Magnesium in PDB 3iff: 2'-Seme-A Modified Dna Decamer

The structure of 2'-Seme-A Modified Dna Decamer, PDB code: 3iff was solved by J.Sheng, J.Gan, J.Salon, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.75
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	38.748, 38.748, 76.628, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 27.8

The binding sites of Magnesium atom in the 2'-Seme-A Modified Dna Decamer (pdb code 3iff). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 2'-Seme-A Modified Dna Decamer, PDB code: 3iff:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the 2'-Seme-A Modified Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2'-Seme-A Modified Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg60 b:59.2 occ:1.00 O A:HOH38 2.0 65.3 1.0 O A:HOH29 2.6 51.4 1.0 O A:HOH45 2.7 50.7 1.0 O A:HOH51 3.4 53.7 1.0 O A:HOH13 3.4 33.0 1.0 O A:HOH19 4.4 49.7 1.0 O B:HOH32 4.5 49.0 1.0 OP2 A:DC6 4.8 50.1 1.0 C5 A:DC6 4.9 40.1 1.0 O A:HOH34 4.9 48.7 1.0 OP2 A:DG5 5.0 57.8 1.0

Magnesium binding site 2 out of 3 in the 2'-Seme-A Modified Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2'-Seme-A Modified Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg61 b:65.2 occ:1.00 OP2 B:DT2 1.9 50.3 1.0 O5' B:DG1 2.5 46.3 1.0 P B:DT2 3.0 49.9 1.0 C3' B:DG1 3.1 44.8 1.0 O3' B:DG1 3.2 47.6 1.0 C5' B:DG1 3.3 44.8 1.0 C7 B:DT2 3.5 48.5 1.0 C4' B:DG1 3.7 42.8 1.0 OP1 B:DT2 3.9 52.3 1.0 O5' B:DT2 4.2 49.5 1.0 C2' B:DG1 4.5 43.2 1.0 O4' B:DG1 4.6 41.8 1.0 C5 B:DT2 4.6 47.5 1.0 C6 B:DT2 4.8 48.3 1.0 C8 B:DG1 4.8 41.3 1.0 O A:HOH40 4.9 63.8 1.0

Magnesium binding site 3 out of 3 in the 2'-Seme-A Modified Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2'-Seme-A Modified Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg62 b:51.1 occ:0.50 O A:HOH36 2.1 52.6 1.0 O A:HOH52 2.2 62.2 1.0 O B:HOH15 2.4 41.4 1.0 N4 B:DC4 3.9 50.2 1.0 N4 A:DC4 4.0 49.8 1.0 O B:HOH28 4.2 48.6 1.0 O A:HOH35 4.6 45.1 1.0 C5 B:DC4 4.7 50.6 1.0 C4 B:DC4 4.7 50.2 1.0 O A:HOH47 4.8 49.9 1.0 O A:HOH34 4.8 48.7 1.0 C4 A:DC4 4.9 50.4 1.0 O6 B:DG5 4.9 42.7 1.0 O6 A:DG5 5.0 42.0 1.0

J.Sheng, J.Gan, J.Salon, Z.Huang. Selenium Modification at 2'-Position of Adenosine For Nucleic Acid Structure Studies To Be Published.