Magnesium in PDB 2h0w: Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme

The structure of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0w 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 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.087, 40.578, 71.799, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24

The binding sites of Magnesium atom in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2h0w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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:Mg501 b:26.0 occ:1.00 O A:HOH324 2.0 26.7 1.0 OP2 B:C36 2.0 25.8 1.0 O B:HOH325 2.0 20.7 1.0 OP2 B:G37 2.2 21.7 1.0 O A:HOH282 2.2 14.8 1.0 OP2 A:C2 2.4 19.5 1.0 P B:C36 3.1 26.0 1.0 O3' B:A35 3.1 24.0 1.0 P B:G37 3.4 21.2 1.0 P A:C2 3.6 20.2 1.0 O3' A:G1 3.7 19.4 1.0 OP1 B:G37 3.8 21.1 1.0 O5' B:C36 3.9 25.2 1.0 C3' B:C36 4.2 21.2 1.0 O2' B:A35 4.2 23.1 1.0 O3' B:C36 4.2 21.2 1.0 OP1 B:C36 4.3 26.3 1.0 C5' A:C2 4.4 21.4 1.0 C3' B:A35 4.4 22.1 1.0 O5' A:C2 4.5 20.6 1.0 C5' B:C36 4.6 22.2 1.0 O5' B:G37 4.6 20.8 1.0 O2' A:G1 4.7 17.2 1.0 OP1 A:C2 4.8 22.3 1.0 C5' B:G37 4.9 19.5 1.0 C2' B:A35 4.9 22.2 1.0 C4' B:C36 5.0 22.0 1.0

Magnesium binding site 2 out of 4 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:Mg502 b:51.3 occ:1.00 O B:HOH291 2.4 21.8 1.0 N7 B:A110 2.5 22.5 1.0 O B:HOH250 2.6 29.5 1.0 O B:HOH293 2.6 26.6 1.0 C8 B:A110 3.4 22.8 1.0 O B:HOH290 3.5 42.5 1.0 C5 B:A110 3.6 22.4 1.0 N4 B:C111 3.7 18.9 1.0 N6 B:A110 3.8 20.1 1.0 OP2 B:A110 3.9 25.4 1.0 C5 B:C109 4.1 22.4 1.0 C6 B:A110 4.1 21.9 1.0 C6 B:C109 4.3 22.7 1.0 C4 B:C109 4.3 21.6 1.0 C4 B:C111 4.5 20.2 1.0 C5 B:C111 4.5 19.9 1.0 N9 B:A110 4.6 24.7 1.0 C4 B:A110 4.7 24.0 1.0 O B:HOH229 4.7 33.0 1.0 N4 B:C109 4.7 17.3 1.0 O B:HOH347 4.8 32.1 1.0 N3 B:C109 4.8 23.0 1.0 N1 B:C109 4.8 22.9 1.0

Magnesium binding site 3 out of 4 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:Mg503 b:24.4 occ:1.00 C2 B:U79 3.0 49.8 1.0 O2' B:U79 3.0 43.1 1.0 O2 B:U79 3.2 49.3 1.0 N1 B:U79 3.3 47.7 1.0 N3 B:U79 3.4 51.9 1.0 N4 B:C82 3.4 39.4 1.0 O B:HOH335 3.5 32.9 1.0 C2' B:U79 3.6 43.7 1.0 N4 B:C81 3.6 39.5 1.0 C1' B:U79 3.8 44.8 1.0 C5 B:C81 3.8 41.8 1.0 C6 B:U79 3.9 50.0 1.0 C4 B:C81 3.9 41.3 1.0 C4 B:U79 4.0 52.9 1.0 C5 B:U79 4.2 52.0 1.0 C5 B:C82 4.3 40.8 1.0 C4 B:C82 4.3 39.6 1.0 C6 B:C81 4.7 41.7 1.0 O4 B:U79 4.7 54.5 1.0 N3 B:C81 4.9 41.1 1.0

Magnesium binding site 4 out of 4 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 4 of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:21.4 occ:1.00 O2' B:A56 2.9 26.9 1.0 O B:HOH281 3.2 22.6 1.0 C4' B:C57 3.2 31.1 1.0 C5' B:C57 3.4 30.4 1.0 O4' B:C57 3.4 30.2 1.0 O B:HOH310 3.4 26.8 1.0 C6 B:U59 3.5 25.9 1.0 C5 B:U59 3.8 23.5 1.0 C2' B:U59 3.9 26.3 1.0 N1 B:U59 3.9 25.3 1.0 OP1 B:U59 3.9 27.9 1.0 C2' B:A56 4.0 25.1 1.0 C5' B:A58 4.1 27.4 1.0 C3' B:A58 4.1 25.9 1.0 O5' B:U59 4.4 26.0 1.0 O5' B:A58 4.4 30.5 1.0 O2' B:U59 4.4 27.7 1.0 C1' B:U59 4.4 26.0 1.0 C4 B:U59 4.5 23.3 1.0 P B:U59 4.6 26.8 1.0 C2 B:U59 4.6 24.9 1.0 O5' B:C57 4.6 29.2 1.0 C4' B:A58 4.6 26.4 1.0 C3' B:C57 4.7 31.6 1.0 O3' B:A58 4.7 26.3 1.0 C1' B:C57 4.8 30.9 1.0 N3 B:U59 4.8 24.8 1.0 O3' B:A56 4.9 26.7 1.0 C1' B:A56 5.0 24.1 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