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Zinc in PDB 5xgw: Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H

Protein crystallography data

The structure of Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H, PDB code: 5xgw 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 / 1.85
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.001, 108.001, 156.236, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H (pdb code 5xgw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H, PDB code: 5xgw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5xgw

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Zinc binding site 1 out of 4 in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:31.9
occ:1.00
NE2 A:HIS71 2.2 17.2 1.0
NE2 A:HIS73 2.2 20.6 1.0
OD1 A:ASP293 2.3 25.2 1.0
OE2 A:GLU166 2.3 22.0 1.0
CE1 A:HIS73 3.1 22.9 1.0
CD A:GLU166 3.1 22.6 1.0
CD2 A:HIS71 3.2 17.4 1.0
CG A:ASP293 3.2 29.7 1.0
CE1 A:HIS71 3.2 15.8 1.0
CD2 A:HIS73 3.3 20.7 1.0
OE1 A:GLU166 3.3 19.0 1.0
OD2 A:ASP293 3.4 39.1 1.0
ZN A:ZN402 3.4 24.1 1.0
O A:HOH760 3.7 48.1 1.0
CD1 A:LEU106 4.3 24.2 1.0
ND1 A:HIS73 4.3 20.8 1.0
CE1 A:HIS234 4.3 16.8 1.0
NE2 A:HIS234 4.3 16.0 1.0
ND1 A:HIS71 4.3 14.5 1.0
CG A:HIS71 4.3 14.9 1.0
CG A:GLU166 4.4 19.0 1.0
CG A:HIS73 4.4 19.3 1.0
CB A:ASP293 4.5 26.0 1.0
CA A:ASP293 4.9 26.0 1.0

Zinc binding site 2 out of 4 in 5xgw

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Zinc binding site 2 out of 4 in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:24.1
occ:1.00
OE1 A:GLU166 2.0 19.0 1.0
NE2 A:HIS234 2.1 16.0 1.0
ND1 A:HIS205 2.1 17.6 1.0
O A:HOH760 2.7 48.1 1.0
CD A:GLU166 2.9 22.6 1.0
CE1 A:HIS205 3.0 18.1 1.0
CD2 A:HIS234 3.0 17.1 1.0
CE1 A:HIS234 3.1 16.8 1.0
OE2 A:GLU166 3.1 22.0 1.0
CG A:HIS205 3.2 17.8 1.0
ZN A:ZN401 3.4 31.9 1.0
CB A:HIS205 3.6 16.9 1.0
CE1 A:HIS71 4.1 15.8 1.0
NE2 A:HIS71 4.1 17.2 1.0
NE2 A:HIS205 4.2 18.2 1.0
CG A:HIS234 4.2 14.9 1.0
ND1 A:HIS234 4.2 15.1 1.0
O A:HOH526 4.2 35.4 1.0
CD2 A:HIS205 4.3 18.2 1.0
CG A:GLU166 4.3 19.0 1.0
CA A:HIS205 4.4 16.5 1.0
OD2 A:ASP293 4.5 39.1 1.0
CE1 A:TYR140 4.5 22.7 1.0
CB A:GLU166 4.9 17.2 1.0
OD1 A:ASP293 4.9 25.2 1.0

Zinc binding site 3 out of 4 in 5xgw

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Zinc binding site 3 out of 4 in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.3
occ:1.00
NE2 B:HIS71 2.2 19.2 1.0
OE1 B:GLU166 2.3 22.7 1.0
NE2 B:HIS73 2.4 22.9 1.0
OD1 B:ASP293 2.4 30.9 1.0
CD2 B:HIS71 3.1 20.1 1.0
CD B:GLU166 3.1 24.9 1.0
CE1 B:HIS71 3.2 20.0 1.0
CG B:ASP293 3.2 35.7 1.0
CE1 B:HIS73 3.3 24.7 1.0
OE2 B:GLU166 3.3 21.2 1.0
CD2 B:HIS73 3.4 21.8 1.0
ZN B:ZN402 3.4 24.9 1.0
OD2 B:ASP293 3.5 42.3 1.0
O B:HOH768 4.1 42.1 1.0
CD1 B:LEU106 4.2 23.3 1.0
CG B:HIS71 4.3 18.5 1.0
NE2 B:HIS234 4.3 19.6 1.0
CE1 B:HIS234 4.3 22.2 1.0
ND1 B:HIS71 4.3 18.1 1.0
CG B:GLU166 4.4 20.9 1.0
O B:HOH759 4.4 38.3 1.0
ND1 B:HIS73 4.4 22.4 1.0
CG B:HIS73 4.5 18.9 1.0
CB B:ASP293 4.5 28.4 1.0
CA B:ASP293 4.9 25.2 1.0

Zinc binding site 4 out of 4 in 5xgw

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Zinc binding site 4 out of 4 in the Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Isoaspartyl Dipeptidase From Colwellia Psychrerythraea Strain 34H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:24.9
occ:1.00
OE2 B:GLU166 2.0 21.2 1.0
ND1 B:HIS205 2.1 19.1 1.0
NE2 B:HIS234 2.1 19.6 1.0
O B:HOH759 2.4 38.3 1.0
CD B:GLU166 2.9 24.9 1.0
CE1 B:HIS205 3.0 20.9 1.0
CD2 B:HIS234 3.0 18.5 1.0
OE1 B:GLU166 3.2 22.7 1.0
CE1 B:HIS234 3.2 22.2 1.0
CG B:HIS205 3.2 18.4 1.0
ZN B:ZN401 3.4 38.3 1.0
CB B:HIS205 3.6 18.7 1.0
O B:HOH768 4.0 42.1 1.0
NE2 B:HIS71 4.1 19.2 1.0
CE1 B:HIS71 4.1 20.0 1.0
NE2 B:HIS205 4.1 20.6 1.0
CG B:HIS234 4.2 17.7 1.0
ND1 B:HIS234 4.3 19.3 1.0
CD2 B:HIS205 4.3 19.2 1.0
CG B:GLU166 4.3 20.9 1.0
CA B:HIS205 4.4 17.9 1.0
O B:HOH510 4.4 30.5 1.0
CE1 B:TYR140 4.5 22.7 1.0
OD2 B:ASP293 4.6 42.3 1.0
CB B:GLU166 4.9 20.4 1.0

Reference:

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
Page generated: Wed Dec 16 11:20:24 2020

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