Atomistry » Palladium » PDB 1ks4-8ejb » 3noz
Atomistry »
  Palladium »
    PDB 1ks4-8ejb »
      3noz »

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

Go back to Palladium Binding Sites List in 3noz
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

Go back to Palladium Binding Sites List in 3noz
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

Go back to Palladium Binding Sites List in 3noz
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

Go back to Palladium Binding Sites List in 3noz
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

Go back to Palladium Binding Sites List in 3noz
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

Go back to Palladium Binding Sites List in 3noz
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: Wed Dec 16 02:02:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy