Zinc in PDB 7cf6: Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide

The structure of Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide, PDB code: 7cf6 was solved by I.Dhanasingh, J.W.La, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.66 / 2.75
Space group	P 2 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.609, 150.425, 151.996, 90, 90, 90
R / Rfree (%)	19.6 / 27.8

The binding sites of Zinc atom in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide (pdb code 7cf6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide, PDB code: 7cf6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:49.8 occ:1.00 ND1 B:HIS195 2.2 35.4 1.0 NE2 B:HIS224 2.2 48.3 1.0 OE1 B:GLU156 2.3 38.2 1.0 CD2 B:HIS224 2.8 46.8 1.0 O02 B:FWO405 2.9 69.8 1.0 CE1 B:HIS195 3.0 36.8 1.0 ZN B:ZN407 3.1 105.3 1.0 CG B:HIS195 3.2 32.8 1.0 CD B:GLU156 3.3 37.4 1.0 CE1 B:HIS224 3.4 52.1 1.0 OE2 B:GLU156 3.6 35.8 1.0 CB B:HIS195 3.6 32.8 1.0 OH B:TYR130 3.7 53.2 1.0 C14 B:FWO405 4.0 66.6 1.0 CG B:HIS224 4.0 45.7 1.0 NE2 B:HIS61 4.2 51.1 1.0 NE2 B:HIS195 4.2 35.1 1.0 N07 B:FWO405 4.3 48.2 1.0 ND1 B:HIS224 4.3 49.6 1.0 CD2 B:HIS195 4.3 33.6 1.0 CE1 B:HIS61 4.4 51.7 1.0 CE1 B:TYR130 4.4 47.6 1.0 CA B:HIS195 4.4 35.7 1.0 CZ B:TYR130 4.5 51.3 1.0 C16 B:FWO405 4.5 49.4 1.0 CG B:GLU156 4.6 37.4 1.0 C13 B:FWO405 4.8 57.6 1.0 CG2 B:THR223 4.8 35.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:105.3 occ:1.00 N07 B:FWO405 2.3 48.2 1.0 NE2 B:HIS63 2.6 44.6 1.0 OD1 B:ASP285 2.7 51.7 1.0 OE2 B:GLU156 2.8 35.8 1.0 NE2 B:HIS61 2.9 51.1 1.0 ZN B:ZN406 3.1 49.8 1.0 C16 B:FWO405 3.3 49.4 1.0 O02 B:FWO405 3.3 69.8 1.0 CG B:ASP285 3.5 50.3 1.0 CD2 B:HIS63 3.6 45.5 1.0 CE1 B:HIS63 3.6 45.2 1.0 CD2 B:HIS61 3.6 46.7 1.0 CD B:GLU156 3.6 37.4 1.0 OE1 B:GLU156 3.7 38.2 1.0 OD2 B:ASP285 3.8 51.3 1.0 NE2 B:HIS224 3.9 48.3 1.0 CE1 B:HIS61 4.1 51.7 1.0 C14 B:FWO405 4.1 66.6 1.0 C13 B:FWO405 4.3 57.6 1.0 C17 B:FWO405 4.3 44.4 1.0 CE1 B:HIS224 4.3 52.1 1.0 ND1 B:HIS63 4.7 43.9 1.0 CB B:ASP285 4.7 44.0 1.0 CG B:HIS63 4.7 45.0 1.0 CG B:HIS61 4.9 44.6 1.0 O05 B:FWO405 4.9 38.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:48.1 occ:1.00 ND1 A:HIS195 1.9 55.9 1.0 OE1 A:GLU156 2.3 44.5 1.0 CE1 A:HIS224 2.5 49.5 1.0 CE1 A:HIS195 2.6 57.7 1.0 CG A:HIS195 3.0 60.0 1.0 CD A:GLU156 3.1 45.9 1.0 O02 A:FWO405 3.2 85.9 1.0 OE2 A:GLU156 3.3 48.4 1.0 NE2 A:HIS224 3.3 51.2 1.0 ND1 A:HIS224 3.4 49.5 1.0 N07 A:FWO405 3.5 80.9 1.0 CB A:HIS195 3.5 58.6 1.0 ZN A:ZN407 3.6 74.1 1.0 NE2 A:HIS195 3.7 57.5 1.0 OH A:TYR130 3.8 37.8 1.0 CD2 A:HIS195 3.9 61.4 1.0 C14 A:FWO405 3.9 86.5 1.0 CE1 A:TYR130 4.2 37.6 1.0 CA A:HIS195 4.4 52.4 1.0 CG A:GLU156 4.4 44.5 1.0 CD2 A:HIS224 4.4 48.9 1.0 CZ A:TYR130 4.4 39.7 1.0 C16 A:FWO405 4.5 79.8 1.0 CG A:HIS224 4.5 42.0 1.0 NE2 A:HIS61 4.5 57.0 1.0 N06 A:FWO405 4.7 95.9 1.0 C13 A:FWO405 4.7 83.0 1.0 C10 A:FWO405 4.8 106.5 1.0 CG2 A:THR223 4.9 34.1 1.0 CE1 A:HIS61 4.9 55.8 1.0 OD2 A:ASP285 5.0 43.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:74.1 occ:1.00 NE2 A:HIS63 2.5 47.1 1.0 OE2 A:GLU156 2.6 48.4 1.0 NE2 A:HIS61 2.7 57.0 1.0 N07 A:FWO405 2.7 80.9 1.0 OD1 A:ASP285 2.7 48.3 1.0 CD2 A:HIS61 3.2 56.8 1.0 CD A:GLU156 3.4 45.9 1.0 CD2 A:HIS63 3.4 42.6 1.0 O02 A:FWO405 3.5 85.9 1.0 OE1 A:GLU156 3.5 44.5 1.0 CG A:ASP285 3.5 43.3 1.0 CE1 A:HIS63 3.6 46.9 1.0 ZN A:ZN406 3.6 48.1 1.0 OD2 A:ASP285 3.7 43.3 1.0 CE1 A:HIS61 3.9 55.8 1.0 C16 A:FWO405 4.2 79.8 1.0 CE1 A:HIS224 4.5 49.5 1.0 CG A:HIS61 4.5 57.8 1.0 C14 A:FWO405 4.5 86.5 1.0 NE2 A:HIS224 4.5 51.2 1.0 CG A:HIS63 4.6 44.6 1.0 ND1 A:HIS63 4.6 45.6 1.0 SG A:CYS96 4.6 41.9 1.0 CG A:GLU156 4.7 44.5 1.0 ND1 A:HIS61 4.8 56.4 1.0 CB A:ASP285 4.8 42.0 1.0 C17 A:FWO405 4.9 64.1 1.0 C13 A:FWO405 4.9 83.0 1.0 O04 A:FWO405 5.0 51.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn406 b:88.8 occ:1.00 OE2 C:GLU156 2.5 44.6 1.0 N07 C:FWO405 2.9 75.8 1.0 NE2 C:HIS61 2.9 53.1 1.0 ZN C:ZN407 3.0 52.6 1.0 OD1 C:ASP285 3.0 49.6 1.0 OE1 C:GLU156 3.0 48.7 1.0 NE2 C:HIS63 3.1 40.7 1.0 CD C:GLU156 3.1 51.1 1.0 OD2 C:ASP285 3.5 54.4 1.0 CG C:ASP285 3.5 48.1 1.0 NE2 C:HIS224 3.5 54.4 1.0 CE1 C:HIS61 3.7 53.4 1.0 CD2 C:HIS61 3.7 51.8 1.0 CE1 C:HIS224 3.9 57.4 1.0 CE1 C:HIS63 3.9 46.5 1.0 C16 C:FWO405 4.0 79.4 1.0 CD2 C:HIS63 4.0 42.5 1.0 O05 C:FWO405 4.1 80.9 1.0 C13 C:FWO405 4.3 77.8 1.0 C17 C:FWO405 4.4 79.5 1.0 CG C:GLU156 4.6 50.0 1.0 ND1 C:HIS61 4.7 49.6 1.0 C14 C:FWO405 4.7 84.2 1.0 CG C:HIS61 4.7 48.4 1.0 CB C:ASP285 4.7 48.2 1.0 CD2 C:HIS224 4.8 47.5 1.0 ND1 C:HIS195 5.0 44.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn407 b:52.6 occ:1.00 ND1 C:HIS195 2.0 44.4 1.0 NE2 C:HIS224 2.4 54.4 1.0 OE1 C:GLU156 2.5 48.7 1.0 CE1 C:HIS195 2.9 48.0 1.0 CD2 C:HIS224 3.0 47.5 1.0 N07 C:FWO405 3.0 75.8 1.0 ZN C:ZN406 3.0 88.8 1.0 CG C:HIS195 3.1 44.0 1.0 CD C:GLU156 3.3 51.1 1.0 OH C:TYR130 3.4 57.9 1.0 CB C:HIS195 3.5 41.6 1.0 OE2 C:GLU156 3.6 44.6 1.0 CE1 C:HIS224 3.6 57.4 1.0 O02 C:FWO405 3.8 82.5 1.0 NE2 C:HIS195 4.0 48.9 1.0 C14 C:FWO405 4.0 84.2 1.0 CD2 C:HIS195 4.1 47.6 1.0 CE1 C:TYR130 4.2 51.7 1.0 CZ C:TYR130 4.2 55.2 1.0 CG C:HIS224 4.2 47.6 1.0 C16 C:FWO405 4.3 79.4 1.0 CA C:HIS195 4.3 43.9 1.0 N06 C:FWO405 4.5 88.9 1.0 CG C:GLU156 4.5 50.0 1.0 ND1 C:HIS224 4.5 53.8 1.0 C13 C:FWO405 4.6 77.8 1.0 C10 C:FWO405 4.8 93.4 1.0 NE2 C:HIS61 4.9 53.1 1.0 CE1 C:HIS61 4.9 53.4 1.0 C08 C:FWO405 5.0 89.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn403 b:123.7 occ:1.00 N07 D:FWO402 2.2 70.8 1.0 OE2 D:GLU156 2.4 54.9 1.0 NE2 D:HIS63 2.7 62.9 1.0 CE1 D:HIS61 2.8 60.7 1.0 OD1 D:ASP285 2.8 51.9 1.0 CD2 D:HIS63 3.3 60.9 1.0 CD D:GLU156 3.3 52.0 1.0 ZN D:ZN404 3.4 66.2 1.0 C16 D:FWO402 3.4 75.0 1.0 OE1 D:GLU156 3.5 43.2 1.0 CG D:ASP285 3.6 56.2 1.0 ND1 D:HIS61 3.7 61.3 1.0 O02 D:FWO402 3.7 88.6 1.0 NE2 D:HIS61 3.7 62.4 1.0 CE1 D:HIS63 3.8 57.4 1.0 CE1 D:HIS224 3.9 73.4 1.0 OD2 D:ASP285 4.0 54.5 1.0 O05 D:FWO402 4.3 72.4 1.0 C14 D:FWO402 4.3 85.7 1.0 C17 D:FWO402 4.3 78.3 1.0 C13 D:FWO402 4.4 78.8 1.0 NE2 D:HIS224 4.5 74.9 1.0 CG D:HIS63 4.6 58.0 1.0 CG D:GLU156 4.7 53.5 1.0 ND1 D:HIS63 4.8 61.7 1.0 CB D:ASP285 4.9 57.8 1.0 CD2 D:HIS61 4.9 63.2 1.0 CG D:HIS61 4.9 61.9 1.0 SG D:CYS96 5.0 58.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide


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 Beta-Aspartyl Dipeptidase From Thermophilic Keratin Degrading Fervidobacterium Islandicum Aw-1 in Complex with Beta-Asp-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn404 b:66.2 occ:1.00 ND1 D:HIS195 2.0 47.9 1.0 OE1 D:GLU156 2.5 43.2 1.0 CE1 D:HIS224 2.7 73.4 1.0 CE1 D:HIS195 2.9 48.1 1.0 ND1 D:HIS224 3.1 71.7 1.0 CG D:HIS195 3.1 49.5 1.0 ZN D:ZN403 3.4 123.7 1.0 CD D:GLU156 3.5 52.0 1.0 OH D:TYR130 3.5 41.5 1.0 CB D:HIS195 3.6 48.0 1.0 O01 D:FWO402 3.8 118.3 1.0 OE2 D:GLU156 3.8 54.9 1.0 NE2 D:HIS224 3.8 74.9 1.0 C14 D:FWO402 4.0 85.7 1.0 O02 D:FWO402 4.0 88.6 1.0 N07 D:FWO402 4.0 70.8 1.0 NE2 D:HIS195 4.1 45.6 1.0 CD2 D:HIS195 4.2 47.4 1.0 C16 D:FWO402 4.2 75.0 1.0 CA D:HIS195 4.3 43.3 1.0 CG D:HIS224 4.3 68.6 1.0 N06 D:FWO402 4.3 96.0 1.0 CE1 D:TYR130 4.3 37.1 1.0 CZ D:TYR130 4.4 35.4 1.0 C13 D:FWO402 4.4 78.8 1.0 CE1 D:HIS61 4.5 60.7 1.0 C15 D:FWO402 4.6 113.9 1.0 CD2 D:HIS224 4.6 75.4 1.0 NE2 D:HIS61 4.7 62.4 1.0 C10 D:FWO402 4.7 110.9 1.0 CG D:GLU156 4.8 53.5 1.0 CG2 D:THR223 4.9 73.7 1.0

J.W.La, I.Dhanasingh, H.Jang, S.H.Lee, D.W.Lee. Functional Characterization of Primordial Protein Repair Enzyme M38 Metallo-Peptidase From Fervidobacterium Islandicum Aw-1. Front Mol Biosci V. 7 00634 2020.
ISSN: ESSN 2296-889X
PubMed: 33392259
DOI: 10.3389/FMOLB.2020.600634