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Zinc in PDB 1pok: Crystal Structure of Isoaspartyl Dipeptidase

Protein crystallography data

The structure of Crystal Structure of Isoaspartyl Dipeptidase, PDB code: 1pok was solved by D.Jozic, J.T.Kaiser, R.Huber, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.475, 117.475, 137.955, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Isoaspartyl Dipeptidase (pdb code 1pok). 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 Isoaspartyl Dipeptidase, PDB code: 1pok:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1pok

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Zinc binding site 1 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:77.3
occ:0.70
OQ2 B:KCX162 2.0 60.5 1.0
OD1 B:ASP285 2.2 41.5 1.0
NE2 B:HIS70 2.6 30.8 1.0
ZN B:ZN604 2.7 66.8 1.0
NE2 B:HIS68 3.0 33.1 1.0
CX B:KCX162 3.1 59.5 1.0
CG B:ASP285 3.1 40.9 1.0
O B:ASN401 3.1 68.7 1.0
CE1 B:HIS70 3.1 29.9 1.0
OQ1 B:KCX162 3.4 60.8 1.0
OD2 B:ASP285 3.4 40.9 1.0
CD2 B:HIS68 3.5 32.1 1.0
O1 B:SO4391 3.6 13.2 0.4
CD2 B:HIS70 3.9 29.8 1.0
CE1 B:HIS230 4.1 52.8 1.0
C B:ASN401 4.1 69.0 1.0
NE2 B:HIS230 4.2 52.5 1.0
CE1 B:HIS68 4.2 33.3 1.0
NZ B:KCX162 4.3 56.0 1.0
CB B:ASP285 4.4 38.2 1.0
ND1 B:HIS70 4.4 29.0 1.0
OXT B:ASN401 4.6 70.8 1.0
OH B:TYR137 4.6 47.6 1.0
S B:SO4391 4.8 15.8 0.4
O4 B:SO4391 4.8 14.1 0.4
CG B:HIS70 4.8 28.6 1.0
CG B:HIS68 4.8 31.6 1.0
CA B:ASP285 5.0 38.3 1.0
ND1 B:HIS201 5.0 45.5 1.0

Zinc binding site 2 out of 4 in 1pok

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Zinc binding site 2 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:66.8
occ:1.00
OQ1 B:KCX162 2.2 60.8 1.0
ND1 B:HIS201 2.3 45.5 1.0
ZN B:ZN603 2.7 77.3 0.7
CX B:KCX162 2.9 59.5 1.0
OQ2 B:KCX162 2.9 60.5 1.0
O B:ASN401 3.0 68.7 1.0
CE1 B:HIS201 3.1 45.8 1.0
CE1 B:HIS230 3.2 52.8 1.0
OH B:TYR137 3.3 47.6 1.0
CG B:HIS201 3.3 43.2 1.0
NE2 B:HIS230 3.4 52.5 1.0
CB B:HIS201 3.8 40.1 1.0
NE2 B:HIS68 3.8 33.1 1.0
CE2 B:TYR137 3.8 46.7 1.0
ND1 B:HIS230 3.9 52.1 1.0
CZ B:TYR137 4.0 47.6 1.0
C B:ASN401 4.0 69.0 1.0
NZ B:KCX162 4.1 56.0 1.0
NE2 B:HIS201 4.2 44.9 1.0
N B:ASN401 4.2 67.1 1.0
CD2 B:HIS230 4.3 50.5 1.0
CD2 B:HIS201 4.3 44.2 1.0
OD1 B:ASP285 4.4 41.5 1.0
CA B:ASN401 4.5 68.0 1.0
CE1 B:HIS68 4.5 33.3 1.0
CG B:HIS230 4.5 49.2 1.0
O1 B:SO4391 4.6 13.2 0.4
CA B:HIS201 4.6 37.5 1.0
OD2 B:ASP285 4.6 40.9 1.0
CG B:ASP285 4.8 40.9 1.0
CE B:KCX162 4.8 50.8 1.0
CD2 B:HIS68 4.9 32.1 1.0

Zinc binding site 3 out of 4 in 1pok

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Zinc binding site 3 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:42.6
occ:0.70
OQ2 A:KCX162 2.1 46.0 1.0
NE2 A:HIS70 2.4 25.3 1.0
OD1 A:ASP285 2.6 34.1 1.0
NE2 A:HIS68 2.7 22.9 1.0
ZN A:ZN602 3.0 42.9 0.7
CX A:KCX162 3.1 43.7 1.0
CG A:ASP285 3.2 36.0 1.0
OD2 A:ASP285 3.3 34.5 1.0
CE1 A:HIS70 3.3 26.1 1.0
CD2 A:HIS68 3.4 25.5 1.0
OQ1 A:KCX162 3.4 41.5 1.0
CD2 A:HIS70 3.4 24.9 1.0
CE1 A:HIS68 3.6 23.6 1.0
O3 A:SO4391 3.8 20.5 0.4
O A:ASN400 4.0 62.7 1.0
CE1 A:HIS230 4.2 41.0 1.0
NE2 A:HIS230 4.2 39.5 1.0
NZ A:KCX162 4.2 41.2 1.0
CD2 A:LEU103 4.4 22.3 1.0
CG A:HIS68 4.5 25.9 1.0
ND1 A:HIS70 4.5 25.9 1.0
CB A:ASP285 4.5 36.2 1.0
ND1 A:HIS68 4.5 25.1 1.0
CG A:HIS70 4.6 24.8 1.0
CA A:ASP285 4.7 37.8 1.0
S A:SO4391 4.8 21.7 0.4
O2 A:SO4391 4.9 19.6 0.4
ND1 A:HIS201 5.0 30.2 1.0

Zinc binding site 4 out of 4 in 1pok

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Zinc binding site 4 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:42.9
occ:0.70
OQ1 A:KCX162 2.0 41.5 1.0
ND1 A:HIS201 2.0 30.2 1.0
CE1 A:HIS230 2.4 41.0 1.0
CE1 A:HIS201 2.5 30.1 1.0
CX A:KCX162 2.8 43.7 1.0
OQ2 A:KCX162 2.8 46.0 1.0
ZN A:ZN601 3.0 42.6 0.7
O A:ASN400 3.2 62.7 1.0
CG A:HIS201 3.3 30.9 1.0
OH A:TYR137 3.3 43.4 1.0
ND1 A:HIS230 3.3 40.4 1.0
NE2 A:HIS230 3.3 39.5 1.0
NE2 A:HIS201 3.7 32.0 1.0
NE2 A:HIS68 3.9 22.9 1.0
OD2 A:ASP285 3.9 34.5 1.0
CE1 A:HIS68 4.0 23.6 1.0
CB A:HIS201 4.0 30.3 1.0
NZ A:KCX162 4.0 41.2 1.0
CD2 A:HIS201 4.1 30.2 1.0
CZ A:TYR137 4.1 41.3 1.0
CE2 A:TYR137 4.1 40.7 1.0
C A:ASN400 4.2 62.1 1.0
N A:ASN400 4.3 60.7 1.0
CG A:HIS230 4.5 39.2 1.0
CD2 A:HIS230 4.5 40.0 1.0
CG A:ASP285 4.7 36.0 1.0
OD1 A:ASP285 4.7 34.1 1.0
CE A:KCX162 4.8 37.0 1.0
CA A:HIS201 4.9 30.4 1.0
CA A:ASN400 4.9 60.4 1.0

Reference:

D.Jozic, J.T.Kaiser, R.Huber, W.Bode, K.Maskos. X-Ray Structure of Isoaspartyl Dipeptidase From E.Coli: A Dinuclear Zinc Peptidase Evolved From Amidohydrolases. J.Mol.Biol. V. 332 243 2003.
ISSN: ISSN 0022-2836
PubMed: 12946361
DOI: 10.1016/S0022-2836(03)00845-3
Page generated: Mon Jan 25 16:11:33 2021

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