 HB3 I:ASP64 4.5 13.6 1.0 HB3 I:TYR63 4.6 14.3 1.0 HB2 I:ASP64 4.6 11.7 1.0 OE2 A:GLU156 4.6 12.1 1.0 N I:ASP64 4.7 11.9 1.0 O I:HOH311 4.8 12.0 1.0 CE A:MET173 4.8 11.8 1.0 HA2 I:GLY103 4.8 11.5 1.0 CA I:ASP64 4.9 10.8 1.0 OE1 A:GLU156 4.9 12.2 1.0 CA I:GLY103 4.9 12.7 1.0 CD1 I:TYR63 5.0 14.2 1.0

Zinc binding site 2 out of 2 in the Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Matrix-Metallopeptidase Inhibitor Potempin A (Pota) From Tannerella Forsythia in Complex with T. Forsythia Karilysin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.4 occ:1.00 OD2 A:ASP104 1.9 15.2 1.0 NE2 A:HIS117 2.0 13.6 1.0 ND1 A:HIS133 2.0 13.0 1.0 NE2 A:HIS102 2.0 15.1 1.0 CG A:ASP104 2.9 16.0 1.0 CE1 A:HIS133 2.9 13.5 1.0 CE1 A:HIS117 2.9 13.6 1.0 CD2 A:HIS102 3.0 14.0 1.0 CE1 A:HIS102 3.0 15.1 1.0 CD2 A:HIS117 3.1 12.7 1.0 HE1 A:HIS133 3.1 15.5 1.0 HE1 A:HIS117 3.1 15.5 1.0 CG A:HIS133 3.1 12.4 1.0 HB2 A:HIS133 3.2 13.8 1.0 HD2 A:HIS102 3.2 13.8 1.0 OD1 A:ASP104 3.3 16.1 1.0 HE1 A:HIS102 3.3 15.9 1.0 HD2 A:HIS117 3.4 11.4 1.0 HE1 A:PHE119 3.6 15.5 1.0 CB A:HIS133 3.6 12.7 1.0 HB3 A:HIS133 3.7 12.2 1.0 ND1 A:HIS117 4.1 13.6 1.0 NE2 A:HIS133 4.1 13.3 1.0 CG A:HIS102 4.1 16.1 1.0 ND1 A:HIS102 4.2 15.5 1.0 HB2 A:TYR106 4.2 11.5 1.0 CG A:HIS117 4.2 12.8 1.0 HG3 A:GLU98 4.2 15.5 1.0 CB A:ASP104 4.2 16.8 1.0 CD2 A:HIS133 4.2 14.1 1.0 HE2 A:PHE108 4.3 17.1 1.0 HB3 A:ASP104 4.3 16.7 1.0 O A:TYR106 4.4 15.2 1.0 HZ A:PHE108 4.5 14.8 1.0 HZ A:PHE119 4.5 17.8 1.0 HB2 A:ASP104 4.6 16.0 1.0 CE2 A:PHE108 4.6 14.0 1.0 CE1 A:PHE119 4.6 13.0 1.0 CZ A:PHE108 4.7 12.6 1.0 HB2 A:GLU98 4.7 14.1 1.0 H A:TYR106 5.0 15.7 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 2023.
ISSN: ESSN 2041-6539