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Palladium in PDB 2zg9: Crystal Structure of Pd(Allyl)/Apo-H114AFR

Protein crystallography data

The structure of Crystal Structure of Pd(Allyl)/Apo-H114AFR, PDB code: 2zg9 was solved by S.Abe, J.Niemeyer, M.Abe, T.Ueno, T.Hikage, G.Erker, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.13 / 1.75
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.176, 181.176, 181.176, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.1

Other elements in 2zg9:

The structure of Crystal Structure of Pd(Allyl)/Apo-H114AFR also contains other interesting chemical elements:

Cadmium (Cd) 1 atom

Palladium Binding Sites:

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-H114AFR (pdb code 2zg9). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 3 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Apo-H114AFR, PDB code: 2zg9:
Jump to Palladium binding site number: 1; 2; 3;

Palladium binding site 1 out of 3 in 2zg9

Go back to Palladium Binding Sites List in 2zg9
Palladium binding site 1 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-H114AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Crystal Structure of Pd(Allyl)/Apo-H114AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd180

b:28.7
occ:1.00
PD X:PLL180 0.0 28.7 1.0
C21 X:PLL180 2.3 30.7 1.0
C20 X:PLL180 2.3 29.9 1.0
C19 X:PLL180 2.3 30.9 1.0
SG X:CYS126 2.4 25.6 1.0
CB X:CYS126 3.3 24.6 1.0
O X:HOH291 4.3 58.6 0.3
CA X:CYS126 4.8 24.4 1.0

Palladium binding site 2 out of 3 in 2zg9

Go back to Palladium Binding Sites List in 2zg9
Palladium binding site 2 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-H114AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Crystal Structure of Pd(Allyl)/Apo-H114AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd181

b:18.6
occ:1.00
PD X:PLL181 0.0 18.6 1.0
C20 X:PLL181 2.3 23.2 1.0
OE1 X:GLU45 2.3 17.7 1.0
SG X:CYS48 2.3 18.1 1.0
C21 X:PLL181 2.3 22.6 1.0
C19 X:PLL181 2.3 22.0 1.0
PD X:PLL182 3.1 23.5 1.0
CD X:GLU45 3.3 19.5 1.0
CB X:CYS48 3.4 14.0 1.0
OE2 X:GLU45 3.5 22.0 1.0
OD1 X:ASP38 3.5 14.4 1.0
CG X:ASP38 3.8 13.6 1.0
CB X:ASP38 3.8 12.2 1.0
CE1 X:HIS49 3.9 21.0 1.0
ND1 X:HIS49 4.0 20.8 1.0
C20 X:PLL182 4.1 24.3 1.0
O X:HOH323 4.2 28.7 1.0
C21 X:PLL182 4.4 23.3 1.0
OD2 X:ASP38 4.5 13.0 1.0
O X:HOH359 4.6 32.3 1.0
CG X:GLU45 4.7 15.8 1.0
CA X:CYS48 4.8 13.6 1.0
CA X:ASP38 4.8 11.1 1.0
O X:HOH335 4.9 30.5 1.0
C19 X:PLL182 5.0 24.6 1.0

Palladium binding site 3 out of 3 in 2zg9

Go back to Palladium Binding Sites List in 2zg9
Palladium binding site 3 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-H114AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Crystal Structure of Pd(Allyl)/Apo-H114AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd182

b:23.5
occ:1.00
PD X:PLL182 0.0 23.5 1.0
ND1 X:HIS49 2.1 20.8 1.0
C20 X:PLL182 2.3 24.3 1.0
C21 X:PLL182 2.3 23.3 1.0
C19 X:PLL182 2.3 24.6 1.0
SG X:CYS48 2.6 18.1 1.0
CE1 X:HIS49 3.0 21.0 1.0
PD X:PLL181 3.1 18.6 1.0
CG X:HIS49 3.2 18.5 1.0
CA X:HIS49 3.4 14.2 1.0
N X:HIS49 3.5 13.7 1.0
C X:CYS48 3.7 14.2 1.0
CB X:HIS49 3.7 14.9 1.0
CB X:CYS48 3.8 14.0 1.0
C20 X:PLL181 3.8 23.2 1.0
O X:CYS48 3.9 13.5 1.0
NE2 X:HIS49 4.1 22.3 1.0
OE1 X:GLU45 4.2 17.7 1.0
CD2 X:HIS49 4.3 22.2 1.0
CA X:CYS48 4.4 13.6 1.0
O X:HOH323 4.5 28.7 1.0
O X:GLU45 4.6 11.7 1.0
C21 X:PLL181 4.6 22.6 1.0
CB X:ARG52 4.6 14.9 1.0
C19 X:PLL181 4.6 22.0 1.0
O X:HOH316 4.7 26.5 1.0
C X:HIS49 4.7 13.1 1.0

Reference:

S.Abe, J.Niemeyer, M.Abe, Y.Takezawa, T.Ueno, T.Hikage, G.Erker, Y.Watanabe. Control of the Coordination Structure of Organometallic Palladium Complexes in An Apo-Ferritin Cage. J.Am.Chem.Soc. V. 130 10512 2008.
ISSN: ISSN 0002-7863
PubMed: 18636721
DOI: 10.1021/JA802463A
Page generated: Wed Dec 16 02:02:44 2020

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