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Ruthenium in PDB 4e7y: Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg

Protein crystallography data

The structure of Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg, PDB code: 4e7y was solved by J.P.Hall, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.74 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.720, 47.720, 34.660, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.8

Other elements in 4e7y:

The structure of Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg also contains other interesting chemical elements:

Barium (Ba) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg (pdb code 4e7y). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total only one binding site of Ruthenium was determined in the Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg, PDB code: 4e7y:

Ruthenium binding site 1 out of 1 in 4e7y

Go back to Ruthenium Binding Sites List in 4e7y
Ruthenium binding site 1 out of 1 in the Lambda-[Ru(Phen)2(Dppz)]2+ Bound to Ccggatccgg


Mono view


Stereo pair view

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

b:19.5
occ:1.00
RU A:RKP101 0.0 19.5 1.0
N5 A:RKP101 1.9 18.1 1.0
N12 A:RKP101 2.0 19.8 1.0
N9 A:RKP101 2.0 19.4 1.0
N1 A:RKP101 2.0 20.2 1.0
N8 A:RKP101 2.0 19.6 1.0
N2 A:RKP101 2.0 18.8 1.0
C29 A:RKP101 2.8 21.2 1.0
C36 A:RKP101 2.8 22.4 1.0
C19 A:RKP101 2.8 19.6 1.0
C1 A:RKP101 2.8 19.0 1.0
C26 A:RKP101 2.8 19.5 1.0
C10 A:RKP101 2.9 18.3 1.0
C38 A:RKP101 3.1 22.2 1.0
C30 A:RKP101 3.1 21.4 1.0
C20 A:RKP101 3.1 19.1 1.0
C28 A:RKP101 3.1 17.0 1.0
C2 A:RKP101 3.1 20.2 1.0
C12 A:RKP101 3.1 19.4 1.0
C32 A:RKP101 4.2 20.6 1.0
C35 A:RKP101 4.2 19.4 1.0
C5 A:RKP101 4.2 19.1 1.0
C22 A:RKP101 4.2 18.1 1.0
C8 A:RKP101 4.3 19.1 1.0
C25 A:RKP101 4.3 18.6 1.0
C21 A:RKP101 4.4 19.7 1.0
C3 A:RKP101 4.4 20.3 1.0
C37 A:RKP101 4.4 20.6 1.0
C31 A:RKP101 4.4 23.5 1.0
C27 A:RKP101 4.4 20.0 1.0
C11 A:RKP101 4.4 19.6 1.0
O A:HOH228 4.7 43.6 1.0
C4 A:RKP101 4.8 18.0 1.0
C41 A:RKP101 4.8 16.3 1.0
C44 A:RKP101 4.8 20.3 1.0
C43 A:RKP101 4.9 21.8 1.0
C9 A:RKP101 4.9 20.9 1.0
N2 A:DG9 4.9 20.7 1.0
C42 A:RKP101 4.9 18.5 1.0
O A:HOH223 4.9 28.3 1.0

Reference:

H.Niyazi, J.P.Hall, K.O'sullivan, G.Winter, T.Sorensen, J.M.Kelly, C.J.Cardin. Crystal Structure of Lambda-[Ru(Phen)2(Dppz)]2+ with Oligonucleotides Containing Ta/Ta and at/at Steps Show Two Intercalation Modes. Nat Chem V. 4 621 2012.
ISSN: ESSN 1755-4349
PubMed: 22824893
DOI: 10.1038/NCHEM.1397
Page generated: Wed Dec 16 02:08:11 2020

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