Zinc in PDB 6fpc: Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei, PDB code: 6fpc was solved by S.D.Weeks, O.I.Klychnikov, P.J.Hensbergen, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.90 / 1.75
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	84.900, 84.900, 113.272, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei also contains other interesting chemical elements:

Cadmium

(Cd)

14 atoms

The binding sites of Zinc atom in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei (pdb code 6fpc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei, PDB code: 6fpc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.9 occ:0.49 CD A:CD302 0.0 25.8 0.5 OE2 A:GLU181 2.0 23.7 1.0 O A:HOH495 2.1 29.6 1.0 NE2 A:HIS137 2.2 25.7 1.0 NE2 A:HIS141 2.2 25.0 1.0 OH A:TYR174 2.7 23.0 1.0 CD A:GLU181 2.7 21.8 1.0 OE1 A:GLU181 2.7 21.4 1.0 CD2 A:HIS141 3.2 25.8 1.0 CD2 A:HIS137 3.2 26.4 1.0 CE1 A:HIS137 3.2 25.4 1.0 CE1 A:HIS141 3.2 24.8 1.0 CZ A:TYR174 3.6 26.6 1.0 CE1 A:TYR174 4.1 23.8 1.0 OE1 A:GLU138 4.1 32.3 1.0 CG A:GLU181 4.2 19.8 1.0 CG A:HIS137 4.3 25.7 1.0 CG A:HIS141 4.3 24.8 1.0 ND1 A:HIS137 4.3 26.8 1.0 ND1 A:HIS141 4.4 25.3 1.0 O D:ILE81 4.4 24.8 1.0 O A:HOH402 4.5 27.9 1.0 O A:HOH421 4.6 47.3 1.0 CE2 A:TYR174 4.7 24.7 1.0 O A:HOH414 4.7 28.2 1.0 O A:HOH460 4.7 36.8 1.0 CD A:GLU138 4.8 40.0 1.0 CB A:GLU181 4.8 19.1 1.0 O A:HOH520 4.8 38.1 1.0 CA A:GLU181 4.8 19.1 1.0 OE2 A:GLU138 4.9 30.7 1.0 CB A:ALA184 4.9 22.5 1.0

Zinc binding site 2 out of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:24.8 occ:0.45 CD B:CD302 0.0 24.8 0.6 OE2 B:GLU181 2.1 20.9 1.0 NE2 B:HIS137 2.1 22.2 1.0 NE2 B:HIS141 2.1 24.3 1.0 O C:HOH501 2.3 29.8 1.0 OH B:TYR174 2.7 24.8 1.0 CD B:GLU181 2.8 18.7 1.0 OE1 B:GLU181 2.8 18.6 1.0 CE1 B:HIS137 3.1 22.1 1.0 CD2 B:HIS141 3.1 24.9 1.0 CD2 B:HIS137 3.1 22.7 1.0 CE1 B:HIS141 3.2 23.7 1.0 CZ B:TYR174 3.7 29.8 1.0 CE1 B:TYR174 4.1 24.2 1.0 ND1 B:HIS137 4.2 23.4 1.0 CG B:HIS137 4.3 21.8 1.0 CG B:GLU181 4.3 20.4 1.0 CG B:HIS141 4.3 24.5 1.0 ND1 B:HIS141 4.3 26.2 1.0 O C:ILE81 4.3 24.7 1.0 OE1 B:GLU138 4.3 30.4 1.0 O B:HOH401 4.5 26.4 1.0 O B:HOH429 4.5 30.6 1.0 CE2 B:TYR174 4.7 22.5 1.0 O B:HOH451 4.7 28.6 1.0 O B:HOH528 4.8 36.1 1.0 CB B:ALA184 4.8 20.8 1.0 OE2 B:GLU138 4.8 22.1 1.0 CD B:GLU138 4.8 29.0 1.0 CA B:GLU181 4.8 17.7 1.0 CB B:GLU181 4.9 17.3 1.0 O B:HOH421 4.9 23.4 1.0

Zinc binding site 3 out of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:26.6 occ:0.33 CD C:CD302 0.0 26.6 0.7 O C:HOH453 1.9 45.5 1.0 OE1 C:GLU181 2.0 25.9 1.0 NE2 C:HIS137 2.2 25.3 1.0 NE2 C:HIS141 2.3 25.4 1.0 OH C:TYR174 2.6 32.6 1.0 CD C:GLU181 2.9 32.1 1.0 OE2 C:GLU181 3.1 30.5 1.0 CD2 C:HIS137 3.2 25.8 1.0 CE1 C:HIS141 3.2 25.1 1.0 CE1 C:HIS137 3.2 24.9 1.0 CD2 C:HIS141 3.3 26.3 1.0 CZ C:TYR174 3.6 35.3 1.0 OE2 C:GLU138 3.8 44.9 1.0 CE1 C:TYR174 4.3 30.4 1.0 CG C:GLU181 4.3 26.0 1.0 CG C:HIS137 4.3 24.4 1.0 ND1 C:HIS137 4.4 25.8 1.0 ND1 C:HIS141 4.4 26.7 1.0 CG C:HIS141 4.4 25.4 1.0 O C:HOH436 4.5 35.0 1.0 CE2 C:TYR174 4.5 32.2 1.0 CD C:GLU138 4.7 49.2 1.0 CD1 C:LEU103 4.8 38.5 1.0 OE1 C:GLU138 4.9 34.0 1.0 CB C:GLU181 4.9 21.9 1.0 CG C:LEU103 4.9 37.8 1.0 CB C:ALA184 5.0 24.3 1.0 CA C:GLU181 5.0 21.0 1.0

Zinc binding site 4 out of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:31.9 occ:0.39 CD D:CD302 0.0 31.8 0.6 O D:HOH427 1.9 44.2 1.0 NE2 D:HIS141 2.3 30.2 1.0 NE2 D:HIS137 2.3 32.5 1.0 OE2 D:GLU181 2.5 32.0 1.0 OE1 D:GLU181 2.5 37.0 1.0 CD D:GLU181 2.8 38.5 1.0 CD2 D:HIS137 3.2 32.2 1.0 CD2 D:HIS141 3.3 30.1 1.0 CE1 D:HIS141 3.3 30.4 1.0 CE1 D:HIS137 3.4 31.6 1.0 OE1 D:GLU138 3.8 50.3 1.0 OH D:TYR174 4.2 51.6 1.0 CG D:GLU181 4.4 32.5 1.0 CG D:HIS137 4.4 29.6 1.0 CG D:HIS141 4.4 29.5 1.0 ND1 D:HIS141 4.5 31.3 1.0 ND1 D:HIS137 4.5 32.2 1.0 CD D:GLU138 4.7 41.7 1.0 OE2 D:GLU138 5.0 40.2 1.0

O.I.Klychnikov, T.M.Shamorkina, S.D.Weeks, H.C.Van Leeuwen, J.Corver, J.W.Drijfhout, P.A.Van Veelen, N.N.Sluchanko, S.V.Strelkov, P.J.Hensbergen. Discovery of A New Pro-Pro Endopeptidase, Ppep-2, Provides Mechanistic Insights Into the Differences in Substrate Specificity Within the Ppep Family. J. Biol. Chem. V. 293 11154 2018.
ISSN: ESSN 1083-351X
PubMed: 29794027
DOI: 10.1074/JBC.RA118.003244