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Silver in PDB 2x17: The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)

Protein crystallography data

The structure of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I), PDB code: 2x17 was solved by A.Ilari, A.Fiorillo, P.Ceci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 157.681, 157.681, 246.437, 90.00, 90.00, 90.00
R / Rfree (%) 26.014 / 28.338

Silver Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Silver atom in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) (pdb code 2x17). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 33 binding sites of Silver where determined in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I), PDB code: 2x17:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 33 in 2x17

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Silver binding site 1 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Ag1172

b:70.7
occ:1.00
NE2 0:HIS53 2.2 67.6 1.0
SD I:MET170 2.2 76.9 1.0
CE1 0:HIS53 3.1 67.0 1.0
CD2 0:HIS53 3.2 66.9 1.0
O 0:HOH2001 3.2 45.9 1.0
CB I:MET170 3.2 78.6 1.0
CG I:MET170 3.4 78.4 1.0
OE1 0:GLU49 3.6 67.3 1.0
CE I:MET170 3.9 78.5 1.0
OE2 0:GLU130 3.9 76.4 1.0
CG 0:GLU126 3.9 71.3 1.0
CH2 0:TRP122 4.0 69.1 1.0
CB 0:GLU49 4.2 66.2 1.0
ND1 0:HIS53 4.3 66.8 1.0
CD 0:GLU49 4.3 67.0 1.0
CG 0:HIS53 4.3 66.5 1.0
O 0:GLU49 4.5 66.2 1.0
CD 0:GLU126 4.5 71.8 1.0
CA I:MET170 4.6 78.7 1.0
OE2 0:GLU126 4.6 72.1 1.0
CZ3 0:TRP122 4.7 69.1 1.0
CG 0:GLU49 4.7 66.6 1.0
O I:MET170 4.7 79.0 1.0
CZ2 0:TRP122 4.8 69.0 1.0
CD 0:GLU130 4.9 76.1 1.0
C 0:GLU49 4.9 66.2 1.0
N I:MET170 4.9 78.4 1.0
CA 0:GLU49 5.0 66.2 1.0
C I:MET170 5.0 79.0 1.0

Silver binding site 2 out of 33 in 2x17

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Silver binding site 2 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ag1173

b:71.0
occ:1.00
SD J:MET170 2.2 76.8 1.0
NE2 1:HIS53 2.2 67.9 1.0
O 1:HOH2001 2.9 47.3 1.0
CG J:MET170 3.0 78.4 1.0
CE1 1:HIS53 3.0 67.2 1.0
OE1 1:GLU49 3.1 67.3 1.0
CD2 1:HIS53 3.2 67.0 1.0
CE J:MET170 3.7 78.4 1.0
OE2 1:GLU126 3.7 72.2 1.0
CG 1:GLU126 3.8 71.3 1.0
CH2 1:TRP122 4.0 69.0 1.0
CB 1:GLU49 4.1 66.3 1.0
CD 1:GLU49 4.1 67.1 1.0
O 1:GLU49 4.1 66.2 1.0
CD 1:GLU126 4.1 71.9 1.0
ND1 1:HIS53 4.2 66.9 1.0
CG 1:HIS53 4.3 66.5 1.0
CB J:MET170 4.4 78.7 1.0
CG 1:GLU49 4.5 66.7 1.0
OE2 1:GLU130 4.6 76.4 1.0
CZ3 1:TRP122 4.7 69.0 1.0
C 1:GLU49 4.7 66.2 1.0
CA 1:GLU49 4.8 66.2 1.0
CZ2 1:TRP122 4.9 69.1 1.0

Silver binding site 3 out of 33 in 2x17

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Silver binding site 3 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ag1174

b:56.1
occ:1.00
SD O:MET153 2.6 79.6 1.0
SD 1:MET153 2.7 79.9 1.0
SD I:MET153 2.9 80.0 1.0
SD 7:MET153 3.0 79.8 1.0
CE 1:MET153 3.5 80.0 1.0
CE I:MET153 3.5 80.1 1.0
CE 7:MET153 3.7 80.0 1.0
CG 1:MET153 3.8 80.0 1.0
CE O:MET153 3.8 79.9 1.0
CG O:MET153 4.1 79.9 1.0
CG 7:MET153 4.1 79.9 1.0
CG I:MET153 4.2 80.0 1.0

Silver binding site 4 out of 33 in 2x17

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Silver binding site 4 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ag1175

b:60.4
occ:1.00
CB 6:MET1 4.0 81.9 1.0
O 6:LEU2 4.1 82.8 1.0
CG 6:MET1 4.2 81.8 1.0
SD 6:MET1 4.7 81.8 1.0
C 6:MET1 4.9 82.1 1.0
O 6:MET1 4.9 82.1 1.0

Silver binding site 5 out of 33 in 2x17

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Silver binding site 5 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ag1172

b:74.1
occ:1.00
NE2 2:HIS53 2.2 68.4 1.0
SD K:MET170 2.2 77.4 1.0
CB K:MET170 2.9 78.6 1.0
CG K:MET170 3.1 78.4 1.0
O 2:HOH2001 3.1 34.9 1.0
CE1 2:HIS53 3.1 67.3 1.0
CD2 2:HIS53 3.1 67.1 1.0
OE1 2:GLU49 3.3 67.5 1.0
CG 2:GLU126 3.8 71.4 1.0
CE K:MET170 3.9 78.6 1.0
CH2 2:TRP122 4.0 69.1 1.0
OE2 2:GLU130 4.1 76.4 1.0
O 2:GLU49 4.1 66.3 1.0
ND1 2:HIS53 4.2 67.0 1.0
CG 2:HIS53 4.2 66.6 1.0
CD 2:GLU49 4.2 67.2 1.0
OE2 2:GLU126 4.3 72.2 1.0
CB 2:GLU49 4.3 66.3 1.0
CA K:MET170 4.3 78.7 1.0
CD 2:GLU126 4.5 71.9 1.0
CZ3 2:TRP122 4.6 69.1 1.0
N K:MET170 4.7 78.4 1.0
C 2:GLU49 4.8 66.3 1.0
CG 2:GLU49 4.8 66.7 1.0
CZ2 2:TRP122 4.9 69.1 1.0
CA 2:GLU49 4.9 66.3 1.0

Silver binding site 6 out of 33 in 2x17

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Silver binding site 6 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ag1172

b:59.5
occ:1.00
SD 3:MET153 2.8 79.7 1.0
SD Q:MET153 2.8 79.7 1.0
SD 9:MET153 2.9 79.8 1.0
SD K:MET153 3.1 79.7 1.0
CE 9:MET153 3.5 80.1 1.0
CE 3:MET153 3.5 79.9 1.0
CE Q:MET153 3.6 80.0 1.0
CE K:MET153 3.8 80.0 1.0
CG 3:MET153 3.9 79.9 1.0
CG Q:MET153 4.1 79.9 1.0
CG 9:MET153 4.1 80.0 1.0
CG K:MET153 4.2 79.9 1.0

Silver binding site 7 out of 33 in 2x17

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Silver binding site 7 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ag1173

b:71.5
occ:1.00
O 3:HOH2002 2.2 72.6 1.0
NE2 3:HIS53 2.2 67.9 1.0
SD L:MET170 2.2 77.2 1.0
CE1 3:HIS53 3.1 67.1 1.0
OE1 3:GLU49 3.2 67.4 1.0
CD2 3:HIS53 3.2 67.0 1.0
CB L:MET170 3.4 78.7 1.0
CG L:MET170 3.4 78.5 1.0
CG 3:GLU126 3.7 71.3 1.0
CE L:MET170 3.8 78.4 1.0
OE2 3:GLU126 4.0 72.1 1.0
CH2 3:TRP122 4.0 69.0 1.0
CD 3:GLU49 4.2 67.0 1.0
CD 3:GLU126 4.2 71.9 1.0
ND1 3:HIS53 4.2 66.8 1.0
CB 3:GLU49 4.2 66.3 1.0
CG 3:HIS53 4.3 66.5 1.0
OE2 3:GLU130 4.3 76.4 1.0
O 3:GLU49 4.4 66.2 1.0
CG 3:GLU49 4.6 66.6 1.0
CZ3 3:TRP122 4.7 69.1 1.0
CA L:MET170 4.7 78.8 1.0
CZ2 3:TRP122 4.8 69.0 1.0
N L:MET170 4.9 78.5 1.0
C 3:GLU49 4.9 66.2 1.0
CA 3:GLU49 4.9 66.2 1.0

Silver binding site 8 out of 33 in 2x17

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Silver binding site 8 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ag1174

b:62.5
occ:1.00
OH Y:TYR91 2.8 75.6 1.0
ND2 3:ASN65 3.3 70.7 1.0
CB 3:MET1 3.7 82.0 1.0
CZ Y:TYR91 3.8 75.6 1.0
SD 3:MET1 3.9 81.8 1.0
CB 3:ASN65 3.9 70.4 1.0
CE2 Y:TYR91 4.0 75.6 1.0
CG 3:ASN65 4.0 70.5 1.0
CG 3:MET1 4.1 81.8 1.0
CE Y:LYS135 4.3 75.7 1.0
CA 3:MET1 4.6 82.1 1.0
N 3:MET1 4.7 82.0 1.0

Silver binding site 9 out of 33 in 2x17

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Silver binding site 9 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Ag1173

b:65.2
occ:1.00
NE2 4:HIS53 2.2 66.6 1.0
SD M:MET170 2.6 78.3 1.0
CE1 4:HIS53 2.9 66.8 1.0
O 4:HOH2002 3.2 43.6 1.0
OE1 4:GLU49 3.2 67.4 1.0
CD2 4:HIS53 3.4 66.6 1.0
CG M:MET170 3.5 78.6 1.0
CE M:MET170 3.6 78.8 1.0
CG 4:GLU126 3.8 71.4 1.0
CB M:MET170 3.9 78.5 1.0
CH2 4:TRP122 4.0 69.1 1.0
OE2 4:GLU130 4.0 76.4 1.0
CB 4:GLU49 4.1 66.3 1.0
ND1 4:HIS53 4.1 66.6 1.0
CD 4:GLU49 4.2 67.1 1.0
OE2 4:GLU126 4.3 72.2 1.0
CG 4:HIS53 4.4 66.3 1.0
CD 4:GLU126 4.4 72.0 1.0
CG 4:GLU49 4.6 66.7 1.0
O 4:GLU49 4.6 66.2 1.0
CZ2 4:TRP122 4.7 69.1 1.0
CZ3 4:TRP122 4.8 69.1 1.0
CA 4:GLU49 4.9 66.2 1.0
C 4:GLU49 5.0 66.2 1.0

Silver binding site 10 out of 33 in 2x17

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Silver binding site 10 out of 33 in the The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of The X-Ray Structure of Ferritin From Pyrococcus Furiosus Loaded with Ag(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Ag1174

b:56.1
occ:1.00
SD Z:MET153 2.7 79.7 1.0
SD P:MET153 2.8 79.8 1.0
SD 4:MET153 2.9 79.8 1.0
SD R:MET153 3.0 79.9 1.0
CE Z:MET153 3.5 79.9 1.0
CE P:MET153 3.6 80.0 1.0
CE 4:MET153 3.6 80.0 1.0
CE R:MET153 3.6 80.0 1.0
CG Z:MET153 3.7 79.9 1.0
CG 4:MET153 3.9 79.9 1.0
CG P:MET153 4.0 79.9 1.0
CG R:MET153 4.3 80.0 1.0

Reference:

O.Kasyutich, A.Ilari, A.Fiorillo, D.Tatchev, A.Hoell, P.Ceci. Silver Ion Incorporation and Nanoparticle Formation Inside the Cavity of Pyrococcus Furiosus Ferritin: Structural and Size-Distribution Analyses. J.Am.Chem.Soc. V. 132 3621 2010.
ISSN: ISSN 0002-7863
PubMed: 20170158
DOI: 10.1021/JA910918B
Page generated: Sat Dec 12 01:21:29 2020

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