Magnesium in PDB 4qjh: Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution

The structure of Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution, PDB code: 4qjh 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)	198.12 / 3.88
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	228.770, 228.770, 101.060, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 23.2

The binding sites of Magnesium atom in the Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution (pdb code 4qjh). 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 the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution, PDB code: 4qjh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 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 the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.4 occ:0.50 O6 B:GTP27 3.6 0.6 1.0 C6 B:GTP27 4.6 0.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 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 the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:0.6 occ:1.00 O C:HOH202 2.2 0.5 1.0 O C:HOH203 2.2 0.7 1.0 O C:HOH201 2.2 0.2 1.0 O C:HOH204 2.2 0.6 1.0 N4 C:C17 3.0 73.0 1.0 C4 C:C17 4.1 69.7 1.0 C5 C:C17 4.4 73.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 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 the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:19.7 occ:1.00 O C:HOH205 3.6 64.9 1.0 N4 C:C14 3.7 70.3 1.0 N6 C:A15 4.5 81.2 1.0 C4 C:C14 4.6 66.3 1.0 C5 C:C14 4.7 67.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 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 the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:44.0 occ:1.00 OP1 C:A11 1.9 57.9 1.0 P C:A11 3.1 57.2 1.0 C5' C:A11 3.3 55.2 1.0 OP2 C:U12 3.4 51.2 1.0 O2' C:A10 3.5 53.1 1.0 O3' C:A10 3.6 51.5 1.0 O3' C:A11 3.6 50.8 1.0 O5' C:A11 3.7 58.4 1.0 P C:U12 3.9 52.2 1.0 C4' C:A11 4.1 51.1 1.0 OP1 C:U12 4.2 57.1 1.0 C3' C:A11 4.3 50.3 1.0 OP2 C:A11 4.4 60.5 1.0 C2' C:A10 4.7 58.0 1.0 C3' C:A10 4.7 54.3 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