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

The structure of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2gcs 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 (°)	181.199, 39.713, 71.038, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.5

The binding sites of Magnesium atom in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2gcs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2gcs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 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:Mg501 b:29.7 occ:1.00 OP2 B:C36 2.1 26.3 1.0 O B:HOH289 2.1 25.0 1.0 O B:HOH288 2.1 18.2 1.0 O B:HOH261 2.1 14.3 1.0 OP2 A:C2 2.2 22.9 1.0 OP2 B:G37 2.3 21.1 1.0 P B:C36 3.2 27.1 1.0 O3' B:A35 3.2 25.7 1.0 P B:G37 3.5 22.7 1.0 P A:C2 3.5 24.6 1.0 O3' A:G1 3.5 21.9 1.0 OP1 B:G37 3.8 21.2 1.0 O2' B:A35 4.1 25.0 1.0 O5' B:C36 4.1 27.1 1.0 C3' B:C36 4.2 21.4 1.0 C5' A:C2 4.2 24.1 1.0 O3' B:C36 4.3 23.2 1.0 O5' A:C2 4.3 23.7 1.0 OP1 B:C36 4.4 21.0 1.0 C3' B:A35 4.4 24.3 1.0 O2' A:G1 4.5 22.2 1.0 OP1 A:C2 4.6 23.1 1.0 O5' B:G37 4.7 21.5 1.0 C5' B:C36 4.7 24.5 1.0 C8 B:G37 4.9 18.6 1.0 C3' A:G1 4.9 20.7 1.0 C2' B:A35 4.9 23.7 1.0 C5' B:G37 4.9 23.1 1.0

Magnesium binding site 2 out of 6 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:Mg502 b:68.8 occ:1.00 N7 B:A110 2.4 22.1 1.0 O B:HOH235 2.4 30.4 1.0 O B:HOH266 2.7 33.2 1.0 O B:HOH374 2.8 33.4 1.0 C8 B:A110 3.2 19.2 1.0 C5 B:A110 3.5 23.2 1.0 OP2 B:A110 3.6 22.1 1.0 N6 B:A110 3.9 24.1 1.0 N4 B:C111 3.9 18.0 1.0 C5 B:C109 4.0 18.9 1.0 C6 B:C109 4.1 14.6 1.0 C6 B:A110 4.2 24.4 1.0 C4 B:C109 4.3 21.4 1.0 C5 B:C111 4.5 17.2 1.0 N9 B:A110 4.5 22.3 1.0 N1 B:C109 4.6 17.9 1.0 C4 B:C111 4.6 22.4 1.0 C3' B:C109 4.6 23.9 1.0 C4 B:A110 4.6 23.5 1.0 O5' B:A110 4.7 22.4 1.0 N3 B:C109 4.7 17.8 1.0 P B:A110 4.7 24.8 1.0 N4 B:C109 4.8 19.1 1.0 C2 B:C109 4.8 20.7 1.0 OP2 B:C109 4.9 24.9 1.0 O5' B:C109 4.9 22.8 1.0 O B:HOH305 4.9 32.1 1.0

Magnesium binding site 3 out of 6 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:Mg503 b:29.0 occ:1.00 C2 B:U79 3.1 46.4 1.0 O2' B:U79 3.2 43.3 1.0 O B:HOH299 3.2 38.5 1.0 O2 B:U79 3.2 45.8 1.0 N4 B:C82 3.3 37.4 1.0 N3 B:U79 3.5 48.0 1.0 N1 B:U79 3.5 45.0 1.0 O B:HOH392 3.5 31.1 1.0 N4 B:C81 3.7 34.0 1.0 C5 B:C81 3.7 36.3 1.0 C2' B:U79 3.8 42.6 1.0 C4 B:C81 3.9 34.7 1.0 C1' B:U79 4.0 42.9 1.0 C5 B:C82 4.0 38.5 1.0 C4 B:C82 4.1 39.2 1.0 C6 B:U79 4.1 48.2 1.0 C4 B:U79 4.1 48.9 1.0 C5 B:U79 4.4 50.2 1.0 C6 B:C81 4.6 37.5 1.0 N3 B:C81 4.8 34.9 1.0 O4 B:U83 4.9 41.7 1.0 O4 B:U79 4.9 50.2 1.0

Magnesium binding site 4 out of 6 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:Mg504 b:27.9 occ:1.00 O2' B:A56 3.0 29.5 1.0 O B:HOH350 3.1 30.8 1.0 O B:HOH260 3.1 28.4 1.0 C4' B:C57 3.1 36.3 1.0 O B:HOH278 3.2 24.7 1.0 C5' B:C57 3.3 34.8 1.0 O4' B:C57 3.4 35.7 1.0 C6 B:U59 3.5 25.0 1.0 C2' B:U59 3.8 27.5 1.0 C5 B:U59 3.9 23.5 1.0 OP1 B:U59 3.9 28.4 1.0 N1 B:U59 4.0 26.5 1.0 C5' B:A58 4.0 27.1 1.0 C3' B:A58 4.1 25.6 1.0 C2' B:A56 4.1 28.3 1.0 O2' B:U59 4.1 29.1 1.0 O5' B:A58 4.2 33.4 1.0 O5' B:U59 4.4 26.6 1.0 C1' B:U59 4.4 26.8 1.0 C3' B:C57 4.5 37.5 1.0 C4' B:A58 4.6 27.4 1.0 P B:U59 4.6 28.3 1.0 O3' B:A58 4.6 26.6 1.0 O5' B:C57 4.6 29.3 1.0 C4 B:U59 4.7 21.6 1.0 C2 B:U59 4.7 25.4 1.0 C1' B:C57 4.8 37.7 1.0 O3' B:A56 4.9 27.6 1.0 C3' B:U59 4.9 27.8 1.0 N3 B:U59 5.0 23.8 1.0

Magnesium binding site 5 out of 6 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:Mg505 b:43.2 occ:1.00 O B:HOH330 2.0 36.7 1.0 O B:HOH211 2.0 27.7 1.0 O B:HOH331 2.0 32.8 1.0 O B:HOH332 2.1 42.9 1.0 O B:HOH333 2.2 37.0 1.0 O B:HOH300 2.2 43.3 1.0 O4 B:U100 3.6 50.1 1.0 O6 B:G102 4.1 33.2 1.0 O6 B:G101 4.1 34.0 1.0 OP2 B:A129 4.2 26.4 1.0 O B:HOH340 4.3 26.5 1.0 C4 B:U100 4.3 49.3 1.0 N7 B:G101 4.3 41.2 1.0 OP1 B:A129 4.3 25.0 1.0 C5 B:U100 4.4 47.6 1.0 O B:HOH341 4.6 39.9 1.0 C6 B:G102 4.7 37.0 1.0 N1 B:G102 4.7 32.5 1.0 P B:A129 4.8 26.2 1.0 O B:HOH210 4.8 44.3 1.0 C6 B:G101 4.9 35.9 1.0

Magnesium binding site 6 out of 6 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 6 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:46.0 occ:1.00 O B:HOH399 2.1 40.9 1.0 O B:HOH400 2.3 45.2 1.0 O B:HOH378 3.3 40.2 1.0 N2 B:G122 3.4 16.8 1.0 O B:HOH322 4.1 32.1 1.0 C2 B:G122 4.3 20.6 1.0 N3 B:G122 4.4 14.8 1.0 C1' B:G123 4.4 20.9 1.0 C1' B:A110 4.5 21.4 1.0 O4' B:G123 4.5 20.9 1.0 O4' B:A110 4.7 23.1 1.0 O2' B:A110 4.8 18.3 1.0 O2' B:G123 4.8 22.0 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