Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn403 b:15.1 occ:0.88 NE2 A:HIS234 2.0 12.6 1.0 NE2 A:HIS224 2.0 11.3 1.0 NE2 A:HIS228 2.1 11.8 1.0 SG A:CSX23 2.2 23.1 1.0 CD2 A:HIS224 2.9 11.9 1.0 CD2 A:HIS234 2.9 13.5 1.0 CE1 A:HIS234 3.0 12.3 1.0 OD A:CSX23 3.0 22.7 1.0 CD2 A:HIS228 3.0 12.4 1.0 CE1 A:HIS224 3.0 12.1 1.0 CE1 A:HIS228 3.1 11.2 1.0 CB A:CSX23 3.2 29.0 1.0 CG A:HIS224 4.0 11.7 1.0 CG A:HIS234 4.1 12.6 1.0 ND1 A:HIS234 4.1 12.3 1.0 ND1 A:HIS224 4.1 12.2 1.0 CE1 A:TYR286 4.2 16.7 1.0 CG A:HIS228 4.2 11.3 1.0 ND1 A:HIS228 4.3 11.9 1.0 O A:SER25 4.4 19.5 1.0 CB A:SER25 4.5 19.8 1.0 OH A:TYR286 4.5 20.9 1.0 CA A:CSX23 4.6 27.1 1.0 CE A:MSE284 4.7 10.8 1.0 N A:SER25 4.7 20.0 1.0 OE2 A:GLU26 4.8 89.5 1.0 CZ A:TYR286 4.8 18.0 1.0 C A:SER25 4.9 19.1 1.0 CA A:SER25 4.9 17.2 1.0 C A:CSX23 5.0 29.1 1.0

Zinc binding site 2 out of 2 in the Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Selenomethionine Variant of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.4 occ:1.00 NE2 B:HIS234 2.0 13.4 1.0 NE2 B:HIS228 2.0 12.9 1.0 NE2 B:HIS224 2.1 12.9 1.0 SG B:CSX23 2.1 31.2 1.0 CD2 B:HIS234 2.9 13.5 1.0 OD B:CSX23 3.0 30.7 1.0 CD2 B:HIS224 3.0 13.5 1.0 CD2 B:HIS228 3.0 13.2 1.0 CE1 B:HIS234 3.0 12.8 1.0 CE1 B:HIS228 3.0 11.7 1.0 CE1 B:HIS224 3.1 12.7 1.0 CB B:CSX23 3.2 36.4 1.0 CG B:HIS234 4.1 13.3 1.0 ND1 B:HIS234 4.1 14.7 1.0 CG B:HIS228 4.1 12.2 1.0 CG B:HIS224 4.1 12.4 1.0 ND1 B:HIS228 4.1 12.7 1.0 CE1 B:TYR286 4.2 18.7 1.0 ND1 B:HIS224 4.2 13.7 1.0 O B:SER25 4.3 19.4 1.0 OH B:TYR286 4.4 26.6 1.0 CB B:SER25 4.4 18.0 1.0 CA B:CSX23 4.6 38.3 1.0 N B:SER25 4.7 21.9 1.0 CE B:MSE284 4.7 9.2 1.0 C B:SER25 4.8 20.2 1.0 CZ B:TYR286 4.8 22.1 1.0 CA B:SER25 4.9 17.2 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