Magnesium in PDB 8pjl: Dna Duplex Forming Base Triplets in Minor Groove

The structure of Dna Duplex Forming Base Triplets in Minor Groove, PDB code: 8pjl was solved by A.Abdullrahman, C.J.Cardin, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.87 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	39.833, 39.833, 58.964, 90, 90, 90
R / Rfree (%)	19.1 / 23.5

The structure of Dna Duplex Forming Base Triplets in Minor Groove also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Dna Duplex Forming Base Triplets in Minor Groove (pdb code 8pjl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Duplex Forming Base Triplets in Minor Groove, PDB code: 8pjl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna Duplex Forming Base Triplets in Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Duplex Forming Base Triplets in Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:31.3 occ:1.00 O A:HOH216 2.1 23.3 1.0 O A:HOH206 2.2 21.8 1.0 O B:HOH214 4.1 20.6 1.0 N7 A:DG4 4.1 14.6 1.0 O A:HOH223 4.2 41.3 1.0 H5 A:DC3 4.2 27.7 1.0 O A:HOH235 4.3 45.9 1.0 O4 A:DT5 4.3 19.9 1.0 O6 A:DG4 4.4 21.7 1.0 H61 B:DA10 4.4 21.0 1.0 H62 B:DA10 4.6 21.0 1.0 C5 A:DC3 4.6 23.0 1.0 OP2 A:DC3 4.8 25.9 1.0 H73 A:DT5 4.8 18.7 1.0 N6 B:DA10 4.9 17.4 1.0 H6 A:DC3 5.0 23.7 1.0 C5 A:DG4 5.0 12.2 1.0 O B:HOH207 5.0 28.2 1.0

Magnesium binding site 2 out of 4 in the Dna Duplex Forming Base Triplets in Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Duplex Forming Base Triplets in Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:38.4 occ:1.00 O A:HOH230 2.1 33.5 1.0 OP2 A:DT7 2.1 26.9 1.0 O A:HOH224 2.3 38.1 1.0 P A:DT7 3.3 20.7 1.0 OP1 A:DT7 3.8 23.8 1.0 H3' A:DC6 4.0 25.5 1.0 H72 A:DT7 4.0 22.9 1.0 O A:HOH246 4.1 22.3 1.0 O3' A:DC6 4.3 22.0 1.0 O5' A:DT7 4.5 24.4 1.0 C3' A:DC6 4.6 21.2 1.0 H71 A:DT7 4.7 22.9 1.0 C7 A:DT7 4.8 19.0 1.0 O A:HOH238 4.9 20.7 1.0 H5' A:DC6 4.9 26.7 1.0 H6 A:DT7 5.0 24.6 1.0

Magnesium binding site 3 out of 4 in the Dna Duplex Forming Base Triplets in Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Duplex Forming Base Triplets in Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:21.9 occ:1.00 O2 A:DT1 2.5 22.6 1.0 H1' A:DT1 3.3 33.0 1.0 C2 A:DT1 3.6 17.0 1.0 C1' A:DT1 4.1 27.4 1.0 H2'' A:DT1 4.2 28.1 1.0 N1 A:DT1 4.4 25.9 1.0 H3 A:DT1 4.6 21.6 1.0 O A:HOH220 4.6 22.4 1.0 N3 A:DT1 4.6 18.3 1.0 OP2 A:DA2 4.7 24.6 1.0 C2' A:DT1 4.7 23.3 1.0 O3' A:DT1 4.9 23.8 1.0

Magnesium binding site 4 out of 4 in the Dna Duplex Forming Base Triplets in Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Duplex Forming Base Triplets in Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:65.1 occ:1.00 OP1 B:DA10 2.3 38.8 1.0 O B:HOH229 3.0 44.2 1.0 P B:DA10 3.2 31.4 1.0 OP2 B:DA10 3.5 34.0 1.0 O3' B:DG9 3.8 30.9 1.0 O B:HOH223 4.0 32.9 1.0 O B:HOH205 4.2 25.3 1.0 H3' B:DG9 4.3 29.6 1.0 O5' B:DA10 4.6 28.4 1.0 C3' B:DG9 4.7 24.6 1.0

A.Abdullrahman, C.J.Cardin, J.P.Hall. Dna Duplex with Triplets Bases in Minor Groove To Be Published.