Magnesium in PDB 2ho6: Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme

The structure of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2ho6 was solved by D.J.Klein, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.625, 40.456, 71.958, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.2

The binding sites of Magnesium atom in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2ho6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2ho6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:35.9 occ:1.00 O A:HOH302 1.9 31.3 1.0 O B:HOH304 1.9 20.0 1.0 O A:HOH303 1.9 26.6 1.0 OP2 B:G37 2.0 20.0 1.0 OP2 B:C36 2.2 20.0 1.0 OP2 A:C2 2.5 20.1 1.0 O3' B:A35 3.1 20.0 1.0 P B:C36 3.2 20.0 1.0 P B:G37 3.2 20.0 1.0 O3' A:G1 3.5 20.0 1.0 P A:C2 3.6 20.0 1.0 OP1 B:G37 3.7 20.0 1.0 O5' B:C36 3.8 20.2 1.0 C3' B:C36 3.9 20.0 1.0 O3' B:C36 4.0 20.0 1.0 O2' B:A35 4.2 20.2 1.0 C3' B:A35 4.4 20.0 1.0 O2' A:G1 4.4 20.0 1.0 C5' A:C2 4.4 20.0 1.0 O5' B:G37 4.5 20.0 1.0 OP1 B:C36 4.5 20.5 1.0 O5' A:C2 4.5 20.0 1.0 C5' B:C36 4.6 20.0 1.0 C5' B:G37 4.7 20.0 1.0 OP1 A:C2 4.8 22.1 1.0 C4' B:C36 4.8 20.0 1.0 C3' A:G1 4.9 20.0 1.0 C8 B:G37 4.9 20.0 1.0 C2' B:A35 5.0 20.0 1.0

Magnesium binding site 2 out of 3 in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:22.1 occ:1.00 C2 B:U79 3.1 41.9 1.0 O2' B:U79 3.2 35.0 1.0 O2 B:U79 3.3 42.1 1.0 N3 B:U79 3.4 44.2 1.0 N1 B:U79 3.4 39.6 1.0 N4 B:C82 3.4 24.2 1.0 N4 B:C81 3.5 20.1 1.0 C5 B:C81 3.6 22.5 1.0 C2' B:U79 3.7 34.4 1.0 C4 B:C81 3.8 22.4 1.0 C1' B:U79 3.9 36.0 1.0 C4 B:U79 4.0 45.2 1.0 C6 B:U79 4.0 42.5 1.0 C5 B:C82 4.2 26.1 1.0 C5 B:U79 4.2 44.4 1.0 C4 B:C82 4.3 26.0 1.0 C6 B:C81 4.5 23.0 1.0 O4 B:U79 4.7 47.6 1.0 OP2 B:C81 4.8 34.9 1.0 N3 B:C81 4.8 22.0 1.0

Magnesium binding site 3 out of 3 in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:23.3 occ:1.00 O2' B:A56 3.0 20.0 1.0 C4' B:C57 3.2 22.1 1.0 C5' B:C57 3.5 21.1 1.0 O4' B:C57 3.5 21.1 1.0 C6 B:U59 3.5 21.8 1.0 C2' B:U59 3.7 21.5 1.0 C5 B:U59 3.9 20.6 1.0 N1 B:U59 3.9 21.4 1.0 OP1 B:U59 4.0 20.0 1.0 C5' B:A58 4.0 22.2 1.0 C3' B:A58 4.1 20.8 1.0 C2' B:A56 4.1 20.0 1.0 O2' B:U59 4.2 22.0 1.0 O5' B:A58 4.3 23.9 1.0 C1' B:U59 4.3 21.1 1.0 O5' B:U59 4.4 20.1 1.0 C4' B:A58 4.5 21.6 1.0 O3' B:A58 4.6 21.3 1.0 C4 B:U59 4.6 20.0 1.0 C2 B:U59 4.6 21.9 1.0 P B:U59 4.6 20.0 1.0 C3' B:C57 4.6 22.8 1.0 O5' B:C57 4.8 20.0 1.0 N3 B:U59 4.8 20.4 1.0 C1' B:C57 4.8 21.4 1.0 C3' B:U59 5.0 21.4 1.0

D.J.Klein, A.R.Ferre-D'amare. Structural Basis of Glms Ribozyme Activation By Glucosamine-6-Phosphate Science V. 313 1752 2006.
ISSN: ISSN 0036-8075
PubMed: 16990543
DOI: 10.1126/SCIENCE.1129666