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Zinc in PDB 4p36: Crystal Structure of Dj-1 with Zn(II) Bound (Crystal 2)

Protein crystallography data

The structure of Crystal Structure of Dj-1 with Zn(II) Bound (Crystal 2), PDB code: 4p36 was solved by S.Tashiro, C.-X.Wu, Q.Q.Hoang, J.M.M.Caaveiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 1.18
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.015, 75.015, 75.525, 90.00, 90.00, 120.00
R / Rfree (%) 11.9 / 13.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dj-1 with Zn(II) Bound (Crystal 2) (pdb code 4p36). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Dj-1 with Zn(II) Bound (Crystal 2), PDB code: 4p36:

Zinc binding site 1 out of 1 in 4p36

Go back to Zinc Binding Sites List in 4p36
Zinc binding site 1 out of 1 in the Crystal Structure of Dj-1 with Zn(II) Bound (Crystal 2)


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 Dj-1 with Zn(II) Bound (Crystal 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:14.6
occ:0.50
SG A:CSO106 1.9 12.9 0.5
O A:HOH304 2.0 32.9 0.9
OE2 A:GLU18 2.1 15.1 1.0
SG A:CSO106 2.2 21.3 0.5
OD A:CSO106 2.3 12.7 0.5
HD3 A:PRO158 2.9 14.4 1.0
CD A:GLU18 2.9 12.4 1.0
CB A:CSO106 3.0 12.4 0.5
HG3 A:GLU15 3.0 12.7 1.0
CB A:CSO106 3.0 17.9 0.5
OE1 A:GLU18 3.1 11.9 1.0
H A:GLY75 3.2 14.2 1.0
HA2 A:GLY157 3.6 13.3 1.0
HB2 A:GLU15 3.7 12.3 1.0
O A:HOH353 3.8 33.5 1.0
HG3 A:PRO158 3.8 14.9 1.0
CD A:PRO158 3.8 12.0 1.0
CG A:GLU15 3.8 10.6 1.0
HA3 A:GLY74 3.9 12.5 1.0
N A:GLY75 3.9 11.8 1.0
O A:HOH512 4.0 45.0 1.0
H A:ALA107 4.1 16.0 1.0
HG2 A:GLU15 4.1 12.7 1.0
CB A:GLU15 4.2 10.2 1.0
HA2 A:GLY75 4.2 15.4 1.0
HB3 A:GLU15 4.2 12.3 1.0
HD2 A:HIS126 4.3 14.4 1.0
CG A:PRO158 4.3 12.4 1.0
CG A:GLU18 4.3 10.7 1.0
HD2 A:PRO158 4.4 14.4 1.0
CA A:CSO106 4.4 12.9 0.5
CA A:CSO106 4.5 14.7 0.5
HG3 A:GLU18 4.5 12.9 1.0
CA A:GLY157 4.5 11.1 1.0
HB2 A:HIS126 4.6 13.2 1.0
N A:PRO158 4.6 10.6 1.0
HG2 A:PRO158 4.6 14.9 1.0
CA A:GLY75 4.6 12.8 1.0
C A:GLY74 4.7 10.2 1.0
CA A:GLY74 4.7 10.4 1.0
HG2 A:GLU18 4.7 12.9 1.0
N A:ALA107 4.8 13.3 1.0
HA3 A:GLY157 4.8 13.3 1.0
CD2 A:HIS126 4.8 12.0 1.0
C A:GLY157 4.9 10.6 1.0
CD A:GLU15 5.0 10.8 1.0

Reference:

S.Tashiro, J.M.Caaveiro, C.X.Wu, Q.Q.Hoang, K.Tsumoto. Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein Dj-1. Biochemistry V. 53 2218 2014.
ISSN: ISSN 1520-4995
PubMed: 24697266
DOI: 10.1021/BI500294H
Page generated: Wed Dec 16 05:39:57 2020

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