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

The structure of Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2gcv 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 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.550, 40.460, 71.080, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24

The binding sites of Magnesium atom in the Post-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2gcv). 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: 2gcv:
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:Mg401 b:37.0 occ:1.00 O B:HOH324 2.0 31.1 1.0 OP2 B:C36 2.1 35.9 1.0 O B:HOH325 2.1 28.3 1.0 O B:HOH282 2.1 14.7 1.0 OP2 B:G37 2.2 23.4 1.0 OP2 A:C2 2.3 22.7 1.0 P B:C36 3.2 32.5 1.0 O3' B:A35 3.2 33.3 1.0 P B:G37 3.4 26.1 1.0 O3' A:G1 3.5 22.2 1.0 P A:C2 3.5 25.2 1.0 OP1 B:G37 3.8 22.1 1.0 O5' B:C36 3.9 32.7 1.0 C3' B:C36 4.2 24.3 1.0 O2' B:A35 4.2 31.1 1.0 O3' B:C36 4.3 24.5 1.0 C5' A:C2 4.3 22.1 1.0 O5' A:C2 4.4 20.4 1.0 OP1 B:C36 4.5 33.1 1.0 C3' B:A35 4.5 29.0 1.0 O5' B:G37 4.6 24.3 1.0 O2' A:G1 4.6 19.4 1.0 C5' B:C36 4.6 26.0 1.0 OP1 A:C2 4.7 24.6 1.0 C5' B:G37 4.8 25.9 1.0 C3' A:G1 4.9 22.2 1.0 C8 B:G37 4.9 21.6 1.0 C2' B:A35 5.0 28.6 1.0 C4' B:C36 5.0 25.5 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:Mg402 b:48.7 occ:1.00 O B:HOH291 2.3 30.5 1.0 N7 B:A110 2.3 26.4 1.0 O B:HOH250 2.6 29.6 1.0 O B:HOH293 2.8 32.0 1.0 C8 B:A110 3.2 23.8 1.0 C5 B:A110 3.4 23.0 1.0 O B:HOH290 3.6 40.5 1.0 N6 B:A110 3.8 20.8 1.0 N4 B:C111 3.8 17.9 1.0 OP2 B:A110 3.8 28.5 1.0 C5 B:C109 4.0 25.1 1.0 C6 B:A110 4.0 21.5 1.0 C4 B:C109 4.2 20.8 1.0 C6 B:C109 4.3 21.6 1.0 N9 B:A110 4.4 24.9 1.0 C5 B:C111 4.5 22.5 1.0 C4 B:C111 4.5 23.1 1.0 C4 B:A110 4.5 26.1 1.0 N4 B:C109 4.6 19.5 1.0 N3 B:C109 4.6 22.8 1.0 N1 B:C109 4.7 23.4 1.0 O B:HOH347 4.7 25.3 1.0 O B:HOH229 4.8 25.0 1.0 C2 B:C109 4.9 24.5 1.0 O5' B:A110 4.9 25.4 1.0 C3' B:C109 5.0 26.1 1.0 P B:A110 5.0 28.8 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:Mg403 b:24.7 occ:1.00 C2 B:U79 3.0 48.8 1.0 N4 B:C82 3.1 40.2 1.0 O2 B:U79 3.2 49.3 1.0 O2' B:U79 3.2 41.7 1.0 N3 B:U79 3.3 50.5 1.0 O B:HOH335 3.4 41.7 1.0 N1 B:U79 3.4 46.2 1.0 N4 B:C81 3.6 31.3 1.0 C5 B:C81 3.7 35.1 1.0 C2' B:U79 3.7 40.4 1.0 C4 B:C81 3.9 35.6 1.0 C1' B:U79 3.9 42.6 1.0 C4 B:C82 4.0 39.7 1.0 C5 B:C82 4.0 40.5 1.0 C6 B:U79 4.0 48.4 1.0 C4 B:U79 4.0 51.2 1.0 C5 B:U79 4.3 52.2 1.0 C6 B:C81 4.6 36.7 1.0 O4 B:U79 4.8 53.4 1.0 N3 B:C81 4.8 33.1 1.0 OP2 B:C81 5.0 45.8 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:Mg404 b:25.4 occ:1.00 O2' B:A56 2.9 25.9 1.0 C4' B:C57 3.1 37.6 1.0 O B:HOH310 3.3 31.0 1.0 O4' B:C57 3.3 37.0 1.0 O B:HOH281 3.3 24.3 1.0 C5' B:C57 3.3 35.5 1.0 C6 B:U59 3.6 28.4 1.0 C2' B:U59 3.8 28.0 1.0 C5 B:U59 4.0 27.9 1.0 C2' B:A56 4.0 27.2 1.0 N1 B:U59 4.0 26.1 1.0 C5' B:A58 4.0 28.1 1.0 OP1 B:U59 4.0 27.9 1.0 C3' B:A58 4.2 25.9 1.0 O2' B:U59 4.2 31.5 1.0 O5' B:A58 4.3 35.9 1.0 O5' B:U59 4.4 25.8 1.0 C1' B:U59 4.4 28.1 1.0 C3' B:C57 4.5 37.9 1.0 O5' B:C57 4.5 32.6 1.0 C4' B:A58 4.6 27.7 1.0 C1' B:C57 4.7 36.1 1.0 C4 B:U59 4.7 25.4 1.0 C2 B:U59 4.7 27.0 1.0 P B:U59 4.7 28.3 1.0 O3' B:A58 4.8 24.5 1.0 O3' B:A56 4.8 29.4 1.0 N3 B:U59 4.9 28.5 1.0 C1' B:A56 5.0 26.9 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