Zinc in PDB 9g3t: Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F From Geobacillus Thermodenitrificans

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F From Geobacillus Thermodenitrificans, PDB code: 9g3t 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)	62.81 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.622, 125.622, 63.483, 90, 90, 90
R / Rfree (%)	15.7 / 17.7

The binding sites of Zinc atom in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F From Geobacillus Thermodenitrificans (pdb code 9g3t). 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) E153A Y189F From Geobacillus Thermodenitrificans, PDB code: 9g3t:
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) E153A Y189F 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) E153A Y189F From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:21.9 occ:1.00 OE1 A:GLU197 2.0 22.7 0.6 OE1 A:GLU197 2.0 20.8 0.4 NE2 A:HIS157 2.1 20.9 1.0 NE2 A:HIS153 2.2 20.3 1.0 O4 A:BCN702 2.2 29.7 0.8 O22 A:BCN702 2.2 25.2 0.8 N1 A:BCN702 2.3 30.1 0.8 CD A:GLU197 2.8 19.8 0.4 HO4 A:BCN702 2.8 35.7 0.8 H52 A:BCN702 2.8 52.1 0.8 C1 A:BCN702 2.9 43.0 0.8 C2 A:BCN702 2.9 42.6 0.8 OE2 A:GLU197 2.9 23.4 0.4 CD A:GLU197 2.9 26.6 0.6 C4 A:BCN702 2.9 40.9 0.8 C5 A:BCN702 3.0 43.4 0.8 CD2 A:HIS153 3.0 19.7 1.0 C3 A:BCN702 3.1 37.2 0.8 HD2 A:HIS153 3.1 23.6 1.0 CD2 A:HIS157 3.1 21.5 1.0 CE1 A:HIS157 3.1 25.5 1.0 H12 A:BCN702 3.1 51.6 0.8 H42 A:BCN702 3.2 49.1 0.8 H51 A:BCN702 3.2 52.1 0.8 OE2 A:GLU197 3.2 26.2 0.6 CE1 A:HIS153 3.2 20.6 1.0 HD2 A:HIS157 3.3 25.8 1.0 HE1 A:HIS157 3.3 30.6 1.0 H31 A:BCN702 3.5 44.7 0.8 HE1 A:HIS153 3.5 24.7 1.0 H11 A:BCN702 3.8 51.6 0.8 H41 A:BCN702 3.8 49.1 0.8 H32 A:BCN702 3.9 44.7 0.8 O21 A:BCN702 4.1 33.5 0.8 HA A:GLU197 4.1 22.4 1.0 CG A:HIS153 4.2 15.7 1.0 ND1 A:HIS157 4.2 19.5 1.0 CG A:HIS157 4.2 19.9 1.0 ND1 A:HIS153 4.3 19.4 1.0 CG A:GLU197 4.3 21.0 0.6 HB3 A:ALA200 4.3 21.0 1.0 CG A:GLU197 4.3 21.7 0.4 HG2 A:GLU197 4.4 25.3 0.6 C6 A:BCN702 4.4 51.6 0.8 H61 A:BCN702 4.6 62.0 0.8 HB3 A:GLU197 4.6 24.8 0.4 HG3 A:GLU197 4.7 26.1 0.4 HE1 A:PHE191 4.7 29.3 1.0 HB1 A:ALA200 4.7 21.0 1.0 H62 A:BCN702 4.8 62.0 0.8 HG2 A:GLU197 4.8 26.1 0.4 CB A:ALA200 4.9 17.5 1.0 CB A:GLU197 4.9 20.6 0.4 HG3 A:GLU197 4.9 25.3 0.6 CA A:GLU197 4.9 18.7 0.4 HB2 A:ALA200 5.0 21.0 1.0 CA A:GLU197 5.0 18.6 0.6

Zinc binding site 2 out of 2 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F 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) E153A Y189F From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:19.8 occ:1.00 O4 B:BCN303 2.0 28.5 1.0 OE1 B:GLU197 2.1 23.6 1.0 NE2 B:HIS157 2.1 20.1 1.0 O21 B:BCN303 2.2 26.5 1.0 NE2 B:HIS153 2.2 19.4 1.0 N1 B:BCN303 2.4 25.5 1.0 HO4 B:BCN303 2.6 34.2 1.0 H51 B:BCN303 2.9 45.1 1.0 C2 B:BCN303 2.9 50.2 1.0 C4 B:BCN303 2.9 35.5 1.0 CD2 B:HIS153 3.0 18.0 1.0 CD B:GLU197 3.0 29.6 1.0 C1 B:BCN303 3.0 34.5 1.0 HD2 B:HIS153 3.0 21.7 1.0 C3 B:BCN303 3.0 31.1 1.0 CD2 B:HIS157 3.1 23.0 1.0 CE1 B:HIS157 3.1 21.1 1.0 C5 B:BCN303 3.2 37.6 1.0 OE2 B:GLU197 3.2 34.2 1.0 HD2 B:HIS157 3.2 27.6 1.0 CE1 B:HIS153 3.3 19.2 1.0 HE1 B:HIS157 3.3 25.3 1.0 H11 B:BCN303 3.4 41.5 1.0 H41 B:BCN303 3.5 42.6 1.0 H32 B:BCN303 3.5 37.4 1.0 HE1 B:HIS153 3.5 23.1 1.0 H52 B:BCN303 3.6 45.1 1.0 H42 B:BCN303 3.7 42.6 1.0 H12 B:BCN303 3.8 41.5 1.0 H31 B:BCN303 3.9 37.4 1.0 O22 B:BCN303 4.1 38.5 1.0 CG B:HIS153 4.2 15.4 1.0 HA B:GLU197 4.2 20.7 1.0 ND1 B:HIS157 4.2 20.4 1.0 CG B:HIS157 4.2 18.2 1.0 ND1 B:HIS153 4.3 18.1 1.0 O B:HOH404 4.3 33.3 1.0 HB3 B:ALA200 4.3 18.6 1.0 CG B:GLU197 4.4 17.8 1.0 C6 B:BCN303 4.5 54.1 1.0 H61 B:BCN303 4.6 64.9 1.0 HE1 B:PHE191 4.6 24.6 1.0 HB3 B:GLU197 4.7 23.7 1.0 HB1 B:ALA200 4.8 18.6 1.0 HG3 B:GLU197 4.8 21.3 1.0 CB B:ALA200 4.9 15.5 1.0 CB B:GLU197 4.9 19.8 1.0 HB2 B:ALA200 5.0 18.6 1.0 HG2 B:GLU197 5.0 21.3 1.0 CA B:GLU197 5.0 17.3 1.0

B.Claushuis, F.Wojtalla, H.Van Leeuwen, J.Corver, U.Baumann, P.Hensbergen. Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F From Geobacillus Thermodenitrificans To Be Published.