Magnesium in PDB 4qjd: Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution

The structure of Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution, PDB code: 4qjd was solved by D.R.Eiler, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	102.37 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.910, 53.070, 106.750, 90.00, 106.86, 90.00
R / Rfree (%)	19 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution (pdb code 4qjd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution, PDB code: 4qjd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution


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 Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:55.4 occ:1.00 OP2 A:G18 2.5 0.3 1.0 OP1 A:G18 3.4 0.5 1.0 P A:G18 3.4 0.9 1.0 O3' A:U17 4.5 0.3 1.0 O5' A:G18 4.6 92.5 1.0 OP1 A:U17 4.8 92.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution


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 Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:54.9 occ:1.00 O2B F:GTP27 2.4 0.8 1.0 PB F:GTP27 3.5 0.5 1.0 O1B F:GTP27 3.8 0.8 1.0 O2 E:U24 3.9 69.3 1.0 O3B F:GTP27 4.6 0.6 1.0 O3A F:GTP27 4.7 0.6 1.0 O2' E:U24 4.7 53.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution


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 Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg102 b:63.6 occ:1.00 OP1 F:U72 3.1 93.9 1.0 C5' G:U3 3.3 0.3 1.0 OP2 F:U72 3.4 81.4 1.0 P F:U72 3.6 91.7 1.0 C4' G:U3 4.0 0.4 1.0 OP1 G:U3 4.1 0.7 1.0 O5' G:U3 4.2 0.4 1.0 O3' F:A71 4.2 92.9 1.0 OP1 F:A71 4.5 0.2 1.0 P G:U3 4.7 0.8 1.0 O3' G:A2 4.7 0.4 1.0 O4' G:U3 4.9 1.0 1.0 C5' F:A71 4.9 92.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:50.6 occ:1.00 OP2 H:G54 3.6 55.3 1.0 OP1 H:A58 3.9 75.2 1.0 OP2 H:A59 3.9 73.6 1.0 P H:A58 4.8 78.0 1.0

D.Eiler, J.Wang, T.A.Steitz. Structural Basis For the Fast Self-Cleavage Reaction Catalyzed By the Twister Ribozyme. Proc.Natl.Acad.Sci.Usa V. 111 13028 2014.
ISSN: ISSN 0027-8424
PubMed: 25157168
DOI: 10.1073/PNAS.1414571111