Magnesium in PDB 2h0s: Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme

The structure of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0s 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 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.540, 41.260, 71.404, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25

The structure of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Magnesium atom in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2h0s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Pre-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 Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:35.2 occ:1.00 O B:HOH220 2.0 26.4 1.0 O A:HOH229 2.0 48.7 1.0 OP2 B:C36 2.2 35.4 1.0 OP2 B:G37 2.4 35.9 1.0 OP2 A:C2 2.4 43.2 1.0 O B:HOH230 2.4 19.9 1.0 O3' B:A35 3.2 34.8 1.0 P B:C36 3.3 35.4 1.0 P B:G37 3.4 25.0 1.0 P A:C2 3.6 38.2 1.0 O3' A:G1 3.6 32.1 1.0 OP1 B:G37 3.7 34.2 1.0 C5' A:C2 4.1 37.6 1.0 O5' B:C36 4.2 37.8 1.0 O2' B:A35 4.3 41.5 1.0 C3' B:C36 4.3 24.4 1.0 O5' A:C2 4.4 37.2 1.0 O3' B:C36 4.4 35.6 1.0 C3' B:A35 4.5 31.6 1.0 OP1 B:C36 4.5 38.4 1.0 O2' A:G1 4.6 27.4 1.0 O5' B:G37 4.7 27.3 1.0 OP1 A:C2 4.8 44.4 1.0 C5' B:C36 4.8 30.0 1.0 C3' A:G1 4.9 28.9 1.0 C2' B:A35 5.0 34.2 1.0

Magnesium binding site 2 out of 5 in the Pre-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 Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:37.6 occ:1.00 C2 B:U79 3.1 71.9 1.0 O2 B:U79 3.2 72.5 1.0 N4 B:C82 3.2 40.3 1.0 N3 B:U79 3.4 74.6 1.0 N1 B:U79 3.6 69.8 1.0 C5 B:C81 3.6 44.4 1.0 N4 B:C81 3.6 46.3 1.0 O2' B:U79 3.6 70.6 1.0 C2' B:U79 3.8 64.5 1.0 C4 B:C81 3.8 44.7 1.0 C5 B:C82 3.9 44.9 1.0 C4 B:C82 4.0 45.9 1.0 C1' B:U79 4.1 65.6 1.0 C4 B:U79 4.1 76.4 1.0 C6 B:U79 4.2 74.1 1.0 C6 B:C81 4.4 46.5 1.0 C5 B:U79 4.5 76.4 1.0 N3 B:C81 4.7 44.3 1.0 OP2 B:C81 4.8 70.1 1.0 O4 B:U79 4.9 77.8 1.0

Magnesium binding site 3 out of 5 in the Pre-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 Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:32.6 occ:1.00 C4' B:C57 2.9 48.2 1.0 O2' B:A56 2.9 33.8 1.0 C5' B:C57 3.0 47.5 1.0 O B:HOH242 3.1 33.4 1.0 O4' B:C57 3.3 42.7 1.0 C6 B:U59 3.7 23.4 1.0 C5 B:U59 3.9 13.0 1.0 C2' B:A56 3.9 31.4 1.0 C2' B:U59 4.1 32.7 1.0 OP1 B:U59 4.1 38.2 1.0 C5' B:A58 4.1 36.3 1.0 N1 B:U59 4.2 24.1 1.0 C3' B:A58 4.2 38.3 1.0 C3' B:C57 4.3 48.0 1.0 O5' B:C57 4.3 43.9 1.0 O5' B:A58 4.4 48.1 1.0 O2' B:U59 4.4 34.4 1.0 O5' B:U59 4.5 31.1 1.0 C1' B:C57 4.7 43.0 1.0 C4 B:U59 4.7 19.1 1.0 C1' B:U59 4.7 30.4 1.0 C4' B:A58 4.7 39.5 1.0 O3' B:A56 4.7 34.8 1.0 P B:U59 4.8 36.1 1.0 O3' B:A58 4.9 37.5 1.0 O3' B:C57 4.9 50.6 1.0 C2 B:U59 4.9 21.5 1.0 C3' B:A56 5.0 31.6 1.0

Magnesium binding site 4 out of 5 in the Pre-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 4 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:62.7 occ:1.00 O3' B:A107 3.4 28.6 1.0 OP1 B:C108 3.7 30.0 1.0 P B:C108 4.1 26.7 1.0 O3' B:A56 4.4 34.8 1.0 OP1 B:C57 4.4 39.5 1.0 C4' B:A107 4.4 24.9 1.0 C3' B:A107 4.5 24.9 1.0 C5' B:A56 4.5 33.7 1.0 O2' B:A107 4.6 25.4 1.0 OP2 B:C108 4.6 30.0 1.0 C4' B:A56 4.7 27.3 1.0 C5' B:A107 4.8 24.0 1.0 P B:C57 4.9 42.8 1.0

Magnesium binding site 5 out of 5 in the Pre-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 5 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:39.9 occ:1.00 O B:HOH217 2.5 39.8 1.0 N7 B:G114 2.6 20.3 1.0 O B:HOH267 2.6 50.4 1.0 O B:HOH234 2.8 33.4 1.0 O6 B:G114 3.5 27.2 1.0 C5 B:G114 3.6 26.5 1.0 C8 B:G114 3.6 31.1 1.0 C6 B:G114 3.9 24.5 1.0 N7 B:G113 4.0 22.1 1.0 C5 B:G113 4.5 21.4 1.0 O6 B:G113 4.5 22.3 1.0 OP2 B:G116 4.6 46.7 1.0 C8 B:G113 4.7 23.4 1.0 C6 B:G113 4.7 26.6 1.0 C4 B:G114 4.8 28.0 1.0 N9 B:G114 4.8 32.9 1.0 OP1 B:G116 4.9 41.7 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