Atomistry » Palladium » PDB 1ks4-8j8e » 2zg9
Atomistry »
  Palladium »
    PDB 1ks4-8j8e »
      2zg9 »

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: Thu Oct 10 10:17:09 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy