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Terbium in PDB 5obb: Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium

Enzymatic activity of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium

All present enzymatic activity of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium:
1.16.3.1;

Protein crystallography data

The structure of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium, PDB code: 5obb was solved by P.Baiocco, M.C.Trabuco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 2.65
Space group I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 237.251, 237.563, 237.572, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 17.4

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Terbium atom in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium (pdb code 5obb). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 32 binding sites of Terbium where determined in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium, PDB code: 5obb:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 32 in 5obb

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Terbium binding site 1 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


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Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:63.6
occ:1.00
OE1 C:GLU134 2.2 52.9 1.0
OE1 A:GLU134 2.3 54.1 1.0
OE1 B:GLU134 2.3 60.8 1.0
CD C:GLU134 3.4 53.0 1.0
CD B:GLU134 3.5 60.7 1.0
CD A:GLU134 3.5 54.0 1.0
OD1 A:ASP131 3.9 54.4 1.0
OD1 B:ASP131 3.9 59.9 1.0
OE2 C:GLU134 3.9 53.1 1.0
OE2 A:GLU134 4.0 54.1 1.0
OE2 B:GLU134 4.0 60.7 1.0
OD1 C:ASP131 4.2 52.7 1.0
CG C:GLU134 4.6 52.9 1.0
CG B:GLU134 4.7 60.5 1.0
CB B:GLU134 4.7 60.5 1.0
CG A:ASP131 4.7 54.2 1.0
CG A:GLU134 4.7 54.0 1.0
CB C:GLU134 4.7 52.8 1.0
CA A:ASP131 4.7 54.0 1.0
CG B:ASP131 4.7 59.9 1.0
CB A:GLU134 4.7 53.9 1.0
CB A:ASP131 4.8 54.1 1.0
CA B:ASP131 4.8 59.8 1.0
CB B:ASP131 4.8 59.8 1.0
CA C:ASP131 4.9 52.5 1.0
CG C:ASP131 4.9 52.6 1.0
CB C:ASP131 5.0 52.5 1.0

Terbium binding site 2 out of 32 in 5obb

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Terbium binding site 2 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


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Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb202

b:90.6
occ:0.75
OE2 A:GLU27 2.6 57.2 1.0
OE2 A:GLU62 2.9 55.5 1.0
OE1 A:GLN141 2.9 52.5 1.0
OE1 A:GLU62 3.1 55.9 1.0
CD A:GLU62 3.3 55.7 1.0
CD A:GLU27 3.4 57.1 1.0
ND1 A:HIS65 3.5 57.0 1.0
OE1 A:GLU27 3.5 57.2 1.0
CG A:HIS65 3.7 56.8 1.0
CE1 A:HIS65 4.0 57.1 1.0
CB A:HIS65 4.1 56.4 1.0
CD A:GLN141 4.1 52.5 1.0
CG1 A:VAL110 4.3 52.7 1.0
CD2 A:HIS65 4.3 57.0 1.0
NE2 A:HIS65 4.5 57.2 1.0
OE1 A:GLU107 4.6 52.9 1.0
CG A:GLU62 4.7 55.5 1.0
CG A:GLU27 4.9 56.9 1.0
NE2 A:GLN141 4.9 52.4 1.0
CD2 A:TYR137 4.9 52.8 1.0

Terbium binding site 3 out of 32 in 5obb

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Terbium binding site 3 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb201

b:1.0
occ:0.60
OE1 B:GLN141 2.3 56.6 1.0
OE1 B:GLU62 2.9 61.4 1.0
OE2 B:GLU62 3.0 61.1 1.0
OE2 B:GLU27 3.0 54.2 1.0
OE1 B:GLU27 3.1 54.0 1.0
CD B:GLU62 3.3 61.1 1.0
CD B:GLN141 3.4 56.6 1.0
CD B:GLU27 3.4 54.1 1.0
ND1 B:HIS65 3.5 60.3 1.0
CG1 B:VAL110 3.6 58.3 1.0
OE1 B:GLU107 4.1 59.6 1.0
NE2 B:GLN141 4.2 56.5 1.0
CE1 B:HIS65 4.3 60.4 1.0
CG B:GLN141 4.4 56.6 1.0
CG B:HIS65 4.6 60.2 1.0
CB B:VAL110 4.6 58.3 1.0
CB B:HIS65 4.8 59.9 1.0
CG B:GLU62 4.8 60.8 1.0
CG B:GLU27 4.9 53.9 1.0
CD B:GLU107 5.0 59.6 1.0

Terbium binding site 4 out of 32 in 5obb

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Terbium binding site 4 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb201

b:79.1
occ:0.75
OE2 C:GLU27 2.7 45.0 1.0
OE2 C:GLU62 2.9 50.9 1.0
OE1 C:GLN141 2.9 51.4 1.0
OE1 C:GLU62 3.2 51.1 1.0
OE1 C:GLU27 3.3 44.9 1.0
CD C:GLU62 3.3 50.9 1.0
CD C:GLU27 3.4 44.9 1.0
ND1 C:HIS65 3.5 52.1 1.0
CG C:HIS65 3.7 51.9 1.0
CB C:HIS65 4.0 51.6 1.0
CE1 C:HIS65 4.0 52.1 1.0
CD C:GLN141 4.1 51.2 1.0
CG1 C:VAL110 4.4 49.7 1.0
CD2 C:HIS65 4.4 52.0 1.0
NE2 C:HIS65 4.5 52.1 1.0
OE1 C:GLU107 4.6 50.9 1.0
CG C:GLU62 4.8 50.8 1.0
CD2 C:TYR137 4.8 51.4 1.0
CG C:GLU27 4.9 44.9 1.0
NE2 C:GLN141 4.9 51.2 1.0
CA C:GLU62 5.0 50.7 1.0

Terbium binding site 5 out of 32 in 5obb

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Terbium binding site 5 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb201

b:63.0
occ:1.00
OE1 E:GLU134 2.3 59.0 1.0
OE1 F:GLU134 2.3 54.0 1.0
OE1 D:GLU134 2.3 53.9 1.0
CD E:GLU134 3.5 58.7 1.0
CD F:GLU134 3.5 54.0 1.0
CD D:GLU134 3.5 53.9 1.0
OD1 D:ASP131 3.8 54.2 1.0
OD1 E:ASP131 3.9 59.3 1.0
OE2 F:GLU134 4.0 54.0 1.0
OE2 D:GLU134 4.0 54.1 1.0
OE2 E:GLU134 4.0 58.9 1.0
OD1 F:ASP131 4.1 52.8 1.0
CG D:ASP131 4.6 54.0 1.0
CB E:GLU134 4.6 58.5 1.0
CG E:GLU134 4.6 58.6 1.0
CG E:ASP131 4.7 59.3 1.0
CG F:GLU134 4.7 53.9 1.0
CG D:GLU134 4.7 53.7 1.0
CB D:ASP131 4.7 53.8 1.0
CB D:GLU134 4.7 53.6 1.0
CB F:GLU134 4.7 53.7 1.0
CA E:ASP131 4.7 59.2 1.0
CA D:ASP131 4.8 53.6 1.0
CB E:ASP131 4.8 59.3 1.0
CA F:ASP131 4.9 52.7 1.0
CG F:ASP131 4.9 52.7 1.0
CB F:ASP131 4.9 52.7 1.0

Terbium binding site 6 out of 32 in 5obb

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Terbium binding site 6 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb202

b:84.5
occ:0.70
OE2 D:GLU27 2.6 48.2 1.0
OE2 D:GLU62 2.8 54.2 1.0
OE1 D:GLN141 2.8 52.9 1.0
OE1 D:GLU62 3.3 54.4 1.0
CD D:GLU62 3.4 54.4 1.0
CD D:GLU27 3.4 48.0 1.0
OE1 D:GLU27 3.5 47.8 1.0
ND1 D:HIS65 3.6 56.5 1.0
CG D:HIS65 3.9 56.4 1.0
CD D:GLN141 4.0 52.8 1.0
CG1 D:VAL110 4.1 52.6 1.0
CB D:HIS65 4.2 56.1 1.0
CE1 D:HIS65 4.2 56.6 1.0
CD2 D:HIS65 4.7 56.6 1.0
OE1 D:GLU107 4.7 51.4 1.0
NE2 D:GLN141 4.7 52.8 1.0
CG D:GLU62 4.8 54.3 1.0
NE2 D:HIS65 4.8 56.6 1.0
CG D:GLU27 4.8 47.8 1.0
CG D:GLN141 4.9 52.8 1.0
CD2 D:TYR137 5.0 52.8 1.0

Terbium binding site 7 out of 32 in 5obb

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Terbium binding site 7 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Tb201

b:89.1
occ:0.75
OE2 E:GLU27 2.6 52.9 1.0
OE2 E:GLU62 2.9 57.7 1.0
OE1 E:GLN141 3.0 55.2 1.0
OE1 E:GLU62 3.1 57.6 1.0
ND1 E:HIS65 3.2 59.2 1.0
CD E:GLU62 3.3 57.7 1.0
CD E:GLU27 3.4 53.0 1.0
OE1 E:GLU27 3.5 53.0 1.0
CG E:HIS65 3.5 59.0 1.0
CE1 E:HIS65 3.7 59.2 1.0
CB E:HIS65 3.8 58.6 1.0
CD2 E:HIS65 4.1 59.1 1.0
CD E:GLN141 4.2 55.1 1.0
NE2 E:HIS65 4.2 59.2 1.0
CG1 E:VAL110 4.5 53.6 1.0
OE1 E:GLU107 4.6 54.1 1.0
CG E:GLU62 4.7 57.4 1.0
CA E:GLU62 4.8 57.3 1.0
CG E:GLU27 4.9 52.9 1.0
CD2 E:TYR137 5.0 57.5 1.0

Terbium binding site 8 out of 32 in 5obb

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Terbium binding site 8 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Tb201

b:73.5
occ:0.70
OE2 F:GLU27 2.6 49.5 1.0
OE1 F:GLN141 3.0 56.9 1.0
OE2 F:GLU62 3.0 51.7 1.0
OE1 F:GLU62 3.1 51.9 1.0
CD F:GLU62 3.4 51.8 1.0
CD F:GLU27 3.4 49.2 1.0
OE1 F:GLU27 3.4 49.4 1.0
ND1 F:HIS65 3.5 53.0 1.0
CG F:HIS65 3.8 52.8 1.0
CE1 F:HIS65 4.0 53.1 1.0
CB F:HIS65 4.1 52.6 1.0
CD F:GLN141 4.1 56.7 1.0
CG1 F:VAL110 4.3 54.5 1.0
CD2 F:HIS65 4.5 53.0 1.0
OE1 F:GLU107 4.6 55.5 1.0
NE2 F:HIS65 4.6 53.1 1.0
CG F:GLU62 4.8 51.7 1.0
OE1 F:GLU140 4.8 57.5 1.0
CG F:GLU27 4.8 49.0 1.0
NE2 F:GLN141 4.9 56.6 1.0
CD2 F:TYR137 5.0 54.0 1.0

Terbium binding site 9 out of 32 in 5obb

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Terbium binding site 9 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Tb201

b:67.6
occ:1.00
OE1 G:GLU134 2.3 56.7 1.0
OE1 I:GLU134 2.3 55.9 1.0
OE1 H:GLU134 2.4 59.4 1.0
CD G:GLU134 3.5 56.5 1.0
CD I:GLU134 3.5 56.1 1.0
CD H:GLU134 3.6 59.2 1.0
OD1 I:ASP131 3.9 55.8 1.0
OD1 G:ASP131 3.9 57.2 1.0
OD1 H:ASP131 4.0 59.1 1.0
OE2 I:GLU134 4.0 56.2 1.0
OE2 G:GLU134 4.0 56.8 1.0
OE2 H:GLU134 4.1 59.3 1.0
CG I:GLU134 4.6 55.9 1.0
CG I:ASP131 4.6 55.7 1.0
CG G:GLU134 4.6 56.2 1.0
CB I:GLU134 4.7 55.8 1.0
CA I:ASP131 4.7 55.4 1.0
CB G:GLU134 4.7 55.9 1.0
CG G:ASP131 4.7 57.1 1.0
CB I:ASP131 4.7 55.5 1.0
CA G:ASP131 4.8 56.8 1.0
CG H:GLU134 4.8 59.0 1.0
CB G:ASP131 4.8 56.9 1.0
CG H:ASP131 4.8 59.1 1.0
CB H:GLU134 4.8 58.9 1.0
CA H:ASP131 4.9 58.9 1.0
CB H:ASP131 4.9 59.0 1.0

Terbium binding site 10 out of 32 in 5obb

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Terbium binding site 10 out of 32 in the Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Structure of A Modified Mouse H Chain Ferritin with A Lanthanide Binding Motif in Complex with Terbium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Tb202

b:84.2
occ:0.75
OE2 G:GLU27 2.7 54.1 1.0
OE2 G:GLU62 2.9 57.2 1.0
OE1 G:GLN141 2.9 51.4 1.0
OE1 G:GLU62 3.1 57.0 1.0
ND1 G:HIS65 3.3 57.2 1.0
CD G:GLU62 3.3 56.9 1.0
CD G:GLU27 3.5 53.8 1.0
OE1 G:GLU27 3.5 53.7 1.0
CG G:HIS65 3.6 57.1 1.0
CE1 G:HIS65 3.8 57.2 1.0
CB G:HIS65 4.0 57.0 1.0
CD G:GLN141 4.1 51.4 1.0
CD2 G:HIS65 4.3 57.2 1.0
NE2 G:HIS65 4.4 57.3 1.0
CG1 G:VAL110 4.5 56.6 1.0
OE1 G:GLU107 4.6 56.1 1.0
CG G:GLU62 4.7 56.6 1.0
CA G:GLU62 4.9 56.3 1.0
CG G:GLU27 4.9 53.5 1.0
NE2 G:GLN141 4.9 51.4 1.0

Reference:

L.Calisti, M.C.Trabuco, A.Boffi, C.Testi, L.C.Montemiglio, A.Des Georges, I.Benni, A.Ilari, B.Taciak, M.Bialasek, T.Rygiel, M.Krol, P.Baiocco, A.Bonamore. Engineered Ferritin For Lanthanide Binding. Plos One V. 13 01859 2018.
ISSN: ESSN 1932-6203
PubMed: 30102720
DOI: 10.1371/JOURNAL.PONE.0201859
Page generated: Wed Dec 16 02:26:50 2020

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