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Zinc in PDB 1po9: Crytsal Structure of Isoaspartyl Dipeptidase

Protein crystallography data

The structure of Crytsal Structure of Isoaspartyl Dipeptidase, PDB code: 1po9 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 / 2.00
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.644, 116.644, 137.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crytsal Structure of Isoaspartyl Dipeptidase (pdb code 1po9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crytsal Structure of Isoaspartyl Dipeptidase, PDB code: 1po9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1po9

Go back to Zinc Binding Sites List in 1po9
Zinc binding site 1 out of 4 in the Crytsal 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 Crytsal Structure of Isoaspartyl Dipeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:30.5
occ:0.70
O A:HOH774 2.0 40.6 1.0
OQ2 A:KCX162 2.2 37.2 1.0
NE2 A:HIS70 2.2 18.1 1.0
OD1 A:ASP285 2.3 27.5 1.0
NE2 A:HIS68 2.3 19.6 1.0
CE1 A:HIS70 3.0 17.8 1.0
CD2 A:HIS68 3.0 20.5 1.0
CX A:KCX162 3.0 39.4 0.8
ZN A:ZN602 3.3 33.4 0.7
CG A:ASP285 3.3 26.9 1.0
OQ1 A:KCX162 3.3 40.5 1.0
CD2 A:HIS70 3.4 18.9 1.0
CE1 A:HIS68 3.5 21.5 1.0
OD2 A:ASP285 3.7 26.3 1.0
NE2 A:HIS230 4.0 36.3 1.0
CD1 A:LEU103 4.0 17.1 1.0
NZ A:KCX162 4.1 34.2 1.0
ND1 A:HIS70 4.2 17.6 1.0
CG A:HIS68 4.3 18.1 1.0
CG A:HIS70 4.4 18.1 1.0
CE1 A:HIS230 4.4 36.0 1.0
ND1 A:HIS68 4.5 20.4 1.0
CB A:ASP285 4.5 24.4 1.0
CA A:ASP285 4.8 23.1 1.0

Zinc binding site 2 out of 4 in 1po9

Go back to Zinc Binding Sites List in 1po9
Zinc binding site 2 out of 4 in the Crytsal 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 Crytsal Structure of Isoaspartyl Dipeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:33.4
occ:0.70
ND1 A:HIS201 2.0 29.8 1.0
O A:HOH774 2.0 40.6 1.0
OQ1 A:KCX162 2.2 40.5 1.0
NE2 A:HIS230 2.3 36.3 1.0
CE1 A:HIS201 2.8 29.9 1.0
CD2 A:HIS230 2.8 34.1 1.0
CG A:HIS201 3.0 27.4 1.0
CX A:KCX162 3.0 39.4 0.8
OQ2 A:KCX162 3.1 37.2 1.0
OH A:TYR137 3.3 35.0 1.0
ZN A:ZN601 3.3 30.5 0.7
CB A:HIS201 3.5 24.6 1.0
CE1 A:HIS230 3.5 36.0 1.0
NE2 A:HIS68 3.8 19.6 1.0
CE2 A:TYR137 3.8 29.7 1.0
NE2 A:HIS201 3.9 31.7 1.0
CZ A:TYR137 4.0 30.8 1.0
CE1 A:HIS68 4.0 21.5 1.0
CD2 A:HIS201 4.0 28.9 1.0
CG A:HIS230 4.1 30.9 1.0
NZ A:KCX162 4.3 34.2 1.0
CA A:HIS201 4.3 22.8 1.0
ND1 A:HIS230 4.3 31.8 1.0
OD2 A:ASP285 4.7 26.3 1.0
OD1 A:ASP285 4.7 27.5 1.0
CE A:KCX162 4.9 34.4 1.0
CG A:ASP285 5.0 26.9 1.0
CG2 A:THR229 5.0 20.0 1.0

Zinc binding site 3 out of 4 in 1po9

Go back to Zinc Binding Sites List in 1po9
Zinc binding site 3 out of 4 in the Crytsal 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 Crytsal Structure of Isoaspartyl Dipeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:24.1
occ:0.70
O B:HOH624 2.1 42.7 1.0
OQ2 B:KCX162 2.1 27.6 1.0
NE2 B:HIS70 2.2 20.9 1.0
NE2 B:HIS68 2.3 19.0 1.0
OD1 B:ASP285 2.5 26.4 1.0
CX B:KCX162 3.0 32.7 0.8
CE1 B:HIS70 3.1 20.6 1.0
CD2 B:HIS68 3.1 21.9 1.0
OQ1 B:KCX162 3.2 32.8 1.0
ZN B:ZN604 3.3 25.4 0.7
CD2 B:HIS70 3.3 20.0 1.0
CG B:ASP285 3.3 28.5 1.0
CE1 B:HIS68 3.4 20.6 1.0
OD2 B:ASP285 3.7 29.9 1.0
O B:HOH879 3.8 42.4 1.0
CD1 B:LEU103 4.0 16.7 1.0
O B:HOH810 4.1 45.7 1.0
NE2 B:HIS230 4.1 29.7 1.0
NZ B:KCX162 4.1 27.1 1.0
ND1 B:HIS70 4.2 17.5 1.0
CG B:HIS68 4.3 18.8 1.0
CG B:HIS70 4.4 18.0 1.0
CE1 B:HIS230 4.4 29.7 1.0
ND1 B:HIS68 4.5 18.0 1.0
CB B:ASP285 4.5 24.7 1.0
CA B:ASP285 4.8 23.2 1.0

Zinc binding site 4 out of 4 in 1po9

Go back to Zinc Binding Sites List in 1po9
Zinc binding site 4 out of 4 in the Crytsal 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 Crytsal Structure of Isoaspartyl Dipeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:25.4
occ:0.70
ND1 B:HIS201 2.0 25.0 1.0
O B:HOH624 2.1 42.7 1.0
OQ1 B:KCX162 2.1 32.8 1.0
NE2 B:HIS230 2.2 29.7 1.0
CE1 B:HIS201 2.9 25.0 1.0
CD2 B:HIS230 2.9 27.8 1.0
CX B:KCX162 3.0 32.7 0.8
CG B:HIS201 3.1 23.2 1.0
OQ2 B:KCX162 3.1 27.6 1.0
ZN B:ZN603 3.3 24.1 0.7
OH B:TYR137 3.3 29.6 1.0
CE1 B:HIS230 3.4 29.7 1.0
CB B:HIS201 3.5 20.7 1.0
NE2 B:HIS68 3.8 19.0 1.0
CE1 B:HIS68 3.9 20.6 1.0
CE2 B:TYR137 4.0 25.7 1.0
NE2 B:HIS201 4.0 25.7 1.0
CZ B:TYR137 4.1 27.6 1.0
O B:HOH879 4.1 42.4 1.0
CD2 B:HIS201 4.1 26.1 1.0
CG B:HIS230 4.1 25.8 1.0
NZ B:KCX162 4.2 27.1 1.0
ND1 B:HIS230 4.3 27.0 1.0
CA B:HIS201 4.3 20.5 1.0
OD2 B:ASP285 4.4 29.9 1.0
CE B:KCX162 4.8 29.9 1.0
OD1 B:ASP285 4.9 26.4 1.0
CG B:ASP285 4.9 28.5 1.0
CG2 B:THR229 4.9 20.9 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: Wed Dec 16 03:00:52 2020

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