Magnesium in PDB 2ho7: Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate

The structure of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate, PDB code: 2ho7 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 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.443, 40.840, 72.097, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 23.9

The binding sites of Magnesium atom in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate (pdb code 2ho7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate, PDB code: 2ho7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:52.7 occ:1.00 O A:HOH303 1.8 20.0 1.0 O B:HOH301 1.9 24.0 1.0 O B:HOH302 2.1 20.0 1.0 OP2 B:C36 2.2 29.4 1.0 OP2 A:C2 2.5 35.2 1.0 OP2 B:G37 2.7 22.7 1.0 O3' B:A35 3.1 26.3 1.0 P B:C36 3.2 28.6 1.0 O3' A:G1 3.6 34.7 1.0 P A:C2 3.6 34.7 1.0 P B:G37 3.7 21.3 1.0 OP1 B:G37 3.8 22.9 1.0 O5' B:C36 4.0 27.4 1.0 O2' B:A35 4.1 26.9 1.0 C5' A:C2 4.1 32.3 1.0 C3' B:A35 4.3 24.1 1.0 C3' B:C36 4.4 22.9 1.0 O5' A:C2 4.4 33.4 1.0 O3' B:C36 4.5 21.8 1.0 OP1 B:C36 4.5 28.5 1.0 O2' A:G1 4.7 34.2 1.0 C5' B:C36 4.8 25.2 1.0 C2' B:A35 4.8 24.4 1.0 OP1 A:C2 4.9 35.5 1.0 C3' A:G1 5.0 35.1 1.0 O5' B:G37 5.0 22.1 1.0

Magnesium binding site 2 out of 4 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:51.2 occ:1.00 C6 B:U59 3.2 29.6 1.0 O2' B:A56 3.3 22.3 1.0 C5 B:U59 3.5 27.9 1.0 OP1 B:U59 3.5 28.1 1.0 C4' B:C57 3.6 26.2 1.0 C5' B:C57 3.7 24.9 1.0 O5' B:U59 3.7 28.5 1.0 N1 B:U59 3.8 30.1 1.0 C2' B:U59 3.8 31.6 1.0 O4' B:C57 4.0 26.7 1.0 C3' B:A58 4.1 25.4 1.0 C5' B:A58 4.2 26.6 1.0 P B:U59 4.2 25.7 1.0 O5' B:A58 4.2 28.4 1.0 C1' B:U59 4.3 30.5 1.0 C4 B:U59 4.4 26.4 1.0 C2' B:A56 4.5 22.6 1.0 O3' B:A58 4.5 25.4 1.0 O2' B:U59 4.6 32.5 1.0 C2 B:U59 4.7 30.1 1.0 C4' B:A58 4.7 26.2 1.0 N3 B:U59 4.8 26.9 1.0 C3' B:U59 4.8 31.9 1.0 C5' B:U59 5.0 29.8 1.0 C3' B:C57 5.0 26.8 1.0

Magnesium binding site 3 out of 4 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:60.4 occ:1.00 O6 B:G64 2.5 33.1 1.0 O2P A:G6P401 2.8 76.4 1.0 C6 B:G64 3.6 31.4 1.0 O6 A:G6P401 3.7 76.7 1.0 P A:G6P401 3.7 75.9 1.0 N4 B:C63 3.8 34.0 1.0 O6 B:G65 3.9 34.9 1.0 O3P A:G6P401 4.0 76.3 1.0 N7 B:G64 4.2 32.0 1.0 C5 B:G64 4.3 31.4 1.0 N4 A:C2 4.6 27.1 1.0 C6 B:G65 4.6 34.5 1.0 C4 B:C63 4.6 34.7 1.0 N1 B:G64 4.8 29.8 1.0 N7 B:G65 4.8 36.1 1.0 C6 A:G6P401 4.9 76.6 1.0 C5 B:C63 4.9 35.5 1.0

Magnesium binding site 4 out of 4 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:54.9 occ:1.00 O2 B:U79 2.1 49.8 1.0 C2 B:U79 2.9 49.6 1.0 N3 B:U79 3.2 51.1 1.0 N4 B:C82 3.6 25.8 1.0 C5 B:C81 3.7 42.5 1.0 O2' B:U79 3.7 48.1 1.0 C4 B:C81 3.9 43.0 1.0 N4 B:C81 3.9 41.7 1.0 C5 B:C82 3.9 29.4 1.0 N1 B:U79 4.0 48.7 1.0 C2' B:U79 4.1 47.2 1.0 C4 B:C82 4.2 28.9 1.0 C6 B:C81 4.4 43.6 1.0 C4 B:U79 4.5 51.4 1.0 C1' B:U79 4.5 47.5 1.0 N3 B:C81 4.7 43.2 1.0 OP2 B:C81 4.8 50.8 1.0 O4 B:U83 4.9 35.0 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