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Palladium in PDB 2z5q: Apo-Fr with Intermediate Content of Pd Ion

Protein crystallography data

The structure of Apo-Fr with Intermediate Content of Pd Ion, PDB code: 2z5q 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) 40.39 / 2.10
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.570, 180.570, 180.570, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.4

Other elements in 2z5q:

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

Cadmium (Cd) 1 atom

Palladium Binding Sites:

The binding sites of Palladium atom in the Apo-Fr with Intermediate Content of Pd Ion (pdb code 2z5q). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 9 binding sites of Palladium where determined in the Apo-Fr with Intermediate Content of Pd Ion, PDB code: 2z5q:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Palladium binding site 1 out of 9 in 2z5q

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Palladium binding site 1 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd201

b:58.3
occ:0.80
 CB A:HIS49 2.2 30.2 1.0
ND1 A:HIS173 2.5 58.8 1.0
CE1 A:HIS173 2.8 60.5 1.0
OE2 A:GLU45 2.9 38.9 1.0
CA A:HIS49 3.3 29.3 1.0
O A:GLU45 3.3 27.7 1.0
PD A:PD203 3.4 57.7 0.6
N A:HIS49 3.5 29.8 1.0
CG A:HIS173 3.7 58.4 1.0
CD A:GLU45 3.9 40.2 1.0
C A:HIS49 4.0 29.4 1.0
NE2 A:HIS173 4.1 60.8 1.0
O A:GLY46 4.2 28.8 1.0
N A:PHE50 4.3 27.7 1.0
C A:GLU45 4.3 27.9 1.0
CA A:GLY46 4.3 27.8 1.0
PD A:PD209 4.4 35.4 0.1
CG A:GLU45 4.4 31.0 1.0
CB A:HIS173 4.5 56.8 1.0
CD2 A:HIS173 4.5 60.4 1.0
C A:GLY46 4.5 28.1 1.0
NH2 A:ARG52 4.6 23.6 0.4
O A:HIS49 4.7 29.9 1.0
N A:GLY46 4.7 26.9 1.0
C A:CYS48 4.9 30.4 1.0
OE1 A:GLU45 4.9 43.4 1.0

Palladium binding site 2 out of 9 in 2z5q

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Palladium binding site 2 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd202

b:58.0
occ:0.70
 OE1 A:GLU45 2.4 43.4 1.0
SG A:CYS48 2.5 34.1 1.0
PD A:PD209 2.6 35.4 0.1
NH2 A:ARG52 2.6 30.9 0.6
OD1 A:ASP38 3.4 26.5 1.0
CZ A:ARG52 3.4 31.6 0.6
CB A:CYS48 3.5 29.1 1.0
CD A:GLU45 3.5 40.2 1.0
O A:HOH1095 3.7 42.3 1.0
CG A:ASP38 3.8 21.8 1.0
CB A:ASP38 3.8 17.4 1.0
OE2 A:GLU45 3.9 38.9 1.0
NH1 A:ARG52 4.0 32.3 0.6
NE A:ARG52 4.2 30.6 0.6
NE A:ARG52 4.5 26.8 0.4
OD2 A:ASP38 4.7 22.2 1.0
CA A:ASP38 4.7 16.9 1.0
CA A:CYS48 4.8 29.9 1.0
CG A:GLU45 4.8 31.0 1.0
C A:CYS48 4.9 30.4 1.0
NH2 A:ARG52 4.9 23.6 0.4
O A:GLY34 5.0 17.2 1.0

Palladium binding site 3 out of 9 in 2z5q

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Palladium binding site 3 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd203

b:57.7
occ:0.60
 NH2 A:ARG52 2.3 23.6 0.4
OE2 A:GLU45 2.7 38.9 1.0
CB A:HIS49 3.3 30.2 1.0
PD A:PD201 3.4 58.3 0.8
PD A:PD209 3.5 35.4 0.1
CZ A:ARG52 3.6 27.6 0.4
CD A:GLU45 3.8 40.2 1.0
NE A:ARG52 4.4 26.8 0.4
NH1 A:ARG52 4.4 30.6 0.4
CA A:HIS49 4.4 29.3 1.0
OE1 A:GLU45 4.6 43.4 1.0
CE1 A:HIS173 4.7 60.5 1.0
ND1 A:HIS173 4.8 58.8 1.0
CG A:GLU45 4.9 31.0 1.0
N A:HIS49 5.0 29.8 1.0

Palladium binding site 4 out of 9 in 2z5q

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Palladium binding site 4 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd204

b:58.5
occ:0.70
 SG A:CYS126 2.2 54.7 1.0
NE2 A:HIS114 2.3 44.7 1.0
CD2 A:HIS114 3.0 42.0 1.0
PD A:PD208 3.1 0.8 0.1
CB A:CYS126 3.3 51.7 1.0
O A:CYS126 3.4 51.6 1.0
CE1 A:HIS114 3.5 45.0 1.0
C A:CYS126 3.7 51.2 1.0
CA A:CYS126 3.7 51.3 1.0
PD A:PD207 4.0 52.5 0.4
CG A:HIS114 4.3 41.3 1.0
CB A:GLU130 4.4 48.5 1.0
ND1 A:HIS114 4.5 43.6 1.0
N A:ASP127 4.5 50.5 1.0

Palladium binding site 5 out of 9 in 2z5q

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Palladium binding site 5 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


Mono view


Stereo pair view

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

b:52.9
occ:0.50
 OE1 A:GLU53 2.4 44.4 1.0
CD A:GLU53 2.8 40.3 1.0
OE2 A:GLU53 2.9 42.7 1.0
CG A:GLU53 4.0 32.4 1.0

Palladium binding site 6 out of 9 in 2z5q

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Palladium binding site 6 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd206

b:53.9
occ:0.40
 N A:SER2 2.3 43.1 1.0
N A:GLN3 2.9 37.8 1.0
CA A:SER2 3.0 42.4 1.0
C A:SER2 3.2 40.3 1.0
NH1 A:ARG75 3.4 6.5 0.2
N A:ILE4 3.8 32.4 1.0
CA A:GLN3 4.0 36.3 0.5
CA A:GLN3 4.0 36.3 0.5
O A:SER2 4.2 40.0 1.0
CG A:GLN3 4.3 36.8 0.5
C A:GLN3 4.4 35.0 1.0
CB A:GLN3 4.5 36.2 0.5
CB A:GLN3 4.5 36.3 0.5
CB A:SER2 4.5 43.4 1.0
CZ A:ARG75 4.5 3.3 0.2
CG1 A:ILE4 4.6 27.6 1.0
O A:GLY73 4.8 17.6 1.0
N A:ARG5 4.8 26.5 1.0
CA A:GLY73 4.9 18.6 1.0
OG A:SER2 5.0 46.9 1.0
CA A:ILE4 5.0 29.0 1.0

Palladium binding site 7 out of 9 in 2z5q

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Palladium binding site 7 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd207

b:52.5
occ:0.40
 PD A:PD208 2.8 0.8 0.1
OG A:SER118 3.2 50.5 1.0
CB A:CYS126 3.4 51.7 1.0
SG A:CYS126 3.4 54.7 1.0
NE2 A:HIS114 3.9 44.7 1.0
CB A:SER118 3.9 49.0 1.0
PD A:PD204 4.0 58.5 0.7
CE1 A:HIS114 4.1 45.0 1.0
CA A:SER118 4.3 48.6 1.0
CA A:CYS126 4.7 51.3 1.0
CD2 A:HIS114 4.9 42.0 1.0
N A:SER118 4.9 47.4 1.0

Palladium binding site 8 out of 9 in 2z5q

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Palladium binding site 8 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


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 Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd208

b:0.8
occ:0.10
 SG A:CYS126 2.1 54.7 1.0
PD A:PD207 2.8 52.5 0.4
PD A:PD204 3.1 58.5 0.7
CB A:CYS126 3.4 51.7 1.0
NE2 A:HIS114 4.6 44.7 1.0
CA A:CYS126 4.8 51.3 1.0
C A:CYS126 4.9 51.2 1.0

Palladium binding site 9 out of 9 in 2z5q

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Palladium binding site 9 out of 9 in the Apo-Fr with Intermediate Content of Pd Ion


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 9 of Apo-Fr with Intermediate Content of Pd Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd209

b:35.4
occ:0.10
 PD A:PD202 2.6 58.0 0.7
NE A:ARG52 2.7 26.8 0.4
SG A:CYS48 2.7 34.1 1.0
OE2 A:GLU45 2.8 38.9 1.0
NH2 A:ARG52 2.8 23.6 0.4
OE1 A:GLU45 3.0 43.4 1.0
N A:HIS49 3.1 29.8 1.0
CZ A:ARG52 3.2 27.6 0.4
CD A:GLU45 3.3 40.2 1.0
C A:CYS48 3.4 30.4 1.0
CA A:HIS49 3.4 29.3 1.0
CB A:HIS49 3.4 30.2 1.0
PD A:PD203 3.5 57.7 0.6
NH2 A:ARG52 3.5 30.9 0.6
CB A:CYS48 3.6 29.1 1.0
NE A:ARG52 3.6 30.6 0.6
O A:CYS48 3.7 30.9 1.0
CZ A:ARG52 3.7 31.6 0.6
CD A:ARG52 3.9 27.7 0.4
CA A:CYS48 4.1 29.9 1.0
O A:GLU45 4.2 27.7 1.0
CG A:ARG52 4.3 28.5 0.6
PD A:PD201 4.4 58.3 0.8
NH1 A:ARG52 4.5 30.6 0.4
CD A:ARG52 4.5 31.2 0.6
NH1 A:ARG52 4.6 32.3 0.6
CG A:ARG52 4.6 27.9 0.4
CG A:GLU45 4.8 31.0 1.0
C A:HIS49 4.9 29.4 1.0
CB A:ARG52 4.9 27.4 0.4
CB A:ARG52 5.0 27.7 0.6

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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