Atomistry » Ruthenium » PDB 3m0b-4kgc » 4jd8
Atomistry »
  Ruthenium »
    PDB 3m0b-4kgc »
      4jd8 »

Ruthenium in PDB 4jd8: Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution

Protein crystallography data

The structure of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution, PDB code: 4jd8 was solved by D.S.Cook, 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) 32.52 / 1.16
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 37.550, 37.550, 54.371, 90.00, 90.00, 120.00
R / Rfree (%) 13.8 / 16.2

Other elements in 4jd8:

The structure of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution also contains other interesting chemical elements:

Potassium (K) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution (pdb code 4jd8). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution, PDB code: 4jd8:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 4jd8

Go back to Ruthenium Binding Sites List in 4jd8
Ruthenium binding site 1 out of 2 in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution


Mono view


Stereo pair view

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

b:12.8
occ:1.00
RU B:0TN101 0.0 12.8 1.0
N12 B:0TN101 2.0 13.3 1.0
N8 B:0TN101 2.0 12.9 1.0
N1 B:0TN101 2.1 13.8 1.0
N5 B:0TN101 2.1 12.2 1.0
N2 B:0TN101 2.1 13.0 1.0
N9 B:0TN101 2.1 13.2 1.0
C36 B:0TN101 2.9 13.7 1.0
C29 B:0TN101 2.9 13.3 1.0
C10 B:0TN101 2.9 13.2 1.0
C1 B:0TN101 2.9 13.2 1.0
C19 B:0TN101 2.9 12.8 1.0
C26 B:0TN101 2.9 13.0 1.0
C2 B:0TN101 3.0 13.7 1.0
C28 B:0TN101 3.0 14.2 1.0
C38 B:0TN101 3.0 13.6 1.0
C20 B:0TN101 3.1 12.5 1.0
C12 B:0TN101 3.1 13.5 1.0
C30 B:0TN101 3.1 14.1 1.0
H1 B:0TN101 3.2 16.5 1.0
H16 B:0TN101 3.2 17.1 1.0
H22 B:0TN101 3.2 16.3 1.0
H11 B:0TN101 3.2 15.0 1.0
H6 B:0TN101 3.2 16.2 1.0
H17 B:0TN101 3.2 16.9 1.0
C35 B:0TN101 4.2 14.2 1.0
C8 B:0TN101 4.2 14.2 1.0
C5 B:0TN101 4.2 13.6 1.0
C25 B:0TN101 4.3 14.2 1.0
C32 B:0TN101 4.3 14.4 1.0
C22 B:0TN101 4.3 13.5 1.0
C27 B:0TN101 4.3 15.3 1.0
C3 B:0TN101 4.3 14.4 1.0
C37 B:0TN101 4.3 14.3 1.0
C11 B:0TN101 4.3 14.8 1.0
C21 B:0TN101 4.4 13.0 1.0
C31 B:0TN101 4.4 15.0 1.0
C44 B:0TN101 4.8 14.4 1.0
C9 B:0TN101 4.8 14.7 1.0
C42 B:0TN101 4.8 15.4 1.0
H21 A:DG3 4.8 16.1 1.0
C41 B:0TN101 4.8 13.6 1.0
C4 B:0TN101 4.8 14.7 1.0
C43 B:0TN101 4.9 14.8 1.0
O2 A:DT2 4.9 16.3 1.0
O4' A:DG3 5.0 16.6 1.0

Ruthenium binding site 2 out of 2 in 4jd8

Go back to Ruthenium Binding Sites List in 4jd8
Ruthenium binding site 2 out of 2 in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru102

b:14.8
occ:1.00
RU B:RKP102 0.0 14.8 1.0
N9 B:RKP102 2.0 14.8 1.0
N12 B:RKP102 2.1 16.4 1.0
N5 B:RKP102 2.1 15.6 1.0
N8 B:RKP102 2.1 17.0 1.0
N2 B:RKP102 2.1 14.6 1.0
N1 B:RKP102 2.1 13.1 1.0
C36 B:RKP102 2.9 15.5 1.0
C29 B:RKP102 2.9 14.7 1.0
C1 B:RKP102 2.9 13.6 1.0
C19 B:RKP102 2.9 16.7 1.0
C26 B:RKP102 2.9 18.0 1.0
C10 B:RKP102 2.9 13.2 1.0
C30 B:RKP102 3.0 14.2 1.0
C2 B:RKP102 3.0 15.8 1.0
C28 B:RKP102 3.0 18.4 1.0
C38 B:RKP102 3.1 18.2 1.0
C20 B:RKP102 3.1 15.7 1.0
C12 B:RKP102 3.1 12.9 1.0
H30 B:RKP102 3.1 17.0 1.0
H2 B:RKP102 3.2 19.0 1.0
H28 B:RKP102 3.2 22.0 1.0
H38 B:RKP102 3.2 21.9 1.0
H12 B:RKP102 3.2 15.4 1.0
H20 B:RKP102 3.2 18.8 1.0
C32 B:RKP102 4.2 15.9 1.0
C35 B:RKP102 4.2 17.0 1.0
C5 B:RKP102 4.2 14.8 1.0
C22 B:RKP102 4.2 18.0 1.0
C25 B:RKP102 4.3 19.6 1.0
C8 B:RKP102 4.3 12.7 1.0
C31 B:RKP102 4.3 15.4 1.0
C3 B:RKP102 4.3 18.1 1.0
C27 B:RKP102 4.3 19.9 1.0
C37 B:RKP102 4.4 18.6 1.0
C21 B:RKP102 4.4 17.2 1.0
C11 B:RKP102 4.4 12.8 1.0
O B:HOH209 4.8 17.2 1.0
C42 B:RKP102 4.8 20.0 1.0
C43 B:RKP102 4.8 16.0 1.0
C41 B:RKP102 4.8 17.5 1.0
C4 B:RKP102 4.8 17.0 1.0
C44 B:RKP102 4.8 17.6 1.0
C9 B:RKP102 4.9 12.9 1.0
H2 A:DA5 5.0 15.9 1.0
H21 B:DG3 5.0 14.0 0.9

Reference:

J.P.Hall, D.Cook, S.R.Morte, P.Mcintyre, K.Buchner, H.Beer, D.J.Cardin, J.A.Brazier, G.Winter, J.M.Kelly, C.J.Cardin. X-Ray Crystal Structure of Rac-[Ru(Phen)2DPPZ](2+) with D(Atgcat)2 Shows Enantiomer Orientations and Water Ordering. J.Am.Chem.Soc. V. 135 12652 2013.
ISSN: ISSN 0002-7863
PubMed: 23875832
DOI: 10.1021/JA403590E
Page generated: Wed Dec 16 02:08:14 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy