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Terbium in PDB 359d: Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)

Protein crystallography data

The structure of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III), PDB code: 359d was solved by A.L.Feig, W.G.Scott, O.C.Uhlenbeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.80 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.540, 65.540, 138.080, 90.00, 90.00, 120.00
R / Rfree (%) 25.6 / 30.2

Terbium Binding Sites:

The binding sites of Terbium atom in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) (pdb code 359d). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 5 binding sites of Terbium where determined in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III), PDB code: 359d:
Jump to Terbium binding site number: 1; 2; 3; 4; 5;

Terbium binding site 1 out of 5 in 359d

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Terbium binding site 1 out of 5 in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb4

b:52.7
occ:0.42
N1 A:G50 3.8 48.1 1.0
N2 A:G50 3.9 61.4 1.0
C2 A:G50 4.4 53.4 1.0
O6 A:G50 4.7 46.9 1.0
C6 A:G50 4.7 42.9 1.0
C2 A:A60 5.0 42.4 1.0

Terbium binding site 2 out of 5 in 359d

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Terbium binding site 2 out of 5 in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb3

b:64.5
occ:0.22
N4 B:C170 3.9 36.0 1.0
N4 A:C30 4.0 23.8 1.0
OP1 A:U70 4.0 19.7 1.0
OP2 A:G80 4.1 20.5 1.0
O5' A:U70 4.1 10.8 1.0
P A:U70 4.4 19.1 1.0
OP2 A:U70 4.5 19.7 1.0
C5' A:U70 4.7 11.4 1.0
N6 B:A11 4.7 29.1 1.0
C4 B:C170 5.0 36.9 1.0
OP1 A:G80 5.0 28.6 1.0

Terbium binding site 3 out of 5 in 359d

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Terbium binding site 3 out of 5 in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb1

b:52.0
occ:0.27
N4 B:C12 3.6 38.5 1.0
C4 B:C12 4.5 38.1 1.0
C5 B:C12 4.6 31.7 1.0
N6 B:A11 5.0 29.1 1.0

Terbium binding site 4 out of 5 in 359d

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Terbium binding site 4 out of 5 in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb7

b:57.1
occ:0.20
N3 B:A11 3.4 37.8 1.0
O4' B:C12 3.7 34.5 1.0
C2 B:A11 3.8 40.1 1.0
O2' A:C30 3.9 28.2 1.0
C1' A:C30 4.0 23.0 1.0
C1' B:C12 4.1 34.6 1.0
O4' A:C30 4.2 27.3 1.0
O2' B:A11 4.4 42.6 1.0
C4 B:A11 4.6 32.4 1.0
C2' A:C30 4.6 24.3 1.0
C2' B:A11 4.7 38.5 1.0
O2 A:C30 4.8 33.5 1.0
N1 B:C12 4.8 33.3 1.0
O2 A:U21 4.8 27.1 1.0
C1' B:A11 4.8 33.9 1.0
C4' B:C12 4.9 34.5 1.0

Terbium binding site 5 out of 5 in 359d

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Terbium binding site 5 out of 5 in the Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III)


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb8

b:51.2
occ:0.23
O4' B:A163 3.6 23.4 1.0
O2' B:G164 3.8 13.6 1.0
C1' B:A163 4.1 15.7 1.0
N2 B:G164 4.2 15.4 1.0
N3 B:G164 4.3 13.9 1.0
N6 B:A34L 4.3 36.9 1.0
C4' B:A163 4.3 20.7 1.0
O2' B:A163 4.4 22.4 1.0
C2' B:G164 4.6 12.8 1.0
C2 B:G164 4.8 16.4 1.0
C2' B:A163 4.9 20.4 1.0

Reference:

A.L.Feig, W.G.Scott, O.C.Uhlenbeck. Inhibition of the Hammerhead Ribozyme Cleavage Reaction By Site-Specific Binding of Tb. Science V. 279 81 1998.
ISSN: ISSN 0036-8075
PubMed: 9417029
DOI: 10.1126/SCIENCE.279.5347.81
Page generated: Wed Dec 16 02:26:37 2020

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