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Rubidium in PDB 460d: 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: 460d 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 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.111, 39.731, 65.829, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / n/a

Other elements in 460d:

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) 3 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove (pdb code 460d). 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: 460d:

Rubidium binding site 1 out of 1 in 460d

Go back to Rubidium Binding Sites List in 460d
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
B:Rb110

b:23.8
occ:0.50
O2 B:TAF19 2.7 18.6 1.0
O2 A:TAF7 2.8 17.6 1.0
O B:HOH145 2.8 27.6 1.0
O B:HOH131 2.9 26.3 1.0
O A:HOH265 3.3 41.6 0.5
O4' B:DT20 3.3 22.3 1.0
O4' A:DT8 3.5 18.6 1.0
C4' B:DT20 3.8 23.4 1.0
C2 B:TAF19 3.9 16.7 1.0
C2 A:TAF7 3.9 16.0 1.0
C4' A:DT8 4.0 20.1 1.0
C5' B:DT20 4.1 23.0 1.0
C1' B:TAF19 4.2 19.3 1.0
C1' A:TAF7 4.3 17.5 1.0
C1' B:DT20 4.3 20.9 1.0
C1' A:DT8 4.4 17.4 1.0
C5' A:DT8 4.4 19.1 1.0
C2 B:DA18 4.5 16.3 1.0
C2 A:DA6 4.5 17.3 1.0
N1 B:TAF19 4.6 17.7 1.0
N1 A:TAF7 4.7 15.6 1.0
N1 B:DT20 4.7 20.6 1.0
O B:HOH115 4.7 20.3 1.0
O B:HOH104 4.8 19.2 1.0
N1 A:DT8 4.8 16.8 1.0
O2 B:DT20 4.9 20.7 1.0
N3 B:TAF19 4.9 18.1 1.0
O2 A:DT8 4.9 16.8 1.0
N3 A:TAF7 4.9 15.2 1.0
O A:HOH186 4.9 49.8 1.0
C2 B:DT20 5.0 20.1 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 02:06:49 2020

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