Ruthenium in PDB 8oyr: Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+

The structure of Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+, PDB code: 8oyr was solved by T.D.Prieto-Otoya, C.J.Cardin, K.T.Mcquaid, N.G.Paterson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.66 / 2.21
Space group	P 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.99, 56.99, 30.892, 90, 90, 90
R / Rfree (%)	23 / 26.3

The structure of Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+ also contains other interesting chemical elements:

Strontium

(Sr)

2 atoms

The binding sites of Ruthenium atom in the Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+ (pdb code 8oyr). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+, PDB code: 8oyr:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:114.4 occ:0.50 RU01 A:V7F101 0.0 114.4 0.5 N04 A:V7F101 2.0 93.8 0.5 N02 A:V7F101 2.0 95.0 0.5 N03 A:V7F101 2.1 98.6 0.5 N01 A:V7F101 2.1 100.3 0.5 N06 A:V7F101 2.1 99.5 0.5 N05 A:V7F101 2.1 100.0 0.5 H24 A:V7F101 2.4 112.5 0.5 H26 A:V7F101 2.7 114.0 0.5 C07 A:V7F101 2.7 98.1 0.5 C03 A:V7F101 2.7 98.2 0.5 C01 A:V7F101 2.9 101.0 0.5 C10 A:V7F101 3.0 100.7 0.5 C04 A:V7F101 3.0 96.7 0.5 C08 A:V7F101 3.0 96.9 0.5 C19 A:V7F101 3.1 116.9 0.5 C12 A:V7F101 3.1 116.2 0.5 C20 A:V7F101 3.1 109.8 0.5 C22 A:V7F101 3.1 111.2 0.5 H06 A:V7F101 3.1 140.3 0.5 H07 A:V7F101 3.2 131.8 0.5 H03 A:V7F101 3.2 139.4 0.5 H09 A:V7F101 3.2 133.4 0.5 C14 A:V7F101 4.1 107.9 0.5 C02 A:V7F101 4.1 106.5 0.5 C13 A:V7F101 4.3 110.0 0.5 C11 A:V7F101 4.3 109.1 0.5 C23 A:V7F101 4.3 93.0 0.5 C17 A:V7F101 4.4 92.2 0.5 H25 A:V7F101 4.4 134.2 0.5 C05 A:V7F101 4.4 117.3 0.5 C21 A:V7F101 4.4 114.4 0.5 C15 A:V7F101 4.4 114.4 0.5 C34 A:V7F101 4.4 115.7 0.5 H05 A:V7F101 4.5 124.5 0.5 O4' A:DC2 4.6 107.7 1.0 C18 A:V7F101 4.8 103.7 0.5 C26 A:V7F101 4.8 111.8 0.5 H1' A:DC2 4.8 122.2 1.0 O2 A:DC2 4.9 103.4 1.0 C06 A:V7F101 4.9 112.8 0.5 C25 A:V7F101 4.9 111.7 0.5 C24 A:V7F101 4.9 89.1 0.5 C33 A:V7F101 5.0 90.5 0.5 O5' A:DC2 5.0 96.2 1.0

Ruthenium binding site 2 out of 3 in the Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru102 b:110.3 occ:1.00 RU01 A:V7F102 0.0 110.3 1.0 N04 A:V7F102 2.0 85.7 1.0 N02 A:V7F102 2.0 65.5 1.0 N05 A:V7F102 2.1 94.3 1.0 N06 A:V7F102 2.1 80.3 1.0 N01 A:V7F102 2.1 80.6 1.0 N03 A:V7F102 2.1 82.2 1.0 H24 A:V7F102 2.4 102.9 1.0 H26 A:V7F102 2.7 78.6 1.0 C04 A:V7F102 2.9 84.9 1.0 C08 A:V7F102 2.9 83.4 1.0 C01 A:V7F102 2.9 70.8 1.0 C10 A:V7F102 2.9 83.7 1.0 C03 A:V7F102 2.9 87.9 1.0 C07 A:V7F102 2.9 60.1 1.0 C22 A:V7F102 3.0 106.4 1.0 C20 A:V7F102 3.1 91.0 1.0 C19 A:V7F102 3.1 113.2 1.0 C12 A:V7F102 3.1 84.9 1.0 H09 A:V7F102 3.1 127.7 1.0 H07 A:V7F102 3.2 109.1 1.0 H06 A:V7F102 3.2 135.8 1.0 H03 A:V7F102 3.2 101.9 1.0 C17 A:V7F102 4.2 95.9 1.0 C23 A:V7F102 4.2 75.3 1.0 C13 A:V7F102 4.3 97.5 1.0 C11 A:V7F102 4.3 86.8 1.0 C34 A:V7F102 4.3 126.9 1.0 C02 A:V7F102 4.3 94.4 1.0 C05 A:V7F102 4.3 95.0 1.0 C14 A:V7F102 4.4 93.3 1.0 C15 A:V7F102 4.4 99.1 1.0 C21 A:V7F102 4.4 94.0 1.0 H22 A:DG4 4.7 132.3 1.0 H05 A:V7F102 4.7 105.0 1.0 H25 A:V7F102 4.7 111.0 1.0 C33 A:V7F102 4.8 108.8 1.0 C24 A:V7F102 4.8 75.4 1.0 C06 A:V7F102 4.8 121.6 1.0 C25 A:V7F102 4.9 90.9 1.0

Ruthenium binding site 3 out of 3 in the Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Dna Major Groove Binding By Lambda-[Ru(Phen)2(Phi)]2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru103 b:120.8 occ:0.50 RU01 A:V7F103 0.0 120.8 0.5 N04 A:V7F103 2.0 96.0 0.5 N02 A:V7F103 2.0 94.2 0.5 N06 A:V7F103 2.1 109.2 0.5 N05 A:V7F103 2.1 104.6 0.5 N01 A:V7F103 2.1 102.5 0.5 N03 A:V7F103 2.1 93.7 0.5 H24 A:V7F103 2.4 115.2 0.5 H26 A:V7F103 2.7 113.0 0.5 C07 A:V7F103 2.8 98.2 0.5 C03 A:V7F103 2.8 97.7 0.5 C04 A:V7F103 2.9 98.8 0.5 C10 A:V7F103 2.9 95.9 0.5 C08 A:V7F103 2.9 94.1 0.5 C01 A:V7F103 2.9 95.6 0.5 C22 A:V7F103 3.1 107.7 0.5 C19 A:V7F103 3.1 105.1 0.5 C20 A:V7F103 3.1 107.3 0.5 C12 A:V7F103 3.1 108.2 0.5 H09 A:V7F103 3.2 129.2 0.5 H06 A:V7F103 3.2 126.1 0.5 H07 A:V7F103 3.2 128.8 0.5 H03 A:V7F103 3.2 129.8 0.5 C14 A:V7F103 4.2 93.2 0.5 C02 A:V7F103 4.2 93.3 0.5 C23 A:V7F103 4.2 100.8 0.5 H71 A:DT5 4.3 115.5 1.0 C17 A:V7F103 4.3 95.9 0.5 C13 A:V7F103 4.3 99.6 0.5 C11 A:V7F103 4.3 92.1 0.5 C05 A:V7F103 4.4 105.8 0.5 C34 A:V7F103 4.4 114.4 0.5 C15 A:V7F103 4.4 102.2 0.5 H25 A:V7F103 4.4 120.6 0.5 C21 A:V7F103 4.4 96.9 0.5 H05 A:V7F103 4.6 121.2 0.5 O4 A:DT5 4.8 108.0 1.0 C24 A:V7F103 4.8 107.2 0.5 C26 A:V7F103 4.8 100.5 0.5 C33 A:V7F103 4.9 107.2 0.5 C06 A:V7F103 4.9 103.2 0.5 C25 A:V7F103 4.9 91.7 0.5 C18 A:V7F103 4.9 101.0 0.5

T.D.Prieto Otoya, K.T.Mcquaid, J.Hennessy, G.Menounou, A.Gibney, N.G.Paterson, D.J.Cardin, A.Kellett, C.J.Cardin. Probing A Major Dna Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Lambda-[Ru(Phen) 2 Phi] 2. Angew.Chem.Int.Ed.Engl. 18863 2024.
ISSN: ESSN 1521-3773
PubMed: 38271265
DOI: 10.1002/ANIE.202318863