Zinc in PDB 8dqn: Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157

All present enzymatic activity of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157:
3.4.19.5;

The structure of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157, PDB code: 8dqn was solved by I.Sharon, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.34 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	153.493, 163.691, 170.453, 90, 90, 90
R / Rfree (%)	16.6 / 18.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 (pdb code 8dqn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157, PDB code: 8dqn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:76.6 occ:1.00 ND1 A:HIS198 2.1 45.6 1.0 NE2 A:HIS227 2.4 57.9 1.0 OE1 A:GLU159 2.4 31.2 1.0 O A:HOH750 2.9 39.1 1.0 CE1 A:HIS198 3.1 45.0 1.0 O A:HOH559 3.1 40.3 1.0 CG A:HIS198 3.1 40.1 1.0 CD2 A:HIS227 3.1 54.5 1.0 CD A:GLU159 3.2 31.7 1.0 OE2 A:GLU159 3.4 30.2 1.0 ZN A:ZN403 3.4 101.4 1.0 CB A:HIS198 3.4 30.5 1.0 CE1 A:HIS227 3.4 56.4 1.0 CE1 A:HIS64 4.2 34.9 1.0 NE2 A:HIS198 4.2 41.1 1.0 NE2 A:HIS64 4.2 35.2 1.0 CD2 A:HIS198 4.2 40.5 1.0 CA A:HIS198 4.3 26.7 1.0 CG A:HIS227 4.3 44.0 1.0 ND1 A:HIS227 4.4 49.9 1.0 CE2 A:TYR133 4.5 30.8 1.0 CG A:GLU159 4.5 27.9 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:101.4 occ:1.00 NE2 A:HIS66 2.6 41.6 1.0 O A:HOH750 2.7 39.1 1.0 OD1 A:ASP286 2.8 37.9 1.0 OE2 A:GLU159 2.8 30.2 1.0 NE2 A:HIS64 2.9 35.2 1.0 ZN A:ZN402 3.4 76.6 1.0 CG A:ASP286 3.4 39.4 1.0 CE1 A:HIS66 3.5 38.6 1.0 CD A:GLU159 3.5 31.7 1.0 OD2 A:ASP286 3.5 45.4 1.0 OE1 A:GLU159 3.6 31.2 1.0 CD2 A:HIS66 3.7 34.6 1.0 O4 A:PO4404 3.8 61.8 1.0 CD2 A:HIS64 3.9 33.7 1.0 CE1 A:HIS64 3.9 34.9 1.0 NE2 A:HIS227 4.3 57.9 1.0 CE1 A:HIS227 4.4 56.4 1.0 O1 A:PO4404 4.5 45.7 1.0 ND1 A:HIS66 4.7 32.7 1.0 P A:PO4404 4.7 50.8 1.0 CB A:ASP286 4.8 39.1 1.0 CG A:HIS66 4.8 32.4 1.0 CD1 A:LEU99 4.8 27.3 1.0 O A:HOH559 4.8 40.3 1.0 O A:HOH563 4.8 50.7 1.0 CG A:GLU159 4.9 27.9 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:83.0 occ:1.00 ND1 B:HIS198 2.2 42.6 1.0 NE2 B:HIS227 2.2 54.9 1.0 OE1 B:GLU159 2.4 36.6 1.0 O B:HOH728 2.7 46.0 1.0 CD2 B:HIS227 3.0 54.5 1.0 ZN B:ZN403 3.1 105.7 1.0 CE1 B:HIS198 3.1 41.4 1.0 CG B:HIS198 3.1 33.3 1.0 CD B:GLU159 3.3 34.1 1.0 CE1 B:HIS227 3.3 54.2 1.0 O B:HOH510 3.4 39.2 1.0 CB B:HIS198 3.4 28.2 1.0 OE2 B:GLU159 3.5 39.5 1.0 O B:HOH516 4.0 44.1 1.0 CE1 B:HIS64 4.1 37.0 1.0 NE2 B:HIS64 4.1 35.4 1.0 CG B:HIS227 4.2 42.3 1.0 NE2 B:HIS198 4.2 37.2 1.0 CD2 B:HIS198 4.3 37.2 1.0 CA B:HIS198 4.3 26.1 1.0 ND1 B:HIS227 4.3 50.6 1.0 CE2 B:TYR133 4.6 32.2 1.0 CG B:GLU159 4.6 27.1 1.0 CG2 B:THR226 5.0 25.4 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:105.7 occ:1.00 O B:HOH728 2.4 46.0 1.0 NE2 B:HIS64 2.7 35.4 1.0 OD1 B:ASP286 2.8 35.6 1.0 OE2 B:GLU159 2.9 39.5 1.0 NE2 B:HIS66 2.9 30.0 1.0 ZN B:ZN402 3.1 83.0 1.0 CG B:ASP286 3.3 46.2 1.0 OE1 B:GLU159 3.4 36.6 1.0 OD2 B:ASP286 3.4 49.6 1.0 CD B:GLU159 3.5 34.1 1.0 O B:HOH516 3.6 44.1 1.0 CE1 B:HIS64 3.7 37.0 1.0 CD2 B:HIS64 3.7 31.3 1.0 CE1 B:HIS66 3.7 30.0 1.0 NE2 B:HIS227 3.9 54.9 1.0 CD2 B:HIS66 4.0 30.0 1.0 CE1 B:HIS227 4.0 54.2 1.0 O2 B:PO4404 4.1 83.7 1.0 CB B:ASP286 4.6 40.7 1.0 ND1 B:HIS64 4.8 29.6 1.0 CG B:HIS64 4.8 29.7 1.0 O3 B:PO4404 4.8 57.4 1.0 O B:HOH510 4.8 39.2 1.0 CG B:GLU159 4.9 27.1 1.0 CD1 B:LEU99 4.9 30.1 1.0 ND1 B:HIS66 4.9 30.0 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:75.7 occ:1.00 ND1 C:HIS198 2.1 43.0 1.0 NE2 C:HIS227 2.1 56.7 1.0 OE1 C:GLU159 2.5 33.3 1.0 O C:HOH739 2.8 41.1 1.0 CD2 C:HIS227 2.9 49.1 1.0 CE1 C:HIS198 3.1 43.2 1.0 CG C:HIS198 3.1 39.5 1.0 O C:HOH572 3.2 39.9 1.0 ZN C:ZN403 3.2 109.3 1.0 CE1 C:HIS227 3.2 53.2 1.0 CD C:GLU159 3.3 38.4 1.0 CB C:HIS198 3.4 33.0 1.0 OE2 C:GLU159 3.5 40.0 1.0 CE1 C:HIS64 4.1 35.8 1.0 CG C:HIS227 4.1 42.0 1.0 NE2 C:HIS64 4.1 38.2 1.0 NE2 C:HIS198 4.2 42.4 1.0 CA C:HIS198 4.2 28.4 1.0 CD2 C:HIS198 4.2 42.9 1.0 ND1 C:HIS227 4.2 51.3 1.0 CE2 C:TYR133 4.6 31.3 1.0 CG C:GLU159 4.6 33.1 1.0 O C:HOH582 4.9 62.3 1.0 CG2 C:THR226 4.9 25.6 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:109.3 occ:1.00 O C:HOH739 2.3 41.1 1.0 NE2 C:HIS64 2.7 38.2 1.0 OD1 C:ASP286 2.7 45.5 1.0 OE2 C:GLU159 2.8 40.0 1.0 NE2 C:HIS66 2.9 26.7 1.0 ZN C:ZN402 3.2 75.7 1.0 OE1 C:GLU159 3.4 33.3 1.0 CG C:ASP286 3.4 51.4 1.0 CD C:GLU159 3.4 38.4 1.0 OD2 C:ASP286 3.5 54.3 1.0 CD2 C:HIS64 3.6 34.5 1.0 CE1 C:HIS64 3.6 35.8 1.0 CE1 C:HIS66 3.7 29.1 1.0 O3 C:PO4404 3.8 97.7 1.0 CD2 C:HIS66 3.9 28.2 1.0 NE2 C:HIS227 4.0 56.7 1.0 CE1 C:HIS227 4.1 53.2 1.0 CB C:ASP286 4.6 45.2 1.0 ND1 C:HIS64 4.8 29.6 1.0 O C:HOH572 4.8 39.9 1.0 CG C:HIS64 4.8 30.2 1.0 CD1 C:LEU99 4.8 28.4 1.0 CG C:GLU159 4.8 33.1 1.0 ND1 C:HIS66 4.9 29.3 1.0 O1 C:PO4404 4.9 68.8 1.0 P C:PO4404 4.9 90.2 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:76.3 occ:1.00 ND1 D:HIS198 2.1 42.5 1.0 NE2 D:HIS227 2.3 50.7 1.0 OE1 D:GLU159 2.4 37.8 1.0 O D:HOH724 2.9 45.3 1.0 CG D:HIS198 3.1 35.5 1.0 CE1 D:HIS198 3.1 41.8 1.0 CD2 D:HIS227 3.1 48.9 1.0 CD D:GLU159 3.2 32.6 1.0 CB D:HIS198 3.4 29.5 1.0 ZN D:ZN403 3.4 96.3 1.0 OE2 D:GLU159 3.4 34.0 1.0 CE1 D:HIS227 3.5 52.0 1.0 O D:HOH504 3.6 48.5 1.0 CE1 D:HIS64 4.2 34.7 1.0 NE2 D:HIS198 4.2 38.3 1.0 CD2 D:HIS198 4.2 37.6 1.0 NE2 D:HIS64 4.2 35.5 1.0 CA D:HIS198 4.2 25.3 1.0 CG D:HIS227 4.3 41.5 1.0 CE2 D:TYR133 4.5 34.0 1.0 ND1 D:HIS227 4.5 45.1 1.0 CG D:GLU159 4.5 29.4 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn403 b:96.3 occ:1.00 O D:HOH724 2.5 45.3 1.0 OD1 D:ASP286 2.7 39.4 1.0 NE2 D:HIS66 2.7 39.6 1.0 NE2 D:HIS64 2.8 35.5 1.0 OE2 D:GLU159 2.9 34.0 1.0 CG D:ASP286 3.3 44.1 1.0 OD2 D:ASP286 3.4 47.0 1.0 ZN D:ZN402 3.4 76.3 1.0 OE1 D:GLU159 3.6 37.8 1.0 CE1 D:HIS66 3.6 40.5 1.0 CD D:GLU159 3.6 32.6 1.0 CD2 D:HIS66 3.7 33.8 1.0 CD2 D:HIS64 3.8 30.8 1.0 CE1 D:HIS64 3.8 34.7 1.0 O2 D:PO4404 3.9 67.4 1.0 NE2 D:HIS227 4.2 50.7 1.0 CE1 D:HIS227 4.3 52.0 1.0 CB D:ASP286 4.6 42.0 1.0 O4 D:PO4404 4.6 56.4 1.0 ND1 D:HIS66 4.7 35.2 1.0 P D:PO4404 4.8 61.2 1.0 CG D:HIS66 4.8 29.5 1.0 CD1 D:LEU99 4.8 24.5 1.0 CG D:HIS64 5.0 27.1 1.0 CG D:GLU159 5.0 29.4 1.0 ND1 D:HIS64 5.0 29.7 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:87.7 occ:1.00 NE2 E:HIS227 2.2 62.9 1.0 ND1 E:HIS198 2.3 48.3 1.0 OE1 E:GLU159 2.5 35.7 1.0 O E:HOH638 2.7 45.0 1.0 ZN E:ZN403 3.0 92.9 1.0 CD2 E:HIS227 3.1 56.7 1.0 CE1 E:HIS198 3.2 47.6 1.0 CD E:GLU159 3.3 35.9 1.0 CG E:HIS198 3.3 37.8 1.0 CE1 E:HIS227 3.3 55.5 1.0 O E:HOH603 3.3 46.1 1.0 OE2 E:GLU159 3.4 35.2 1.0 CB E:HIS198 3.6 28.0 1.0 NE2 E:HIS64 4.1 33.4 1.0 CE1 E:HIS64 4.1 35.2 1.0 CG E:HIS227 4.2 45.1 1.0 ND1 E:HIS227 4.3 49.3 1.0 NE2 E:HIS198 4.3 41.3 1.0 CD2 E:HIS198 4.4 40.3 1.0 CA E:HIS198 4.4 24.0 1.0 CE2 E:TYR133 4.6 34.4 1.0 CG E:GLU159 4.7 29.3 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn403 b:92.9 occ:1.00 O E:HOH638 2.5 45.0 1.0 NE2 E:HIS64 2.7 33.4 1.0 OE2 E:GLU159 2.8 35.2 1.0 NE2 E:HIS66 2.8 37.3 1.0 OD1 E:ASP286 2.8 44.3 1.0 ZN E:ZN402 3.0 87.7 1.0 OE1 E:GLU159 3.3 35.7 1.0 CD E:GLU159 3.3 35.9 1.0 CG E:ASP286 3.5 45.3 1.0 CE1 E:HIS66 3.6 38.3 1.0 OD2 E:ASP286 3.6 42.6 1.0 O2 E:PO4404 3.6 85.6 1.0 CE1 E:HIS64 3.6 35.2 1.0 CD2 E:HIS64 3.7 31.9 1.0 CD2 E:HIS66 3.9 33.9 1.0 NE2 E:HIS227 4.0 62.9 1.0 CE1 E:HIS227 4.2 55.5 1.0 O E:HOH603 4.7 46.1 1.0 CG E:GLU159 4.7 29.3 1.0 CB E:ASP286 4.8 43.3 1.0 CD1 E:LEU99 4.8 28.0 1.0 ND1 E:HIS64 4.8 33.2 1.0 ND1 E:HIS66 4.8 33.5 1.0 CG E:HIS64 4.8 32.5 1.0 P E:PO4404 4.8 74.0 1.0 O3 E:PO4404 4.9 62.0 1.0 CG E:HIS66 5.0 33.6 1.0

I.Sharon, T.M.Schmeing. Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 To Be Published.