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Ruthenium in PDB 3u38: Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2

Protein crystallography data

The structure of Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2, PDB code: 3u38 was solved by C.J.Cardin, J.P.Hall, H.Niyazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.86 / 2.13
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.560, 52.560, 32.430, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.2

Other elements in 3u38:

The structure of Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2 also contains other interesting chemical elements:

Barium (Ba) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2 (pdb code 3u38). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2, PDB code: 3u38:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 3u38

Go back to Ruthenium Binding Sites List in 3u38
Ruthenium binding site 1 out of 2 in the Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru101

b:36.1
occ:1.00
RU A:RKP101 0.0 36.1 1.0
N12 A:RKP101 1.9 37.1 1.0
N8 A:RKP101 1.9 36.4 1.0
N1 A:RKP101 1.9 33.7 1.0
N5 A:RKP101 1.9 38.2 1.0
N9 A:RKP101 2.0 34.4 1.0
N2 A:RKP101 2.0 30.3 1.0
C36 A:RKP101 2.7 37.8 1.0
C29 A:RKP101 2.8 36.7 1.0
C26 A:RKP101 2.8 36.3 1.0
C19 A:RKP101 2.8 34.4 1.0
C38 A:RKP101 2.8 37.5 1.0
C10 A:RKP101 2.8 34.0 1.0
C1 A:RKP101 2.9 31.3 1.0
C12 A:RKP101 2.9 36.8 1.0
C28 A:RKP101 2.9 40.6 1.0
C20 A:RKP101 3.0 35.6 1.0
C2 A:RKP101 3.0 32.1 1.0
C30 A:RKP101 3.1 36.3 1.0
C35 A:RKP101 4.1 37.9 1.0
C37 A:RKP101 4.1 32.2 1.0
C25 A:RKP101 4.1 33.7 1.0
C32 A:RKP101 4.1 34.0 1.0
C22 A:RKP101 4.2 34.3 1.0
C8 A:RKP101 4.2 31.6 1.0
C5 A:RKP101 4.2 30.6 1.0
C27 A:RKP101 4.2 34.8 1.0
C11 A:RKP101 4.2 32.8 1.0
C21 A:RKP101 4.2 34.0 1.0
C3 A:RKP101 4.3 31.4 1.0
C31 A:RKP101 4.3 33.2 1.0
C44 A:RKP101 4.6 33.8 1.0
C42 A:RKP101 4.7 39.0 1.0
C41 A:RKP101 4.7 33.1 1.0
C9 A:RKP101 4.7 32.2 1.0
C4 A:RKP101 4.8 30.3 1.0
C43 A:RKP101 4.8 35.1 1.0
N2 A:DG9 4.8 30.2 1.0

Ruthenium binding site 2 out of 2 in 3u38

Go back to Ruthenium Binding Sites List in 3u38
Ruthenium binding site 2 out of 2 in the Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Intercalation of Lambda-[Ru(Phen)2(Dppz)]2+ Into D(Ccggtaccgg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:37.1
occ:0.50
RU A:RKP102 0.0 37.1 0.5
N12 A:RKP102 1.9 36.4 0.5
N8 A:RKP102 1.9 35.6 0.5
N1 A:RKP102 1.9 36.5 0.5
N5 A:RKP102 1.9 35.7 0.5
N9 A:RKP102 2.0 36.3 0.5
N2 A:RKP102 2.0 36.4 0.5
C26 A:RKP102 2.8 36.2 0.5
C36 A:RKP102 2.8 37.0 0.5
C19 A:RKP102 2.8 36.6 0.5
C10 A:RKP102 2.8 35.1 0.5
C29 A:RKP102 2.8 37.0 0.5
C38 A:RKP102 2.9 39.0 0.5
C1 A:RKP102 2.9 35.0 0.5
C28 A:RKP102 2.9 38.2 0.5
C12 A:RKP102 2.9 35.2 0.5
C20 A:RKP102 3.0 37.2 0.5
C2 A:RKP102 3.0 35.0 0.5
C30 A:RKP102 3.1 37.3 0.5
C35 A:RKP102 4.1 37.0 0.5
C25 A:RKP102 4.1 36.1 0.5
C37 A:RKP102 4.1 37.3 0.5
C22 A:RKP102 4.1 35.5 0.5
C27 A:RKP102 4.2 36.2 0.5
C8 A:RKP102 4.2 33.4 0.5
C32 A:RKP102 4.2 36.2 0.5
C11 A:RKP102 4.2 32.4 0.5
C21 A:RKP102 4.2 35.9 0.5
C5 A:RKP102 4.3 33.2 0.5
C31 A:RKP102 4.3 36.2 0.5
C3 A:RKP102 4.3 32.5 0.5
C44 A:RKP102 4.6 36.8 0.5
C42 A:RKP102 4.7 35.8 0.5
C9 A:RKP102 4.7 32.5 0.5
C41 A:RKP102 4.8 35.4 0.5
C43 A:RKP102 4.8 35.7 0.5
C4 A:RKP102 4.9 33.0 0.5
N3 A:DA6 4.9 35.9 1.0

Reference:

H.Niyazi, J.P.Hall, K.O'sullivan, G.Winter, T.Sorensen, J.M.Kelly, C.J.Cardin. Crystal Structures of Lambda-[Ru(Phen)2DPPZ]2+ with Oligonucleotides Containing Ta/Ta and at/at Steps Show Two Intercalation Modes Nat Chem V. 4 621 2012.
ISSN: ISSN 1755-4349
PubMed: 22824893
DOI: 10.1038/NCHEM.1397
Page generated: Wed Dec 16 02:08:08 2020

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