Magnesium in PDB 3b4c: T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage

The structure of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage, PDB code: 3b4c 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 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.300, 40.400, 77.500, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.2

The binding sites of Magnesium atom in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage (pdb code 3b4c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage, PDB code: 3b4c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:42.6 occ:1.00 O A:HOH401 1.8 47.1 1.0 OP2 B:C36 2.0 36.4 1.0 O B:HOH402 2.1 42.1 1.0 OP2 B:G37 2.6 31.3 1.0 OP2 A:C2 2.6 46.2 1.0 O3' B:A35 2.7 37.3 1.0 P B:C36 2.9 36.2 1.0 O3' A:G1 3.5 46.4 1.0 P A:C2 3.7 46.2 1.0 P B:G37 3.8 31.8 1.0 O5' B:C36 3.8 35.2 1.0 O2' B:A35 3.8 41.3 1.0 C3' B:A35 3.9 39.0 1.0 C5' A:C2 4.1 50.6 1.0 OP1 B:C36 4.1 36.8 1.0 OP1 B:G37 4.2 31.6 1.0 O5' A:C2 4.4 48.0 1.0 C3' B:C36 4.4 30.6 1.0 C2' B:A35 4.5 38.8 1.0 O2' A:G1 4.6 46.7 1.0 O3' B:C36 4.6 30.0 1.0 C5' B:C36 4.6 33.6 1.0 C3' A:G1 4.8 47.4 1.0 OP1 A:C2 5.0 47.0 1.0

Magnesium binding site 2 out of 4 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:60.3 occ:1.00 O6 B:G64 2.6 75.5 1.0 O2P A:GLP201 2.9 66.5 1.0 O3P A:GLP201 3.1 68.9 1.0 N4 B:C63 3.5 74.1 1.0 C6 B:G64 3.5 75.8 1.0 P A:GLP201 3.6 66.7 1.0 N7 B:G64 3.6 77.0 1.0 C5 B:G64 3.9 76.8 1.0 C6 A:GLP201 4.0 62.8 1.0 C4 B:C63 4.2 74.3 1.0 C5 B:C63 4.2 75.1 1.0 O6 A:GLP201 4.4 66.2 1.0 O6 B:G65 4.4 67.8 1.0 O6 A:G3 4.6 68.6 1.0 N1 B:G64 4.8 74.6 1.0 O1P A:GLP201 4.8 66.7 1.0 N4 A:C2 4.9 54.3 1.0 C8 B:G64 4.9 76.8 1.0

Magnesium binding site 3 out of 4 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:50.7 occ:1.00 OP2 B:A38 2.4 37.8 1.0 OP1 A:C2 3.3 47.0 1.0 O6 B:G39 3.5 34.5 1.0 P B:A38 3.8 36.5 1.0 N7 B:A38 3.9 33.6 1.0 N7 B:G39 3.9 32.6 1.0 C8 B:A38 4.0 33.8 1.0 O5' B:A38 4.1 36.1 1.0 C3' B:G37 4.3 31.4 1.0 C6 B:G39 4.3 32.3 1.0 C5 B:G39 4.5 31.4 1.0 O3' B:G37 4.5 33.5 1.0 P A:C2 4.7 46.2 1.0 OP1 B:A38 4.9 36.8 1.0

Magnesium binding site 4 out of 4 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6- Phosphate and A Substrate Rna with A 2'5'-Phosphodiester Linkage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:71.2 occ:1.00 N7 A:G1 4.0 44.8 1.0 O6 A:G1 4.5 40.6 1.0 N4 B:C52 4.6 28.4 1.0 N1 B:A35 4.7 39.6 1.0 O6 B:G53 4.9 40.2 1.0 C2 B:A35 5.0 38.2 1.0 C5 A:G1 5.0 43.9 1.0 C8 A:G1 5.0 44.9 1.0

D.J.Klein, M.D.Been, A.R.Ferre-D'amare. Essential Role of An Active-Site Guanine in Glms Ribozyme Catalysis. J.Am.Chem.Soc. V. 129 14858 2007.
ISSN: ISSN 0002-7863
PubMed: 17990888
DOI: 10.1021/JA0768441