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Rubidium in PDB 461d: A "Hydrat-Ion Spine" in A B-Dna Minor Groove

Protein crystallography data

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 461d was solved by V.Tereshko, G.Minasov, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.070, 39.720, 65.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / n/a

Other elements in 461d:

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove (pdb code 461d). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total only one binding site of Rubidium was determined in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 461d:

Rubidium binding site 1 out of 1 in 461d

Go back to Rubidium Binding Sites List in 461d
Rubidium binding site 1 out of 1 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb110

b:26.9
occ:0.50
O2 B:TAF19 2.7 21.4 1.0
O B:HOH145 2.8 28.3 1.0
O A:HOH131 2.8 28.8 1.0
O2 A:TAF7 2.8 19.3 1.0
O A:HOH265 3.2 0.0 0.0
O4' B:DT20 3.3 22.5 1.0
O4' A:DT8 3.5 20.1 1.0
C4' B:DT20 3.8 24.4 1.0
C2 B:TAF19 3.9 20.0 1.0
C4' A:DT8 4.0 22.1 1.0
C2 A:TAF7 4.0 16.4 1.0
C5' B:DT20 4.1 24.0 1.0
C1' B:TAF19 4.3 20.3 1.0
C1' B:DT20 4.3 22.4 1.0
C1' A:TAF7 4.3 17.7 1.0
C5' A:DT8 4.4 19.4 1.0
C1' A:DT8 4.4 18.5 1.0
C2 B:DA18 4.5 17.1 1.0
C2 A:DA6 4.6 18.8 1.0
N1 B:TAF19 4.6 20.9 1.0
N1 A:TAF7 4.7 17.1 1.0
O A:HOH104 4.7 21.4 1.0
N1 B:DT20 4.7 22.6 1.0
O2 A:DT8 4.8 18.4 1.0
N1 A:DT8 4.8 18.5 1.0
N3 B:TAF19 4.9 19.7 1.0
O B:HOH115 4.9 22.1 1.0
O2 B:DT20 4.9 21.5 1.0
N3 A:TAF7 5.0 16.2 1.0
C2 A:DT8 5.0 16.1 1.0
C2 B:DT20 5.0 21.1 1.0

Reference:

V.Tereshko, G.Minasov, M.Egli. A "Hydrat-Ion Spine" in A B-Dna Minor Groove J.Am.Chem.Soc. V. 121 3590 1999.
ISSN: ISSN 0002-7863
Page generated: Wed Dec 16 02:06:50 2020

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