Zinc in PDB 1hi9: Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.

The structure of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease., PDB code: 1hi9 was solved by H.Remaut, C.Bompard-Gilles, C.Goffin, J.M.Frere, J.Van Beeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	145.110, 165.860, 109.930, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 26.8

The binding sites of Zinc atom in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. (pdb code 1hi9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease., PDB code: 1hi9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:31.8 occ:1.00 NE2 A:HIS104 1.9 31.5 1.0 OE1 A:GLU133 2.0 33.4 1.0 OD2 A:ASP8 2.0 36.5 1.0 O A:HOH2059 2.1 28.8 1.0 CD A:GLU133 2.7 33.1 1.0 OE2 A:GLU133 2.7 30.9 1.0 CE1 A:HIS104 2.9 26.9 1.0 CD2 A:HIS104 2.9 29.8 1.0 CG A:ASP8 3.1 35.7 1.0 ZN A:ZN301 3.1 56.2 1.0 OD1 A:ASP8 3.5 37.2 1.0 NE2 A:HIS115 3.6 36.5 1.0 OE1 A:GLU10 3.8 35.2 1.0 CE1 A:HIS115 3.9 35.5 1.0 ND1 A:HIS104 4.0 30.6 1.0 CG A:HIS104 4.0 29.9 1.0 CG A:GLU133 4.1 33.5 1.0 CE A:MET87 4.2 32.1 1.0 CB A:ASP8 4.4 36.0 1.0 CD A:GLU10 4.5 34.9 1.0 CD2 A:HIS115 4.5 34.4 1.0 CB A:GLU133 4.7 35.0 1.0 OE2 A:GLU10 4.8 36.7 1.0 SD A:MET87 4.8 34.5 1.0 ND1 A:HIS115 5.0 34.7 1.0

Zinc binding site 2 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:56.2 occ:1.00 OD1 A:ASP8 2.3 37.2 1.0 OE1 A:GLU10 2.3 35.2 1.0 ND1 A:HIS60 2.5 36.0 1.0 O A:HOH2059 2.5 28.8 1.0 OE2 A:GLU10 2.8 36.7 1.0 CD A:GLU10 2.9 34.9 1.0 CG A:ASP8 3.1 35.7 1.0 ZN A:ZN300 3.1 31.8 1.0 OD2 A:ASP8 3.2 36.5 1.0 CE1 A:HIS60 3.3 35.3 1.0 CG A:HIS60 3.6 36.5 1.0 CB A:HIS60 3.9 36.0 1.0 CA A:HIS60 4.1 36.4 1.0 NE2 A:HIS115 4.1 36.5 1.0 NE2 A:HIS104 4.2 31.5 1.0 N A:MET9 4.2 33.4 1.0 CG A:GLU10 4.4 35.8 1.0 CE1 A:HIS115 4.4 35.5 1.0 CB A:ASP8 4.4 36.0 1.0 CD2 A:HIS104 4.5 29.8 1.0 NE2 A:HIS60 4.5 35.4 1.0 N A:SER61 4.6 37.3 1.0 N A:GLU10 4.6 30.6 1.0 O A:SER59 4.6 37.6 1.0 CD2 A:HIS60 4.7 35.8 1.0 OE1 A:GLU133 4.8 33.4 1.0 C A:HIS60 4.9 36.7 1.0 CA A:ASP8 4.9 35.1 1.0 CB A:GLU10 5.0 32.9 1.0 CB A:MET9 5.0 32.9 1.0 O A:HOH2001 5.0 39.8 1.0

Zinc binding site 3 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:40.5 occ:1.00 OE1 B:GLU133 2.0 36.5 1.0 NE2 B:HIS104 2.0 35.3 1.0 OD2 B:ASP8 2.0 28.2 1.0 O B:HOH2025 2.1 32.5 1.0 CD B:GLU133 2.6 35.9 1.0 OE2 B:GLU133 2.7 35.8 1.0 CD2 B:HIS104 2.9 33.2 1.0 CE1 B:HIS104 2.9 33.8 1.0 CG B:ASP8 3.1 35.6 1.0 ZN B:ZN301 3.2 63.7 1.0 OD1 B:ASP8 3.5 39.2 1.0 NE2 B:HIS115 3.6 38.9 1.0 O B:HOH2009 3.6 36.9 1.0 OE1 B:GLU10 3.8 38.3 1.0 CE1 B:HIS115 4.0 39.5 1.0 ND1 B:HIS104 4.0 35.3 1.0 CG B:HIS104 4.1 34.5 1.0 CG B:GLU133 4.1 38.2 1.0 CE B:MET87 4.1 34.2 1.0 CB B:ASP8 4.4 37.8 1.0 CD2 B:HIS115 4.5 39.2 1.0 CD B:GLU10 4.6 37.5 1.0 CB B:GLU133 4.6 39.1 1.0 SD B:MET87 4.7 42.1 1.0 OE2 B:GLU10 4.9 38.8 1.0

Zinc binding site 4 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:63.7 occ:1.00 OE1 B:GLU10 2.3 38.3 1.0 OD1 B:ASP8 2.3 39.2 1.0 ND1 B:HIS60 2.5 37.5 1.0 O B:HOH2025 2.6 32.5 1.0 OE2 B:GLU10 2.8 38.8 1.0 CD B:GLU10 2.9 37.5 1.0 CG B:ASP8 3.0 35.6 1.0 OD2 B:ASP8 3.1 28.2 1.0 ZN B:ZN300 3.2 40.5 1.0 CE1 B:HIS60 3.3 39.1 1.0 CG B:HIS60 3.6 38.7 1.0 CB B:HIS60 4.0 39.6 1.0 NE2 B:HIS115 4.1 38.9 1.0 NE2 B:HIS104 4.1 35.3 1.0 CA B:HIS60 4.2 39.1 1.0 N B:MET9 4.3 37.9 1.0 CE1 B:HIS115 4.4 39.5 1.0 CG B:GLU10 4.4 36.6 1.0 CB B:ASP8 4.4 37.8 1.0 CD2 B:HIS104 4.4 33.2 1.0 NE2 B:HIS60 4.5 40.3 1.0 N B:GLU10 4.6 34.4 1.0 N B:SER61 4.6 40.4 1.0 CD2 B:HIS60 4.7 38.9 1.0 O B:SER59 4.7 41.6 1.0 OE1 B:GLU133 4.8 36.5 1.0 C B:HIS60 4.9 38.7 1.0 CA B:ASP8 4.9 37.9 1.0 CB B:GLU10 5.0 34.0 1.0

Zinc binding site 5 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:42.7 occ:1.00 OD2 C:ASP8 2.0 31.4 1.0 NE2 C:HIS104 2.0 34.7 1.0 OE1 C:GLU133 2.0 38.8 1.0 O C:HOH2037 2.1 32.2 1.0 CD C:GLU133 2.6 37.0 1.0 OE2 C:GLU133 2.7 37.9 1.0 CD2 C:HIS104 2.9 33.2 1.0 CE1 C:HIS104 2.9 35.7 1.0 CG C:ASP8 3.1 37.3 1.0 ZN C:ZN301 3.2 60.2 1.0 OD1 C:ASP8 3.5 39.2 1.0 NE2 C:HIS115 3.6 42.4 1.0 OE1 C:GLU10 3.8 37.2 1.0 CE1 C:HIS115 4.0 41.9 1.0 ND1 C:HIS104 4.0 36.8 1.0 CG C:HIS104 4.1 34.9 1.0 CG C:GLU133 4.1 38.1 1.0 CE C:MET87 4.1 34.8 1.0 CB C:ASP8 4.4 36.4 1.0 CD C:GLU10 4.5 37.8 1.0 CD2 C:HIS115 4.6 39.5 1.0 CB C:GLU133 4.6 38.8 1.0 SD C:MET87 4.7 37.7 1.0 OE2 C:GLU10 4.9 38.8 1.0

Zinc binding site 6 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:60.2 occ:1.00 OD1 C:ASP8 2.3 39.2 1.0 OE1 C:GLU10 2.4 37.2 1.0 ND1 C:HIS60 2.5 37.1 1.0 O C:HOH2037 2.6 32.2 1.0 OE2 C:GLU10 2.9 38.8 1.0 CD C:GLU10 3.0 37.8 1.0 CG C:ASP8 3.1 37.3 1.0 OD2 C:ASP8 3.2 31.4 1.0 ZN C:ZN300 3.2 42.7 1.0 CE1 C:HIS60 3.3 36.8 1.0 CG C:HIS60 3.5 36.5 1.0 CB C:HIS60 3.9 39.2 1.0 CA C:HIS60 4.1 39.2 1.0 NE2 C:HIS115 4.2 42.4 1.0 NE2 C:HIS104 4.2 34.7 1.0 N C:MET9 4.3 36.0 1.0 CB C:ASP8 4.4 36.4 1.0 CE1 C:HIS115 4.5 41.9 1.0 CG C:GLU10 4.5 37.3 1.0 NE2 C:HIS60 4.5 37.6 1.0 N C:SER61 4.5 40.7 1.0 CD2 C:HIS104 4.5 33.2 1.0 O C:SER59 4.6 37.1 1.0 CD2 C:HIS60 4.6 38.2 1.0 N C:GLU10 4.6 35.2 1.0 C C:HIS60 4.8 40.4 1.0 OE1 C:GLU133 4.9 38.8 1.0 CA C:ASP8 4.9 36.3 1.0 CB C:MET9 5.0 38.1 1.0

Zinc binding site 7 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:33.5 occ:1.00 OE1 D:GLU133 1.9 35.7 1.0 NE2 D:HIS104 2.0 26.6 1.0 OD2 D:ASP8 2.0 35.2 1.0 O D:HOH2053 2.1 35.3 1.0 CD D:GLU133 2.6 35.7 1.0 OE2 D:GLU133 2.6 35.8 1.0 CE1 D:HIS104 2.9 29.2 1.0 CD2 D:HIS104 3.0 26.0 1.0 CG D:ASP8 3.1 36.5 1.0 ZN D:ZN301 3.2 57.0 1.0 O D:HOH2003 3.4 38.4 1.0 OD1 D:ASP8 3.5 38.5 1.0 NE2 D:HIS115 3.6 37.5 1.0 OE1 D:GLU10 3.9 34.6 1.0 CE1 D:HIS115 4.0 37.6 1.0 CG D:GLU133 4.0 35.5 1.0 ND1 D:HIS104 4.0 26.4 1.0 CG D:HIS104 4.1 28.5 1.0 CE D:MET87 4.2 31.7 1.0 CB D:ASP8 4.4 36.9 1.0 CD2 D:HIS115 4.6 37.4 1.0 CB D:GLU133 4.6 35.4 1.0 CD D:GLU10 4.6 35.5 1.0 SD D:MET87 4.7 34.0 1.0 OE2 D:GLU10 4.9 37.3 1.0 ND1 D:HIS115 5.0 37.1 1.0

Zinc binding site 8 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:57.0 occ:1.00 OE1 D:GLU10 2.3 34.6 1.0 OD1 D:ASP8 2.3 38.5 1.0 O D:HOH2053 2.5 35.3 1.0 ND1 D:HIS60 2.5 34.9 1.0 OE2 D:GLU10 2.8 37.3 1.0 CD D:GLU10 2.9 35.5 1.0 CG D:ASP8 3.1 36.5 1.0 ZN D:ZN300 3.2 33.5 1.0 OD2 D:ASP8 3.2 35.2 1.0 CE1 D:HIS60 3.4 34.0 1.0 CG D:HIS60 3.6 32.9 1.0 CB D:HIS60 4.0 34.3 1.0 NE2 D:HIS115 4.1 37.5 1.0 NE2 D:HIS104 4.1 26.6 1.0 CA D:HIS60 4.2 35.0 1.0 N D:MET9 4.3 36.1 1.0 CE1 D:HIS115 4.3 37.6 1.0 CG D:GLU10 4.3 36.0 1.0 CD2 D:HIS104 4.4 26.0 1.0 CB D:ASP8 4.5 36.9 1.0 NE2 D:HIS60 4.5 33.7 1.0 N D:GLU10 4.6 34.3 1.0 N D:SER61 4.6 35.8 1.0 O D:SER59 4.7 36.4 1.0 CD2 D:HIS60 4.7 34.0 1.0 OE1 D:GLU133 4.8 35.7 1.0 C D:HIS60 4.9 34.5 1.0 CA D:ASP8 4.9 36.8 1.0 CB D:GLU10 5.0 33.6 1.0

Zinc binding site 9 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:28.9 occ:1.00 OE1 E:GLU133 1.9 32.6 1.0 NE2 E:HIS104 2.0 26.6 1.0 O E:HOH2073 2.0 24.0 1.0 OD2 E:ASP8 2.1 29.8 1.0 CD E:GLU133 2.5 33.7 1.0 OE2 E:GLU133 2.6 31.6 1.0 CE1 E:HIS104 2.9 30.4 1.0 CD2 E:HIS104 3.0 30.7 1.0 CG E:ASP8 3.1 33.4 1.0 ZN E:ZN301 3.2 51.3 1.0 NE2 E:HIS115 3.6 38.9 1.0 OD1 E:ASP8 3.6 31.6 1.0 OE1 E:GLU10 3.9 35.2 1.0 CE1 E:HIS115 3.9 38.8 1.0 CG E:GLU133 4.0 35.0 1.0 ND1 E:HIS104 4.0 28.4 1.0 CG E:HIS104 4.1 31.1 1.0 CE E:MET87 4.1 33.1 1.0 CB E:ASP8 4.4 34.0 1.0 CD2 E:HIS115 4.5 36.9 1.0 CD E:GLU10 4.6 33.9 1.0 CB E:GLU133 4.6 34.5 1.0 SD E:MET87 4.8 30.2 1.0 OE2 E:GLU10 4.9 34.4 1.0 ND1 E:HIS115 5.0 36.1 1.0

Zinc binding site 10 out of 10 in the Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis, A Self- Compartmentalizing Protease. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:51.3 occ:1.00 OE1 E:GLU10 2.3 35.2 1.0 OD1 E:ASP8 2.3 31.6 1.0 ND1 E:HIS60 2.5 30.8 1.0 O E:HOH2073 2.5 24.0 1.0 OE2 E:GLU10 2.8 34.4 1.0 CD E:GLU10 2.9 33.9 1.0 CG E:ASP8 3.1 33.4 1.0 OD2 E:ASP8 3.2 29.8 1.0 ZN E:ZN300 3.2 28.9 1.0 CE1 E:HIS60 3.3 32.0 1.0 CG E:HIS60 3.6 31.6 1.0 CB E:HIS60 3.9 33.3 1.0 CA E:HIS60 4.1 34.2 1.0 NE2 E:HIS115 4.2 38.9 1.0 N E:MET9 4.2 33.4 1.0 NE2 E:HIS104 4.2 26.6 1.0 CG E:GLU10 4.4 35.3 1.0 CE1 E:HIS115 4.4 38.8 1.0 CB E:ASP8 4.4 34.0 1.0 CD2 E:HIS104 4.5 30.7 1.0 NE2 E:HIS60 4.5 32.2 1.0 N E:GLU10 4.6 33.5 1.0 O E:HOH2002 4.6 38.0 1.0 N E:SER61 4.6 35.8 1.0 CD2 E:HIS60 4.6 31.9 1.0 O E:SER59 4.6 30.3 1.0 OE1 E:GLU133 4.8 32.6 1.0 C E:HIS60 4.9 35.1 1.0 CA E:ASP8 4.9 33.6 1.0 CB E:MET9 4.9 35.2 1.0 CB E:GLU10 5.0 33.0 1.0 CA E:MET9 5.0 35.1 1.0

H.Remaut, C.Bompard-Gilles, C.Goffin, J.M.Frere, J.Van Beeumen. Structure of the Bacillus Subtilis D-Aminopeptidase Dppa Reveals A Novel Self-Compartmentalizing Protease Nat.Struct.Biol. V. 8 674 2001.
ISSN: ISSN 1072-8368
PubMed: 11473256
DOI: 10.1038/90380