Zinc in PDB 5xgx: Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine

The structure of Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine, PDB code: 5xgx was solved by J.H.Lee, C.W.Lee, S.H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.33
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.878, 107.878, 155.879, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine (pdb code 5xgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine, PDB code: 5xgx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine


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 Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:94.9 occ:1.00 NE2 A:HIS71 2.4 29.1 1.0 OD1 A:ASP293 2.6 42.2 1.0 OE1 A:GLU166 2.6 40.0 1.0 NE2 A:HIS73 2.8 39.8 1.0 OD1 A:DAS403 2.9 52.6 1.0 CG A:DAS403 3.0 68.8 1.0 CB A:DAS403 3.1 60.8 1.0 CG A:ASP293 3.2 45.0 1.0 ZN A:ZN402 3.2 38.3 1.0 OD2 A:ASP293 3.2 54.2 1.0 OE2 A:GLU166 3.3 36.9 1.0 CD A:GLU166 3.3 37.6 1.0 CD2 A:HIS71 3.3 29.0 1.0 CE1 A:HIS71 3.4 26.9 1.0 CD2 A:HIS73 3.8 34.7 1.0 CE1 A:HIS73 3.8 42.3 1.0 CE1 A:HIS234 3.9 27.9 1.0 NE2 A:HIS234 3.9 33.0 1.0 CA A:DAS403 4.0 61.2 1.0 N A:DLY404 4.0 82.4 1.0 ND1 A:HIS71 4.5 32.4 1.0 CG A:HIS71 4.5 30.4 1.0 CB A:ASP293 4.5 41.9 1.0 CB A:DLY404 4.7 0.8 1.0 CG A:GLU166 4.7 37.3 1.0 CD1 A:LEU106 4.8 33.8 1.0 ND1 A:HIS73 4.9 39.8 1.0 N A:DAS403 5.0 67.1 1.0 CG A:HIS73 5.0 37.6 1.0 CA A:DLY404 5.0 92.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine


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 Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:38.3 occ:1.00 OE2 A:GLU166 1.8 36.9 1.0 ND1 A:HIS205 2.0 29.2 1.0 NE2 A:HIS234 2.1 33.0 1.0 OD1 A:DAS403 2.2 52.6 1.0 CD A:GLU166 2.8 37.6 1.0 CE1 A:HIS205 2.9 27.1 1.0 CD2 A:HIS234 3.0 31.9 1.0 CG A:HIS205 3.1 29.5 1.0 CE1 A:HIS234 3.2 27.9 1.0 ZN A:ZN401 3.2 94.9 1.0 CG A:DAS403 3.4 68.8 1.0 OE1 A:GLU166 3.4 40.0 1.0 CB A:HIS205 3.6 31.5 1.0 OH A:TYR140 3.7 36.0 1.0 CB A:DLY404 3.8 0.8 1.0 CG A:GLU166 4.0 37.3 1.0 NE2 A:HIS205 4.1 28.7 1.0 CG A:HIS234 4.2 28.8 1.0 CE1 A:TYR140 4.2 32.3 1.0 CD2 A:HIS205 4.2 30.6 1.0 OXT A:DLY404 4.2 0.5 1.0 CE1 A:HIS71 4.2 26.9 1.0 NE2 A:HIS71 4.2 29.1 1.0 ND1 A:HIS234 4.2 28.0 1.0 N A:DLY404 4.2 82.4 1.0 CZ A:TYR140 4.4 34.9 1.0 CA A:DLY404 4.4 92.2 1.0 CA A:HIS205 4.4 30.5 1.0 CB A:DAS403 4.4 60.8 1.0 C A:DLY404 4.5 92.5 1.0 CA A:DAS403 4.9 61.2 1.0 CG2 A:THR233 4.9 32.5 1.0 OD2 A:ASP293 4.9 54.2 1.0 N A:DAS403 5.0 67.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine


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 Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.5 occ:1.00 N B:DAS403 2.5 61.1 1.0 O B:HOH505 2.5 39.2 1.0 NE2 B:HIS71 2.5 32.2 1.0 OE1 B:GLU166 2.6 30.3 1.0 OD1 B:ASP293 2.9 37.8 1.0 ZN B:ZN402 3.0 39.2 1.0 OD2 B:ASP293 3.1 51.0 1.0 CD B:GLU166 3.3 31.3 1.0 CG B:ASP293 3.3 43.2 1.0 NE2 B:HIS73 3.3 39.7 1.0 OE2 B:GLU166 3.3 31.6 1.0 CE1 B:HIS71 3.5 31.5 1.0 CD2 B:HIS71 3.5 30.4 1.0 NE2 B:HIS234 3.6 32.6 1.0 CE1 B:HIS234 3.7 29.6 1.0 CA B:DAS403 3.8 63.2 1.0 N B:DLY404 4.0 87.7 1.0 CD2 B:HIS73 4.2 37.2 1.0 CE1 B:HIS73 4.2 42.5 1.0 CB B:DAS403 4.3 71.1 1.0 ND1 B:HIS71 4.6 34.2 1.0 CB B:ASP293 4.6 41.7 1.0 CG B:HIS71 4.6 32.8 1.0 CG B:GLU166 4.6 32.7 1.0 CG B:DAS403 4.7 79.2 1.0 CB B:DLY404 4.7 0.2 1.0 CD2 B:HIS234 4.9 30.2 1.0 C B:DAS403 4.9 56.1 1.0 CD1 B:LEU106 5.0 30.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine


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 Colwellia Psychrerythraea Strain 34H Isoaspartyl Dipeptidase E80Q Mutant Complexed with Beta-Isoaspartyl Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:39.2 occ:1.00 O B:HOH505 1.8 39.2 1.0 OE2 B:GLU166 2.1 31.6 1.0 ND1 B:HIS205 2.1 30.4 1.0 NE2 B:HIS234 2.2 32.6 1.0 CD B:GLU166 2.9 31.3 1.0 CD2 B:HIS234 2.9 30.2 1.0 ZN B:ZN401 3.0 0.5 1.0 CG B:HIS205 3.1 27.9 1.0 OE1 B:GLU166 3.1 30.3 1.0 CE1 B:HIS205 3.1 31.2 1.0 CB B:HIS205 3.3 30.0 1.0 CE1 B:HIS234 3.3 29.6 1.0 OH B:TYR140 3.8 43.9 1.0 N B:DLY404 3.9 87.7 1.0 CA B:HIS205 4.1 27.9 1.0 CB B:DLY404 4.1 0.2 1.0 CE1 B:HIS71 4.2 31.5 1.0 NE2 B:HIS71 4.2 32.2 1.0 CG B:HIS234 4.2 29.8 1.0 N B:DAS403 4.2 61.1 1.0 CD2 B:HIS205 4.2 29.4 1.0 NE2 B:HIS205 4.2 30.0 1.0 CE1 B:TYR140 4.2 33.6 1.0 CG B:GLU166 4.3 32.7 1.0 ND1 B:HIS234 4.3 28.3 1.0 CZ B:TYR140 4.5 37.0 1.0 CB B:DAS403 4.5 71.1 1.0 CA B:DLY404 4.6 0.7 1.0 CG B:DAS403 4.7 79.2 1.0 CB B:GLU166 4.8 31.1 1.0 OD2 B:ASP293 5.0 51.0 1.0

S.H.Park, C.W.Lee, S.G.Lee, S.C.Shin, H.J.Kim, H.Park, J.H.Lee. Crystal Structure and Functional Characterization of An Isoaspartyl Dipeptidase (Cpsiada) From Colwellia Psychrerythraea Strain 34H. Plos One V. 12 81705 2017.
ISSN: ESSN 1932-6203
PubMed: 28723955
DOI: 10.1371/JOURNAL.PONE.0181705