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Palladium in PDB 3noz: Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr, PDB code: 3noz was solved by Z.Wang, T.Ueno, S.Abe, Y.Takezawa, H.Aoyagi, T.Hikage, Y.Watanabe, S.Kitagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.34 / 1.52
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.427, 181.427, 181.427, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 20.9

Other elements in 3noz:

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr 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-E45C/R52H-Rhlfr (pdb code 3noz). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 6 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr, PDB code: 3noz:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6;

Palladium binding site 1 out of 6 in 3noz

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Palladium binding site 1 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


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-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd180

b:27.8
occ:1.00
 PD X:PLL180 0.0 27.8 1.0
NE2 X:HIS114 2.2 25.2 1.0
SG X:CYS126 2.2 29.3 1.0
C21 X:PLL180 2.3 84.1 1.0
C20 X:PLL180 2.3 83.8 1.0
C19 X:PLL180 2.3 84.0 1.0
O X:CYS126 3.1 30.1 1.0
CE1 X:HIS114 3.2 24.7 1.0
CD2 X:HIS114 3.2 23.6 1.0
CB X:CYS126 3.3 28.6 1.0
C X:CYS126 3.4 29.4 1.0
CA X:CYS126 3.6 28.5 1.0
PD X:PLL181 3.7 41.7 1.0
O X:HOH259 3.8 13.2 0.3
ND1 X:HIS114 4.3 24.6 1.0
CG X:HIS114 4.3 22.7 1.0
N X:ASP127 4.3 30.0 1.0
C20 X:PLL181 4.6 79.1 1.0
C21 X:PLL181 4.6 79.2 1.0
CA X:ASP127 5.0 30.4 1.0

Palladium binding site 2 out of 6 in 3noz

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Palladium binding site 2 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


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-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd181

b:41.7
occ:1.00
 PD X:PLL181 0.0 41.7 1.0
C21 X:PLL181 2.3 79.2 1.0
C20 X:PLL181 2.3 79.1 1.0
C19 X:PLL181 2.3 79.2 1.0
SG X:CYS126 2.4 29.3 1.0
O X:HOH259 2.5 13.2 0.3
CB X:CYS126 3.4 28.6 1.0
PD X:PLL180 3.7 27.8 1.0
CE1 X:HIS114 4.3 24.7 1.0
NE2 X:HIS114 4.3 25.2 1.0
OG X:SER118 4.8 28.2 1.0
CA X:CYS126 4.8 28.5 1.0
C19 X:PLL180 5.0 84.0 1.0

Palladium binding site 3 out of 6 in 3noz

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Palladium binding site 3 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


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-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd182

b:15.4
occ:1.00
 PD X:PLL182 0.0 15.4 1.0
O X:HOH232 2.3 19.1 1.0
C20 X:PLL182 2.3 18.2 1.0
C21 X:PLL182 2.3 20.5 1.0
C19 X:PLL182 2.3 18.3 1.0
SG X:CYS48 2.4 12.2 1.0
PD X:PLL183 3.3 12.3 1.0
CB X:CYS48 3.4 10.4 1.0
C19 X:PLL183 3.6 14.4 1.0
CB X:ASP38 3.6 10.6 1.0
CG X:ASP38 3.7 10.9 1.0
OD1 X:ASP38 3.9 13.1 1.0
O X:HOH228 4.1 32.9 1.0
OD2 X:ASP38 4.2 13.1 1.0
C21 X:PLL183 4.2 16.5 1.0
O X:HOH220 4.3 20.1 1.0
ND1 X:HIS52 4.6 10.0 1.0
CE1 X:HIS52 4.7 12.4 1.0
CA X:ASP38 4.8 10.5 1.0
CA X:CYS48 4.8 10.6 1.0
O X:GLY34 4.9 11.4 1.0

Palladium binding site 4 out of 6 in 3noz

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Palladium binding site 4 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd183

b:12.3
occ:1.00
 PD X:PLL183 0.0 12.3 1.0
ND1 X:HIS52 2.1 10.0 1.0
C20 X:PLL183 2.3 16.4 1.0
C21 X:PLL183 2.3 16.5 1.0
C19 X:PLL183 2.3 14.4 1.0
SG X:CYS48 2.4 12.2 1.0
CE1 X:HIS52 3.1 12.4 1.0
CG X:HIS52 3.1 11.1 1.0
PD X:PLL182 3.3 15.4 1.0
O X:CYS48 3.3 10.8 1.0
CB X:HIS52 3.4 11.3 1.0
C X:CYS48 3.6 10.5 1.0
CB X:CYS48 3.6 10.4 1.0
C20 X:PLL182 3.7 18.2 1.0
N X:HIS49 4.0 10.6 1.0
CA X:CYS48 4.1 10.6 1.0
NE2 X:HIS52 4.2 11.8 1.0
CD2 X:HIS52 4.2 13.3 1.0
CA X:HIS49 4.3 10.9 1.0
C21 X:PLL182 4.6 20.5 1.0
O X:HOH232 4.7 19.1 1.0
CA X:HIS52 4.8 11.5 1.0
O X:HOH364 4.9 30.0 1.0

Palladium binding site 5 out of 6 in 3noz

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Palladium binding site 5 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd184

b:16.3
occ:1.00
 PD X:PLL184 0.0 16.3 1.0
NE2 X:HIS49 2.0 12.0 1.0
C21 X:PLL184 2.3 20.0 1.0
C19 X:PLL184 2.3 18.0 1.0
C20 X:PLL184 2.3 21.2 1.0
SG X:CYS45 2.4 14.3 1.0
CD2 X:HIS49 3.0 12.6 1.0
CE1 X:HIS49 3.1 11.6 1.0
PD X:PLL185 3.2 20.1 1.0
CB X:CYS45 3.6 12.7 1.0
NE2 X:HIS173 3.6 25.2 1.0
O X:HOH232 3.9 19.1 1.0
CE1 X:HIS173 4.0 26.2 1.0
CG X:HIS49 4.1 12.5 1.0
ND1 X:HIS49 4.2 14.1 1.0
CA X:CYS45 4.2 11.6 1.0
CD2 X:HIS173 4.2 25.7 1.0
O X:CYS45 4.3 10.4 1.0
C19 X:PLL183 4.3 14.4 1.0
C X:CYS45 4.5 11.2 1.0
ND1 X:HIS173 4.7 25.9 1.0
C19 X:PLL185 4.8 22.6 1.0
O X:HOH228 4.8 32.9 1.0
CG X:HIS173 4.9 28.4 1.0

Palladium binding site 6 out of 6 in 3noz

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Palladium binding site 6 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Crystal Structure of Pd(Allyl)/Apo-E45C/R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pd185

b:20.1
occ:1.00
 PD X:PLL185 0.0 20.1 1.0
NE2 X:HIS173 2.2 25.2 1.0
SG X:CYS45 2.3 14.3 1.0
C21 X:PLL185 2.3 20.9 1.0
C19 X:PLL185 2.3 22.6 1.0
C20 X:PLL185 2.3 19.2 1.0
CE1 X:HIS173 3.2 26.2 1.0
PD X:PLL184 3.2 16.3 1.0
CD2 X:HIS173 3.2 25.7 1.0
CB X:CYS45 3.5 12.7 1.0
C19 X:PLL184 3.5 18.0 1.0
C1 X:EDO177 3.6 35.5 1.0
O1 X:EDO177 4.2 36.1 1.0
NE2 X:HIS49 4.2 12.0 1.0
ND1 X:HIS173 4.3 25.9 1.0
CG X:HIS173 4.3 28.4 1.0
C21 X:PLL184 4.4 20.0 1.0
C2 X:EDO177 4.6 34.1 1.0
CD2 X:HIS49 4.8 12.6 1.0
NH2 X:ARG168 4.8 14.9 1.0
C20 X:PLL184 4.8 21.2 1.0
CA X:CYS45 4.9 11.6 1.0

Reference:

Z.Wang, Y.Takezawa, H.Aoyagi, S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Definite Coordination Arrangement of Organometallic Palladium Complexes Accumulated on the Designed Interior Surface of Apo-Ferritin. Chem.Commun.(Camb.) V. 47 170 2011.
ISSN: ISSN 1359-7345
PubMed: 20730233
DOI: 10.1039/C0CC02221G
Page generated: Thu Oct 10 10:19:55 2024

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