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Palladium in PDB 3fi6: Apo-H49AFR with High Content of Pd Ions

Protein crystallography data

The structure of Apo-H49AFR with High Content of Pd Ions, PDB code: 3fi6 was solved by M.Abe, T.Ueno, K.Hirata, M.Suzuki, S.Abe, N.Shimizu, M.Yamaoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.30 / 1.80
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.701, 180.701, 180.701, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.5

Other elements in 3fi6:

The structure of Apo-H49AFR with High Content of Pd Ions also contains other interesting chemical elements:

Cadmium (Cd) 1 atom

Palladium Binding Sites:

The binding sites of Palladium atom in the Apo-H49AFR with High Content of Pd Ions (pdb code 3fi6). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 8 binding sites of Palladium where determined in the Apo-H49AFR with High Content of Pd Ions, PDB code: 3fi6:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Palladium binding site 1 out of 8 in 3fi6

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Palladium binding site 1 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd201

b:27.9
occ:1.00
 O A:HOH1082 2.2 21.3 1.0
PD A:PD204 2.3 26.0 0.5
O A:HOH1145 2.3 23.8 1.0
SG A:CYS48 2.4 19.0 1.0
O A:HOH1113 2.4 39.5 1.0
PD A:PD202 3.3 30.8 1.0
CB A:CYS48 3.4 15.8 1.0
N A:ALA49 3.6 13.8 1.0
OD2 A:ASP38 3.6 12.9 0.5
C A:CYS48 3.7 14.3 1.0
CA A:ALA49 3.8 13.7 1.0
CD A:ARG52 4.1 20.7 0.5
O A:CYS48 4.1 14.4 1.0
OE2 A:GLU45 4.2 33.2 1.0
CA A:CYS48 4.2 14.2 1.0
CB A:ALA49 4.3 14.0 1.0
O A:GLU45 4.3 12.5 1.0
O A:HOH1129 4.4 41.2 1.0
CG A:ARG52 4.6 19.0 0.5
CG A:GLU45 4.6 18.8 1.0
CD A:GLU45 4.7 29.8 1.0
CG A:ASP38 4.8 13.1 0.5
CB A:ARG52 4.9 16.0 0.5
CB A:ARG52 5.0 15.7 0.5

Palladium binding site 2 out of 8 in 3fi6

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Palladium binding site 2 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd202

b:30.8
occ:1.00
 PD A:PD204 2.0 26.0 0.5
OD2 A:ASP38 2.1 12.9 0.5
SG A:CYS48 2.2 19.0 1.0
O A:HOH1134 2.4 19.1 1.0
CG A:ASP38 3.0 13.1 0.5
CB A:ASP38 3.0 13.5 0.5
CB A:ASP38 3.2 13.4 0.5
PD A:PD201 3.3 27.9 1.0
CG A:ASP38 3.3 15.1 0.5
CB A:CYS48 3.5 15.8 1.0
O A:HOH1145 3.7 23.8 1.0
OD1 A:ASP38 3.7 20.4 0.5
OD2 A:ASP38 3.9 19.9 0.5
O A:GLY34 3.9 12.3 1.0
O A:HOH1082 4.2 21.3 1.0
OD1 A:ASP38 4.2 13.7 0.5
CA A:ASP38 4.4 12.7 0.5
CD A:ARG52 4.5 20.7 0.5
CD1 A:PHE35 4.5 13.8 1.0
NE A:ARG52 4.5 25.1 0.5
CA A:ASP38 4.5 12.5 0.5
C A:GLY34 4.5 12.5 1.0
CE1 A:PHE35 4.6 13.9 1.0
CA A:PHE35 4.7 12.6 1.0
N A:ASP38 4.8 12.4 1.0
CA A:CYS48 4.8 14.2 1.0
N A:PHE35 4.9 11.8 1.0

Palladium binding site 3 out of 8 in 3fi6

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Palladium binding site 3 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd203

b:42.5
occ:1.00
 NE2 A:HIS124 2.1 41.4 1.0
O A:HOH1107 2.2 25.3 1.0
O A:HOH1104 2.5 27.9 1.0
O A:HOH1032 2.6 22.4 1.0
CD2 A:HIS124 2.9 41.0 1.0
CE1 A:HIS124 3.1 41.2 1.0
CG A:MET68 3.6 25.6 1.0
CG A:HIS124 4.1 41.0 1.0
ND1 A:HIS124 4.1 40.9 1.0
CD A:ARG72 4.2 20.2 1.0
CG A:ARG72 4.3 17.6 1.0
CB A:PHE128 4.3 36.9 0.8
CD1 A:PHE128 4.4 36.2 0.8
CG A:PHE128 4.4 36.4 0.8
SD A:MET68 4.5 37.7 1.0
OE1 A:GLN71 4.6 29.4 0.8
CB A:MET68 4.8 18.7 1.0
NH2 A:ARG72 4.9 22.7 1.0
O A:HIS124 5.0 40.3 1.0

Palladium binding site 4 out of 8 in 3fi6

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Palladium binding site 4 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd204

b:26.0
occ:0.50
 OD2 A:ASP38 1.4 12.9 0.5
O A:HOH1145 1.7 23.8 1.0
PD A:PD202 2.0 30.8 1.0
PD A:PD201 2.3 27.9 1.0
SG A:CYS48 2.5 19.0 1.0
CG A:ASP38 2.6 13.1 0.5
CB A:CYS48 3.3 15.8 1.0
OD1 A:ASP38 3.3 13.7 0.5
OD1 A:ASP38 3.6 20.4 0.5
O A:HOH1134 3.6 19.1 1.0
CB A:ASP38 3.7 13.4 0.5
CB A:ASP38 3.9 13.5 0.5
CG A:ASP38 3.9 15.1 0.5
O A:HOH1113 4.0 39.5 1.0
CG A:GLU45 4.1 18.8 1.0
O A:HOH1082 4.2 21.3 1.0
CA A:CYS48 4.7 14.2 1.0
O A:GLU45 4.7 12.5 1.0
OD2 A:ASP38 4.8 19.9 0.5
OE2 A:GLU45 4.8 33.2 1.0
CA A:GLU45 4.8 14.2 1.0
CA A:ASP38 4.9 12.7 0.5
CD A:GLU45 4.9 29.8 1.0
CB A:GLU45 4.9 16.0 1.0
C A:CYS48 4.9 14.3 1.0
CA A:ASP38 5.0 12.5 0.5
N A:ALA49 5.0 13.8 1.0

Palladium binding site 5 out of 8 in 3fi6

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Palladium binding site 5 out of 8 in the Apo-H49AFR 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 5 of Apo-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd205

b:58.0
occ:0.90
 NE2 A:HIS173 2.1 38.2 1.0
CE1 A:HIS173 2.7 39.0 1.0
CD2 A:HIS173 3.3 39.2 1.0
ND1 A:HIS173 4.0 39.3 1.0
CG A:HIS173 4.3 38.0 1.0
O A:HOH1091 5.0 26.8 1.0

Palladium binding site 6 out of 8 in 3fi6

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Palladium binding site 6 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd206

b:54.5
occ:0.70
 NE2 A:HIS114 2.0 37.2 1.0
CE1 A:HIS114 2.7 38.0 1.0
CB A:CYS126 3.0 39.9 1.0
CD2 A:HIS114 3.2 36.4 1.0
O A:CYS126 3.2 39.3 0.6
PD A:PD208 3.4 50.4 0.4
C A:CYS126 3.5 39.4 0.6
O A:HOH1139 3.5 38.1 1.0
CA A:CYS126 3.6 39.6 1.0
ND1 A:HIS114 3.9 37.5 1.0
CG A:HIS114 4.2 34.9 1.0
N A:ASP127 4.3 39.3 1.0
O A:HOH1152 4.3 63.9 1.0
CB A:GLU130 4.6 35.8 1.0
CA A:ASP127 5.0 39.1 1.0

Palladium binding site 7 out of 8 in 3fi6

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Palladium binding site 7 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd207

b:55.5
occ:0.80
 O A:HOH1119 2.1 33.7 1.0
O A:SER2 2.6 32.9 1.0
N A:GLN3 2.8 30.4 0.9
C A:SER2 2.9 31.8 1.0
NH1 A:ARG75 3.4 29.9 0.8
N A:ILE4 4.1 25.3 1.0
CA A:GLN3 4.1 28.8 1.0
CA A:SER2 4.2 32.6 1.0
N A:SER2 4.5 33.5 1.0
CZ A:ARG75 4.5 24.6 0.8
C A:GLN3 4.6 27.6 1.0
CG1 A:ILE4 4.7 21.9 1.0
CB A:GLN3 4.7 28.6 1.0
O A:GLY73 4.8 18.9 1.0
O A:HOH1053 5.0 42.9 1.0

Palladium binding site 8 out of 8 in 3fi6

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Palladium binding site 8 out of 8 in the Apo-H49AFR 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-H49AFR with High Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd208

b:50.4
occ:0.40
 O A:HOH1152 2.7 63.9 1.0
CB A:CYS126 3.2 39.9 1.0
PD A:PD206 3.4 54.5 0.7
CE1 A:HIS114 3.4 38.0 1.0
NE2 A:HIS114 4.1 37.2 1.0
OG A:SER118 4.2 39.8 0.6
CB A:SER118 4.2 39.9 1.0
ND1 A:HIS114 4.4 37.5 1.0
O A:HOH1139 4.5 38.1 1.0
CA A:SER118 4.6 39.8 1.0
CA A:CYS126 4.7 39.6 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 10:19:52 2024

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