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Zinc in PDB 1y0r: Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii

Protein crystallography data

The structure of Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii, PDB code: 1y0r was solved by M.Groll, L.Borissenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.91 / 1.75
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 111.572, 111.572, 111.572, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 22.7

Other elements in 1y0r:

The structure of Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii also contains other interesting chemical elements:

Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii (pdb code 1y0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii, PDB code: 1y0r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y0r

Go back to Zinc Binding Sites List in 1y0r
Zinc binding site 1 out of 2 in the Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii


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 the Tetrahedral Aminopeptidase From P. Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:33.7
occ:1.00
OD1 A:ASP182 2.0 25.8 1.0
OD1 A:ASP235 2.2 31.1 1.0
NE2 A:HIS68 2.4 28.4 1.0
OD2 A:ASP235 2.5 31.1 1.0
CG A:ASP235 2.7 29.8 1.0
CG A:ASP182 3.0 26.9 1.0
AS A:ARS1003 3.0 73.5 1.0
CD2 A:HIS68 3.2 27.3 1.0
OD2 A:ASP182 3.5 28.5 1.0
CE1 A:HIS68 3.5 26.4 1.0
CB A:ASP183 3.7 23.9 1.0
ZN A:ZN1002 3.8 36.6 1.0
OE2 A:GLU212 3.9 33.4 1.0
OE1 A:GLU212 4.0 31.2 1.0
OE2 A:GLU213 4.0 30.4 1.0
CD A:GLU212 4.1 32.1 1.0
CG A:ASP183 4.1 24.3 1.0
CB A:ASP235 4.2 27.0 1.0
CB A:ASP182 4.3 25.2 1.0
CG A:HIS68 4.4 24.9 1.0
CG2 A:VAL236 4.4 26.7 1.0
CA A:ASP183 4.5 21.5 1.0
OD2 A:ASP183 4.5 28.1 1.0
N A:ASP183 4.5 23.4 1.0
ND1 A:HIS68 4.5 26.1 1.0
C A:ASP182 4.6 22.9 1.0
CA A:ASP182 4.6 23.6 1.0
OD1 A:ASP183 4.6 24.9 1.0
N A:VAL236 4.7 24.4 1.0
CD A:GLU213 4.8 30.3 1.0
O A:HOH1132 4.9 40.3 1.0
CA A:ASP235 4.9 25.8 1.0

Zinc binding site 2 out of 2 in 1y0r

Go back to Zinc Binding Sites List in 1y0r
Zinc binding site 2 out of 2 in the Crystal Structure of the Tetrahedral Aminopeptidase From P. Horikoshii


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 the Tetrahedral Aminopeptidase From P. Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:36.6
occ:1.00
OD2 A:ASP182 2.1 28.5 1.0
OE2 A:GLU213 2.2 30.4 1.0
NE2 A:HIS323 2.4 32.4 1.0
OE1 A:GLU213 2.5 30.5 1.0
CD A:GLU213 2.7 30.3 1.0
CG A:ASP182 3.0 26.9 1.0
AS A:ARS1003 3.1 73.5 1.0
CD2 A:HIS323 3.2 30.5 1.0
OD1 A:ASP182 3.3 25.8 1.0
CE1 A:HIS323 3.5 33.2 1.0
ZN A:ZN1001 3.8 33.7 1.0
CG A:GLU213 4.2 26.9 1.0
O A:HOH1046 4.3 32.9 1.0
CB A:ASP182 4.4 25.2 1.0
CG A:HIS323 4.4 29.1 1.0
OE1 A:GLU212 4.5 31.2 1.0
ND1 A:HIS323 4.5 33.0 1.0
O A:HOH1037 4.6 28.6 1.0
NE2 A:HIS68 4.8 28.4 1.0
CG2 A:ILE322 4.8 25.5 1.0
CG2 A:ILE72 4.9 23.2 1.0
CE1 A:HIS68 5.0 26.4 1.0

Reference:

L.Borissenko, M.Groll. Crystal Structure of Tet Protease Reveals Complementary Protein Degradation Pathways in Prokaryotes J.Mol.Biol. V. 346 1207 2005.
ISSN: ISSN 0022-2836
PubMed: 15713475
DOI: 10.1016/J.JMB.2004.12.056
Page generated: Wed Dec 16 03:13:28 2020

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