Magnesium in PDB 4rhd: Dna Duplex with Novel Zp Base Pair

The structure of Dna Duplex with Novel Zp Base Pair, PDB code: 4rhd was solved by W.Zhang, L.Zhang, S.Benner, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.05 / 1.70
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	59.429, 59.429, 87.048, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 22.6

The binding sites of Magnesium atom in the Dna Duplex with Novel Zp Base Pair (pdb code 4rhd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Duplex with Novel Zp Base Pair, PDB code: 4rhd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Duplex with Novel Zp Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Duplex with Novel Zp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:77.2 occ:1.00 OP2 C:DA8 2.1 57.0 1.0 OP1 A:DG3 2.9 27.6 1.0 P C:DA8 3.5 57.0 1.0 C5' A:DG3 3.6 27.3 1.0 O5' A:DG3 3.8 22.9 1.0 P A:DG3 3.9 30.2 1.0 OP1 C:DA8 4.1 44.9 1.0 O3' A:DG3 4.2 22.7 1.0 O3' C:DC7 4.3 46.8 1.0 C4' A:DG3 4.5 28.4 1.0 O5' C:DA8 4.6 44.6 1.0 OP2 C:DC9 4.8 35.4 1.0 C3' A:DG3 4.8 27.1 1.0 O3' A:T5S2 4.9 25.9 1.0 OP2 A:DG3 5.0 18.2 1.0

Magnesium binding site 2 out of 2 in the Dna Duplex with Novel Zp Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Duplex with Novel Zp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:79.6 occ:1.00 O2 H:T5S2 2.1 25.9 1.0 C2 H:T5S2 3.3 23.4 1.0 C1' H:DG3 3.6 38.9 1.0 N9 H:DG3 3.6 26.8 1.0 O4' H:DG3 3.7 36.3 1.0 C2 G:DA8 3.7 27.2 1.0 C4 H:DG3 4.0 32.5 1.0 N3 H:T5S2 4.1 22.5 1.0 C8 H:DG3 4.1 25.6 1.0 N3 H:DG3 4.2 32.1 1.0 N1 H:T5S2 4.2 22.3 1.0 C1' H:T5S2 4.2 28.5 1.0 N1 G:DA8 4.3 23.9 1.0 C2' H:T5S2 4.5 26.1 1.0 N3 G:DA8 4.6 30.3 1.0 C5 H:DG3 4.6 28.9 1.0 O2 G:DC9 4.7 26.2 1.0 N7 H:DG3 4.7 27.9 1.0 C2' H:DG3 5.0 32.7 1.0

L.Zhang, Z.Yang, K.Sefah, K.M.Bradley, S.Hoshika, M.J.Kim, H.J.Kim, G.Zhu, E.Jimenez, S.Cansiz, I.T.Teng, C.Champanhac, C.Mclendon, C.Liu, W.Zhang, D.L.Gerloff, Z.Huang, W.Tan, S.A.Benner. Evolution of Functional Six-Nucleotide Dna. J.Am.Chem.Soc. V. 137 6734 2015.
ISSN: ISSN 0002-7863
PubMed: 25966323
DOI: 10.1021/JACS.5B02251