Magnesium in PDB 2h0z: 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: 2h0z 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.877, 39.809, 70.226, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 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 2h0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate, PDB code: 2h0z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 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 A:Mg401 b:48.9 occ:1.00 O B:HOH202 1.9 11.5 1.0 O B:HOH201 2.0 13.4 1.0 OP2 A:C2 2.2 23.3 1.0 O3' A:G1 2.9 24.0 1.0 OP2 B:C36 3.0 26.1 1.0 P A:C2 3.1 24.4 1.0 OP2 B:G37 3.2 23.1 1.0 O3' B:A35 3.2 25.8 1.0 C5' A:C2 3.4 24.9 1.0 O2' B:A35 3.4 27.0 1.0 O5' A:C2 3.7 23.9 1.0 P B:C36 3.8 26.6 1.0 O2' A:G1 3.9 24.2 1.0 C3' B:A35 4.2 24.5 1.0 C3' A:G1 4.3 23.3 1.0 P B:G37 4.4 21.1 1.0 C2' B:A35 4.4 24.8 1.0 OP1 A:C2 4.5 24.9 1.0 O5' B:C36 4.6 26.5 1.0 OP1 B:G37 4.6 20.9 1.0 C4' A:C2 4.6 25.9 1.0 C2' A:G1 4.7 23.4 1.0 OP2 A:G3 4.9 28.4 1.0

Magnesium binding site 2 out of 8 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:Mg402 b:24.4 occ:1.00 O2' B:A56 3.0 24.0 1.0 C4' B:C57 3.2 30.8 1.0 C5' B:C57 3.2 28.4 1.0 C6 B:U59 3.4 33.2 1.0 O4' B:C57 3.4 31.8 1.0 C5 B:U59 3.6 33.0 1.0 N1 B:U59 3.9 31.2 1.0 C2' B:U59 3.9 30.1 1.0 OP1 B:U59 4.0 32.8 1.0 C2' B:A56 4.1 24.0 1.0 C3' B:A58 4.2 29.3 1.0 C5' B:A58 4.2 30.5 1.0 O2' B:U59 4.3 31.6 1.0 O5' B:A58 4.4 31.8 1.0 C1' B:U59 4.4 30.0 1.0 C4 B:U59 4.4 33.0 1.0 O5' B:U59 4.4 32.1 1.0 C2 B:U59 4.6 31.9 1.0 O5' B:C57 4.6 24.1 1.0 C3' B:C57 4.6 31.8 1.0 P B:U59 4.7 32.4 1.0 N3 B:U59 4.7 32.7 1.0 O3' B:A58 4.7 30.7 1.0 C4' B:A58 4.8 29.6 1.0 C1' B:C57 4.8 30.9 1.0 O3' B:A56 4.9 22.8 1.0

Magnesium binding site 3 out of 8 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:Mg403 b:13.2 occ:1.00 O2 B:U79 2.9 47.2 1.0 C2 B:U79 2.9 49.0 1.0 N4 B:C82 3.2 44.6 1.0 N3 B:U79 3.2 50.4 1.0 O2' B:U79 3.3 44.9 1.0 N1 B:U79 3.5 47.9 1.0 N4 B:C81 3.6 41.1 1.0 C5 B:C81 3.6 43.3 1.0 C4 B:C81 3.8 42.5 1.0 C2' B:U79 3.9 45.3 1.0 C4 B:U79 4.0 51.2 1.0 C4 B:C82 4.1 45.7 1.0 C1' B:U79 4.1 46.5 1.0 C5 B:C82 4.2 45.6 1.0 C6 B:U79 4.3 49.6 1.0 C5 B:U79 4.5 51.4 1.0 C6 B:C81 4.5 43.9 1.0 O4 B:U79 4.7 51.8 1.0 N3 B:C81 4.8 44.1 1.0

Magnesium binding site 4 out of 8 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:Mg404 b:41.6 occ:1.00 O6 B:G101 3.5 46.2 1.0 O4 B:U100 3.5 52.8 1.0 O6 B:G102 3.9 53.9 1.0 N7 B:G101 4.0 48.2 1.0 C4 B:U100 4.2 51.8 1.0 OP2 B:A129 4.2 23.4 1.0 C6 B:G101 4.3 46.6 1.0 C6 B:G102 4.4 53.8 1.0 N1 B:G102 4.4 54.1 1.0 C5 B:U100 4.5 51.6 1.0 C5 B:G101 4.5 47.2 1.0 OP1 B:A129 4.7 24.3 1.0

Magnesium binding site 5 out of 8 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 5 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:Mg405 b:20.1 occ:1.00 N2 B:G122 3.6 25.5 1.0 C1' B:A110 4.5 23.1 1.0 O2' B:A110 4.6 21.7 1.0 C2 B:G122 4.6 25.5 1.0 N3 B:G122 4.7 24.1 1.0 O4' B:A110 4.8 23.6 1.0 C1' B:G123 4.9 22.6 1.0 O4' B:G123 5.0 21.4 1.0

Magnesium binding site 6 out of 8 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 6 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:Mg406 b:29.2 occ:1.00 O2P A:G6P301 2.4 45.1 1.0 P A:G6P301 3.2 43.5 1.0 O3P A:G6P301 3.3 45.5 1.0 O6 A:G6P301 3.4 44.6 1.0 O6 B:G64 3.5 32.6 1.0 N4 B:C63 3.8 31.4 1.0 N7 B:G64 4.2 31.3 1.0 C6 B:G64 4.4 30.0 1.0 C4 B:C63 4.6 33.1 1.0 O1P A:G6P301 4.6 43.0 1.0 C6 A:G6P301 4.6 44.5 1.0 C5 B:C63 4.7 33.2 1.0 O6 B:G65 4.7 32.5 1.0 C5 B:G64 4.7 31.0 1.0

Magnesium binding site 7 out of 8 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 7 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:Mg407 b:26.2 occ:1.00 N2 B:G86 3.1 31.8 1.0 O4' B:G139 3.4 50.5 1.0 C1' B:G139 3.7 49.0 1.0 O4' B:A87 4.1 35.0 1.0 C2 B:G86 4.2 33.1 1.0 C1' B:A87 4.2 35.0 1.0 N9 B:G139 4.2 46.0 1.0 N3 B:G86 4.3 33.3 1.0 C4' B:G139 4.7 51.0 1.0 C4 B:G139 4.7 44.4 1.0 O2 B:C78 4.8 39.4 1.0 N3 B:G139 4.8 43.2 1.0 N9 B:A87 4.9 35.0 1.0 C8 B:G139 5.0 44.9 1.0

Magnesium binding site 8 out of 8 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 8 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:Mg408 b:28.0 occ:1.00 N2 B:G142 4.1 46.6 1.0 C1' B:U83 4.7 45.2 1.0 C1' B:G143 4.8 53.8 1.0 N3 B:G142 4.8 47.0 1.0 O2' B:G143 4.9 55.9 1.0 O4' B:G143 4.9 55.1 1.0 O2 B:U83 4.9 43.3 1.0 O4' B:U83 5.0 46.0 1.0 C2 B:G142 5.0 46.8 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