Magnesium in PDB 6gdn: Holliday Junctions Formed From Telomeric Dna

The structure of Holliday Junctions Formed From Telomeric Dna, PDB code: 6gdn was solved by G.N.Parkinson, S.Haider, P.Li, S.Khiali, D.Munnur, A.Ramanathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.38 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.937, 45.374, 63.828, 90.00, 101.01, 90.00
R / Rfree (%)	23.4 / 27.9

The binding sites of Magnesium atom in the Holliday Junctions Formed From Telomeric Dna (pdb code 6gdn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Holliday Junctions Formed From Telomeric Dna, PDB code: 6gdn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Holliday Junctions Formed From Telomeric Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Holliday Junctions Formed From Telomeric Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:59.2 occ:1.00 N7 A:DG14 3.5 28.4 1.0 O6 A:DG14 3.5 36.4 1.0 C5 A:DG14 4.2 29.3 1.0 C6 A:DG14 4.2 33.5 1.0 OP2 A:DT13 4.4 41.5 1.0 N6 A:DA15 4.5 33.0 1.0 C8 A:DG14 4.6 27.8 1.0 C2' A:DT12 4.7 35.6 1.0 O4 B:DT10 4.7 42.4 1.0

Magnesium binding site 2 out of 2 in the Holliday Junctions Formed From Telomeric Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Holliday Junctions Formed From Telomeric Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:50.2 occ:1.00 N7 B:DA33 3.5 56.3 1.0 C8 B:DA33 3.8 54.0 1.0 N7 B:DA34 4.2 57.7 1.0 OP2 A:DA16 4.3 42.3 1.0 N6 B:DA34 4.5 50.5 1.0 C5 B:DA33 4.7 58.1 1.0

S.Haider, P.Li, S.Khiali, D.Munnur, A.Ramanathan, G.N.Parkinson. Holliday Junctions Formed From Human Telomeric Dna. J. Am. Chem. Soc. V. 140 15366 2018.
ISSN: ESSN 1520-5126
PubMed: 30376323
DOI: 10.1021/JACS.8B08699