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Bromine in PDB 6gld: Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2

Protein crystallography data

The structure of Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2, PDB code: 6gld was solved by K.T.Mcquaid, 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) 29.80 / 1.06
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.136, 42.136, 39.092, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 15.8

Other elements in 6gld:

The structure of Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Barium (Ba) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 (pdb code 6gld). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2, PDB code: 6gld:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 6gld

Go back to Bromine Binding Sites List in 6gld
Bromine binding site 1 out of 2 in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br102

b:26.4
occ:0.34
BR1 B:F3K102 0.0 26.4 0.3
H021 B:F3K102 1.0 26.2 0.7
C02 B:F3K102 1.9 21.8 0.7
C01 B:F3K102 1.9 18.5 0.3
C03 B:F3K102 2.8 19.6 0.7
H031 B:F3K102 2.8 23.5 0.7
C04 B:F3K102 2.9 16.2 0.3
C02 B:F3K102 2.9 20.0 0.3
H041 B:F3K102 2.9 19.5 0.3
C01 B:F3K102 3.0 23.6 0.7
H021 B:F3K102 3.0 24.0 0.3
BR1 B:F3K102 3.5 29.6 0.7
O B:HOH254 4.0 48.0 1.0
C06 B:F3K102 4.1 16.8 0.7
C05 B:F3K102 4.2 14.4 0.3
C03 B:F3K102 4.2 16.7 0.3
C04 B:F3K102 4.2 19.6 0.7
C05 B:F3K102 4.7 17.7 0.7
C06 B:F3K102 4.7 15.0 0.3
H031 B:F3K102 4.9 20.1 0.3
H041 B:F3K102 5.0 23.6 0.7

Bromine binding site 2 out of 2 in 6gld

Go back to Bromine Binding Sites List in 6gld
Bromine binding site 2 out of 2 in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br102

b:29.6
occ:0.66
BR1 B:F3K102 0.0 29.6 0.7
H021 B:F3K102 1.0 24.0 0.3
C01 B:F3K102 1.9 23.6 0.7
C02 B:F3K102 2.0 20.0 0.3
C04 B:F3K102 2.8 19.6 0.7
C03 B:F3K102 2.9 16.7 0.3
H031 B:F3K102 2.9 20.1 0.3
C02 B:F3K102 2.9 21.8 0.7
H041 B:F3K102 2.9 23.6 0.7
H021 B:F3K102 3.0 26.2 0.7
C01 B:F3K102 3.0 18.5 0.3
BR1 B:F3K102 3.5 26.4 0.3
O B:HOH278 3.7 42.7 1.0
O B:HOH271 3.8 38.0 1.0
C05 B:F3K102 4.1 17.7 0.7
C06 B:F3K102 4.2 15.0 0.3
C03 B:F3K102 4.2 19.6 0.7
C04 B:F3K102 4.3 16.2 0.3
C06 B:F3K102 4.7 16.8 0.7
C05 B:F3K102 4.8 14.4 0.3
H031 B:F3K102 4.9 23.5 0.7

Reference:

K.Mcquaid, J.P.Hall, J.A.Brazier, D.J.Cardin, C.J.Cardin. X-Ray Crystal Structures Show Dna Stacking Advantage of Terminal Nitrile Substitution in Ru-Dppz Complexes. Chemistry V. 24 15859 2018.
ISSN: ISSN 0947-6539
PubMed: 30063271
DOI: 10.1002/CHEM.201803021
Page generated: Thu Jul 11 01:59:25 2024

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