Magnesium in PDB 5ckk: Crystal Structure of 9DB1* Deoxyribozyme

The structure of Crystal Structure of 9DB1* Deoxyribozyme, PDB code: 5ckk was solved by A.Ponce-Salvatierra, C.Hoebartner, V.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.45 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.155, 83.155, 55.995, 90.00, 90.00, 90.00
R / Rfree (%)	27.5 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of 9DB1* Deoxyribozyme (pdb code 5ckk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of 9DB1* Deoxyribozyme, PDB code: 5ckk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of 9DB1* Deoxyribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 9DB1* Deoxyribozyme within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg101 b:0.6 occ:1.00 OP2 Y:DA15 2.2 98.2 1.0 P Y:DA15 3.6 0.5 1.0 O6 Y:DG31 4.1 0.9 1.0 O6 Y:DG18 4.1 0.9 1.0 C2' Y:DT14 4.2 0.3 1.0 O3' Y:DT14 4.4 0.8 1.0 OP1 Y:DC16 4.4 0.6 1.0 C3' Y:DT14 4.4 0.5 1.0 OP1 Y:DA15 4.5 0.3 1.0 O5' Y:DA15 4.6 0.2 1.0 N4 Y:DC32 4.6 0.7 1.0 N7 Y:DG17 4.7 0.6 1.0 C5' Y:DA15 4.9 0.8 1.0 O6 Y:DG17 5.0 0.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of 9DB1* Deoxyribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 9DB1* Deoxyribozyme within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg102 b:0.3 occ:1.00 OP1 Y:DT14 2.1 0.4 1.0 OP1 Y:DA15 2.1 0.3 1.0 OP2 Y:DT14 2.4 0.4 1.0 P Y:DT14 2.5 0.9 1.0 P Y:DA15 3.4 0.5 1.0 O5' Y:DT14 3.4 0.2 1.0 O3' Y:DA13 3.9 0.6 1.0 OP2 Y:DA15 3.9 98.2 1.0 N7 Y:DG18 4.1 0.7 1.0 O3' Y:DT14 4.2 0.8 1.0 C3' Y:DT14 4.2 0.5 1.0 C5' Y:DT14 4.5 0.1 1.0 C8 Y:DG18 4.6 0.3 1.0 O5' Y:DA15 4.6 0.2 1.0 C3' Y:DA13 4.9 0.8 1.0 OP2 Y:DG17 4.9 0.9 1.0 C4' Y:DT14 5.0 0.3 1.0 N4 Y:DC20 5.0 0.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of 9DB1* Deoxyribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 9DB1* Deoxyribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:0.4 occ:0.34 N1 D:G1 1.9 0.1 1.0 N7 D:A-1 1.9 0.8 1.0 C5 D:A-1 2.1 0.5 1.0 C6 D:G1 2.3 0.9 1.0 C6 D:A-1 2.5 0.6 1.0 O6 D:G1 2.5 0.6 1.0 N6 D:A-1 2.6 0.3 1.0 C2 D:G1 2.8 0.7 1.0 C8 D:A-1 2.9 0.8 1.0 C4 D:A-1 3.2 0.8 1.0 N2 D:G1 3.3 0.0 1.0 C5 D:G1 3.4 1.0 1.0 N9 D:A-1 3.5 0.2 1.0 N1 D:A-1 3.6 0.7 1.0 N3 D:G1 3.7 0.2 1.0 C4 D:G1 3.8 0.3 1.0 N3 D:A-1 4.2 0.7 1.0 C2 D:A-1 4.2 0.9 1.0 O4 Y:DT29 4.4 0.7 1.0 N6 Y:DA15 4.4 0.6 1.0 N7 D:G1 4.5 0.7 1.0 N3 Y:DT29 4.6 0.9 1.0 C1' D:A-1 4.9 0.9 1.0 C4 Y:DT29 5.0 1.0 1.0

A.Ponce-Salvatierra, K.Wawrzyniak-Turek, U.Steuerwald, C.Hobartner, V.Pena. Crystal Structure of A Dna Catalyst. Nature V. 529 231 2016.
ISSN: ESSN 1476-4687
PubMed: 26735012
DOI: 10.1038/NATURE16471