Magnesium in PDB 5cki: Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)

The structure of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals), PDB code: 5cki 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)	45.93 / 2.99
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.845, 80.845, 55.814, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 31.1

The structure of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) also contains other interesting chemical elements:

Cobalt

(Co)

4 atoms

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

Magnesium binding site 1 out of 2 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


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 (Cobalt Hexammine Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg103 b:99.5 occ:1.00 OP2 Y:DA15 2.0 1.0 1.0 P Y:DA15 3.3 0.5 1.0 O5' Y:DA15 3.5 0.2 1.0 OP1 Y:DC16 3.9 99.3 1.0 C5' Y:DA15 3.9 0.9 1.0 OP1 Y:DA15 4.3 0.7 1.0 O3' Y:DT14 4.3 0.8 1.0 C3' Y:DA15 4.5 97.4 1.0 C4' Y:DA15 4.7 0.6 1.0 C2' Y:DT14 4.7 0.0 1.0 N7 Y:DG17 4.8 0.6 1.0 O6 Y:DG17 4.8 0.4 1.0 C3' Y:DT14 4.9 0.5 1.0 O6 Y:DG18 4.9 0.3 1.0 N4 Y:DC32 5.0 0.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


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 (Cobalt Hexammine Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg104 b:93.8 occ:1.00 OP1 Y:DA15 2.0 0.7 1.0 OP1 Y:DT14 2.1 0.5 1.0 P Y:DT14 3.1 0.3 1.0 P Y:DA15 3.1 0.5 1.0 O5' Y:DT14 3.3 0.1 1.0 O5' Y:DA15 3.3 0.2 1.0 O3' Y:DT14 3.7 0.8 1.0 OP2 Y:DT14 3.7 0.9 1.0 OP2 Y:DG17 3.8 0.5 1.0 OP2 Y:DA15 4.5 1.0 1.0 O3' Y:DA13 4.5 0.3 1.0 C5' Y:DA15 4.5 0.9 1.0 C3' Y:DT14 4.6 0.5 1.0 C5' Y:DT14 4.6 0.2 1.0 O5' Y:DG17 4.7 0.9 1.0 C2' Y:DG17 4.8 0.0 1.0 P Y:DG17 4.9 0.1 1.0 C8 Y:DG17 4.9 0.7 1.0 C3' Y:DA13 5.0 0.5 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