Zinc in PDB 9g0j: Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans, PDB code: 9g0j was solved by B.Claushuis, F.Wojtalla, H.Van Leeuwen, J.Corver, U.Baumann, P.Hensbergen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 1.55
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.247, 126.247, 64.043, 90, 90, 90
R / Rfree (%)	17.3 / 19.8

The binding sites of Zinc atom in the Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans (pdb code 9g0j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans, PDB code: 9g0j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans


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-3) From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:16.3 occ:1.00 OE1 A:GLU197 2.0 19.9 1.0 O22 A:BCN702 2.0 23.0 0.9 O6 A:BCN702 2.1 23.8 0.9 NE2 A:HIS157 2.1 17.5 1.0 NE2 A:HIS153 2.2 17.5 1.0 N1 A:BCN702 2.3 24.3 0.9 HO6 A:BCN702 2.8 28.6 0.9 C2 A:BCN702 2.8 28.7 0.9 H32 A:BCN702 2.9 39.9 0.9 C1 A:BCN702 2.9 27.9 0.9 C6 A:BCN702 3.0 29.6 0.9 CD A:GLU197 3.0 23.3 1.0 CD2 A:HIS153 3.0 16.4 1.0 C5 A:BCN702 3.1 29.0 0.9 CE1 A:HIS157 3.1 16.7 1.0 CD2 A:HIS157 3.1 16.2 1.0 HD2 A:HIS153 3.1 19.7 1.0 C3 A:BCN702 3.2 33.2 0.9 H12 A:BCN702 3.2 33.5 0.9 CE1 A:HIS153 3.2 17.4 1.0 HE1 A:HIS157 3.3 20.0 1.0 HD2 A:HIS157 3.3 19.5 1.0 OE2 A:GLU197 3.3 26.1 1.0 H62 A:BCN702 3.4 35.5 0.9 HE1 A:HIS153 3.5 20.9 1.0 H51 A:BCN702 3.6 34.8 0.9 H21 A:PEG703 3.7 33.6 1.0 H31 A:PEG703 3.7 36.2 1.0 H11 A:BCN702 3.8 33.5 0.9 H31 A:BCN702 3.8 39.9 0.9 H52 A:BCN702 3.8 34.8 0.9 H61 A:BCN702 3.8 35.5 0.9 O21 A:BCN702 4.1 27.1 0.9 H41 A:BCN702 4.1 43.6 0.9 HA A:GLU197 4.2 18.6 1.0 ND1 A:HIS157 4.2 16.1 1.0 C4 A:BCN702 4.2 36.3 0.9 CG A:HIS153 4.2 15.2 1.0 CG A:HIS157 4.3 15.1 1.0 ND1 A:HIS153 4.3 15.3 1.0 CG A:GLU197 4.3 20.4 1.0 HB3 A:ALA200 4.4 17.0 1.0 HG2 A:GLU197 4.4 24.5 1.0 H42 A:BCN702 4.5 43.6 0.9 C2 A:PEG703 4.5 28.0 1.0 C3 A:PEG703 4.6 30.2 1.0 H11 A:PEG703 4.7 40.0 1.0 O2 A:PEG703 4.8 38.6 1.0 OE1 A:GLU154 4.8 23.4 1.0 HB1 A:ALA200 4.8 17.0 1.0 HE1 A:PHE191 4.9 27.1 1.0 H32 A:PEG703 4.9 36.2 1.0 CB A:ALA200 4.9 14.2 1.0 HG3 A:GLU197 5.0 24.5 1.0 HB2 A:ALA200 5.0 17.0 1.0

Zinc binding site 2 out of 2 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans


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-3) From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:16.5 occ:1.00 OE1 B:GLU197 2.0 19.2 1.0 O22 B:BCN702 2.1 20.9 0.8 O6 B:BCN702 2.1 18.4 0.8 NE2 B:HIS157 2.1 16.3 1.0 NE2 B:HIS153 2.2 15.4 1.0 N1 B:BCN702 2.4 22.6 0.8 HO6 B:BCN702 2.8 22.1 0.8 C2 B:BCN702 2.9 26.0 0.8 C1 B:BCN702 2.9 26.6 0.8 H32 B:BCN702 3.0 41.6 0.8 CD B:GLU197 3.0 25.2 1.0 C6 B:BCN702 3.0 25.4 0.8 CD2 B:HIS153 3.0 15.7 1.0 C5 B:BCN702 3.1 30.8 0.8 CD2 B:HIS157 3.1 18.0 1.0 CE1 B:HIS157 3.1 17.7 1.0 HD2 B:HIS153 3.1 18.8 1.0 H12 B:BCN702 3.2 31.9 0.8 CE1 B:HIS153 3.2 15.6 1.0 C3 B:BCN702 3.2 34.6 0.8 HD2 B:HIS157 3.3 21.6 1.0 OE2 B:GLU197 3.3 25.8 1.0 HE1 B:HIS157 3.3 21.3 1.0 H62 B:BCN702 3.4 30.6 0.8 HE1 B:HIS153 3.4 18.7 1.0 H51 B:BCN702 3.7 37.0 0.8 H52 B:BCN702 3.8 37.0 0.8 H11 B:BCN702 3.8 31.9 0.8 H61 B:BCN702 3.8 30.6 0.8 H31 B:BCN702 3.9 41.6 0.8 O2 B:PEG703 3.9 42.1 1.0 H31 B:PEG703 4.0 42.4 1.0 H21 B:PEG703 4.1 35.8 1.0 O21 B:BCN702 4.1 20.5 0.8 H41 B:BCN702 4.1 38.6 0.8 HA B:GLU197 4.2 17.8 1.0 CG B:HIS153 4.2 15.2 1.0 ND1 B:HIS157 4.2 14.9 1.0 CG B:HIS157 4.3 15.7 1.0 ND1 B:HIS153 4.3 14.9 1.0 C4 B:BCN702 4.3 32.2 0.8 CG B:GLU197 4.3 18.9 1.0 HB3 B:ALA200 4.4 18.9 1.0 HG2 B:GLU197 4.4 22.7 1.0 C3 B:PEG703 4.5 35.3 1.0 H11 B:PEG703 4.5 41.4 1.0 C2 B:PEG703 4.5 29.8 1.0 H42 B:BCN702 4.5 38.6 0.8 OE1 B:GLU154 4.8 25.3 1.0 HE1 B:PHE191 4.8 25.7 1.0 HB1 B:ALA200 4.9 18.9 1.0 HG3 B:GLU197 4.9 22.7 1.0 CB B:ALA200 5.0 15.8 1.0 H42 B:PEG703 5.0 47.1 1.0 HB2 B:ALA200 5.0 18.9 1.0

B.Claushuis, F.Wojtalla, H.Van Leeuwen, J.Corver, U.Baumann, P.Hensbergen. Structure of the Pro-Pro Endopeptidase (Ppep-3) From Geobacillus Thermodenitrificans To Be Published.