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Palladium in PDB 2z5r: Apo-Fr with High Content of Pd Ions

Protein crystallography data

The structure of Apo-Fr with High Content of Pd Ions, PDB code: 2z5r was solved by T.Ueno, K.Hirata, M.Abe, M.Suzuki, S.Abe, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.41 / 2.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.594, 181.594, 181.594, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 28.7

Other elements in 2z5r:

The structure of Apo-Fr with High Content of Pd Ions also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Palladium Binding Sites:

The binding sites of Palladium atom in the Apo-Fr with High Content of Pd Ions (pdb code 2z5r). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 10 binding sites of Palladium where determined in the Apo-Fr with High Content of Pd Ions, PDB code: 2z5r:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Palladium binding site 1 out of 10 in 2z5r

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Palladium binding site 1 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd201

b:54.3
occ:0.80
 N A:GLN3 2.7 52.3 1.0
N A:SER2 3.0 52.9 1.0
C A:SER2 3.4 53.2 1.0
CB A:GLN3 3.5 50.9 1.0
CA A:GLN3 3.5 50.2 1.0
CA A:SER2 3.5 53.7 1.0
N A:ILE4 3.7 43.6 1.0
OG A:SER2 3.8 54.9 1.0
C A:GLN3 4.1 47.8 1.0
CB A:SER2 4.3 54.0 1.0
O A:SER2 4.4 54.6 1.0
CG1 A:ILE4 4.5 39.7 1.0
O A:GLY73 4.6 27.0 1.0
N A:ARG5 4.6 36.9 1.0
CA A:GLY73 4.8 24.9 1.0
CA A:ILE4 4.9 39.0 1.0
CB A:ARG5 5.0 38.7 1.0

Palladium binding site 2 out of 10 in 2z5r

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Palladium binding site 2 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd202

b:51.1
occ:0.50
 CB A:HIS49 1.8 40.8 1.0
O A:HOH1040 2.5 42.2 1.0
OE2 A:GLU45 2.7 36.0 0.5
CA A:HIS49 3.1 39.9 1.0
PD A:PD207 3.3 52.3 0.4
N A:HIS49 3.5 40.1 1.0
CD A:GLU45 3.6 41.1 0.5
O A:GLU45 3.6 39.2 1.0
C A:HIS49 3.8 38.5 1.0
OE1 A:GLU45 3.9 42.1 0.5
CB A:HIS173 4.1 51.7 1.0
O A:GLY46 4.1 40.7 1.0
N A:PHE50 4.2 35.6 1.0
PD A:PD206 4.3 55.3 0.4
CA A:GLY46 4.3 38.1 1.0
C A:GLU45 4.4 37.8 1.0
C A:GLY46 4.5 40.0 1.0
O A:HIS49 4.5 39.9 1.0
N A:GLY46 4.8 37.6 1.0
C A:CYS48 4.8 41.4 1.0
CG A:GLU45 4.9 37.9 0.5

Palladium binding site 3 out of 10 in 2z5r

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Palladium binding site 3 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd203

b:56.7
occ:0.50
 NE2 A:HIS124 2.0 76.6 1.0
CE1 A:HIS124 2.8 75.5 1.0
CD2 A:HIS124 3.1 75.2 1.0
CG A:MET68 3.7 35.4 1.0
ND1 A:HIS124 3.9 73.7 1.0
CG A:HIS124 4.1 73.7 1.0
CB A:PHE128 4.2 71.2 1.0
CG A:PHE128 4.3 72.7 1.0
CD1 A:PHE128 4.3 74.6 1.0
CD A:ARG72 4.5 27.2 1.0
OE1 A:GLN71 4.7 38.2 1.0
CG A:ARG72 4.8 22.6 1.0
CB A:MET68 4.8 28.1 1.0
SD A:MET68 4.8 59.2 1.0
O A:HIS124 4.9 71.6 1.0

Palladium binding site 4 out of 10 in 2z5r

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Palladium binding site 4 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd204

b:46.9
occ:0.30
 SG A:CYS48 1.9 47.5 0.8
PD A:PD206 2.5 55.3 0.4
CB A:CYS48 3.2 41.3 1.0
CG A:ASP38 3.7 27.5 1.0
CB A:ASP38 3.8 20.3 1.0
OD1 A:ASP38 3.8 31.0 1.0
OD2 A:ASP38 4.1 32.2 1.0
CA A:CYS48 4.5 42.1 1.0
CG A:GLU45 4.6 37.9 0.5
O A:GLY34 4.6 19.2 1.0
C A:CYS48 4.7 41.4 1.0
OE2 A:GLU45 4.8 36.0 0.5
CA A:ASP38 4.8 20.1 1.0
O A:CYS48 4.9 39.5 1.0

Palladium binding site 5 out of 10 in 2z5r

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Palladium binding site 5 out of 10 in the Apo-Fr with High Content of Pd Ions


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Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd205

b:51.0
occ:0.40
 NE2 A:HIS114 1.8 59.2 1.0
CD2 A:HIS114 2.6 57.0 1.0
CE1 A:HIS114 3.0 61.5 1.0
CB A:CYS126 3.4 74.7 1.0
O A:CYS126 3.4 75.8 1.0
C A:CYS126 3.5 75.2 1.0
PD A:PD208 3.6 0.0 0.1
CA A:CYS126 3.8 75.0 1.0
CG A:HIS114 3.8 51.4 1.0
N A:ASP127 3.9 75.1 1.0
ND1 A:HIS114 4.0 59.8 1.0
CB A:GLU130 4.8 65.6 1.0

Palladium binding site 6 out of 10 in 2z5r

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Palladium binding site 6 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd206

b:55.3
occ:0.40
 SG A:CYS48 2.4 47.5 0.8
PD A:PD204 2.5 46.9 0.3
OE2 A:GLU45 2.8 36.0 0.5
N A:HIS49 3.2 40.1 1.0
CB A:CYS48 3.2 41.3 1.0
C A:CYS48 3.3 41.4 1.0
CA A:HIS49 3.5 39.9 1.0
CB A:HIS49 3.5 40.8 1.0
PD A:PD207 3.6 52.3 0.4
CD A:GLU45 3.7 41.1 0.5
O A:GLU45 3.8 39.2 1.0
O A:CYS48 3.8 39.5 1.0
CG A:GLU45 3.8 37.9 0.5
CA A:CYS48 3.9 42.1 1.0
PD A:PD202 4.3 51.1 0.5
C A:GLU45 4.8 37.8 1.0
N A:CYS48 4.9 43.0 1.0
OE1 A:GLU45 4.9 42.1 0.5

Palladium binding site 7 out of 10 in 2z5r

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Palladium binding site 7 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 7 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd207

b:52.3
occ:0.40
 OE2 A:GLU45 2.6 36.0 0.5
CB A:HIS49 3.2 40.8 1.0
PD A:PD202 3.3 51.1 0.5
PD A:PD206 3.6 55.3 0.4
CD A:GLU45 3.6 41.1 0.5
OE1 A:GLU45 4.1 42.1 0.5
CA A:HIS49 4.4 39.9 1.0
O A:HOH1040 4.5 42.2 1.0
CG A:GLU45 4.8 37.9 0.5

Palladium binding site 8 out of 10 in 2z5r

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Palladium binding site 8 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 8 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd208

b:0.0
occ:0.10
 PD A:PD205 3.6 51.0 0.4
CB A:CYS126 4.6 74.7 1.0

Palladium binding site 9 out of 10 in 2z5r

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Palladium binding site 9 out of 10 in the Apo-Fr with High Content of Pd Ions


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Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 9 of Apo-Fr with High Content of Pd Ions within 5.0Å range:

Palladium binding site 10 out of 10 in 2z5r

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Palladium binding site 10 out of 10 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 10 of Apo-Fr with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd210

b:0.4
occ:0.10
 OE2 A:GLU136 1.6 53.8 1.0
NH1 A:ARG64 1.9 56.7 1.0
CD A:GLU136 2.1 48.6 1.0
OE1 A:GLU136 2.2 55.7 1.0
NH2 A:ARG64 2.5 61.2 1.0
CZ A:ARG64 2.5 59.7 1.0
O A:HOH1033 3.4 37.3 1.0
CG A:GLU136 3.7 45.7 1.0
NE A:ARG64 3.8 56.1 1.0
O A:HIS132 4.0 56.9 1.0
CB A:GLU136 4.4 41.0 1.0
CD A:ARG64 4.7 48.0 1.0
CG A:GLU57 5.0 36.2 1.0

Reference:

T.Ueno, M.Abe, K.Hirata, S.Abe, M.Suzuki, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe. Process of Accumulation of Metal Ions on the Interior Surface of Apo-Ferritin: Crystal Structures of A Series of Apo-Ferritins Containing Variable Quantities of Pd(II) Ions. J.Am.Chem.Soc. V. 131 5094 2009.
ISSN: ISSN 0002-7863
PubMed: 19317403
DOI: 10.1021/JA806688S
Page generated: Thu Oct 10 10:17:10 2024

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