Magnesium in PDB 3b4b: T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate and A Substrate Rna with A 2'5'- Phosphodiester Linkage

The structure of T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate and A Substrate Rna with A 2'5'- Phosphodiester Linkage, PDB code: 3b4b 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.992, 39.686, 70.968, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.3

The binding sites of Magnesium atom in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate and A Substrate Rna with A 2'5'- Phosphodiester Linkage (pdb code 3b4b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate and A Substrate Rna with A 2'5'- Phosphodiester Linkage, PDB code: 3b4b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, 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 with G40A Mutation, 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:28.8 occ:1.00 O B:HOH404 1.7 22.9 1.0 O B:HOH403 1.7 24.9 1.0 O B:HOH405 1.9 42.8 1.0 OP2 B:G37 2.2 20.4 1.0 OP2 A:C2 2.3 23.0 1.0 OP2 B:C36 2.4 23.4 1.0 O3' B:A35 3.3 22.1 1.0 P B:G37 3.4 17.1 1.0 P B:C36 3.4 22.5 1.0 P A:C2 3.5 21.8 1.0 O3' A:G1 3.5 22.2 1.0 OP1 B:G37 3.7 17.7 1.0 O5' B:C36 4.1 21.6 1.0 C5' A:C2 4.1 23.7 1.0 C3' B:C36 4.2 18.5 1.0 O3' B:C36 4.2 18.7 1.0 O5' A:C2 4.3 23.4 1.0 O2' B:A35 4.3 22.0 1.0 O2' A:G1 4.5 21.9 1.0 C3' B:A35 4.6 20.3 1.0 O5' B:G37 4.6 17.7 1.0 OP1 A:C2 4.7 25.2 1.0 OP1 B:C36 4.7 22.4 1.0 C5' B:C36 4.8 20.9 1.0 C5' B:G37 4.9 18.1 1.0 C3' A:G1 4.9 23.1 1.0

Magnesium binding site 2 out of 3 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, 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 with G40A Mutation, 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:Mg302 b:38.6 occ:1.00 OP2 B:A38 2.2 21.7 1.0 P B:A38 3.6 19.8 1.0 OP1 A:C2 3.7 25.2 1.0 O6 B:G39 3.9 26.1 1.0 O5' B:A38 4.1 19.3 1.0 N7 B:G39 4.1 25.9 1.0 N7 B:A38 4.3 12.3 1.0 C5' A:3AD-1 4.4 34.1 1.0 C8 B:A38 4.4 14.1 1.0 OP1 B:A38 4.5 19.7 1.0 O3' B:G37 4.6 21.1 1.0 C3' B:G37 4.7 19.7 1.0 C6 B:G39 4.7 26.6 1.0 C5 B:G39 4.8 25.2 1.0 O5' A:3AD-1 4.9 35.2 1.0

Magnesium binding site 3 out of 3 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, 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 with G40A Mutation, 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:Mg303 b:41.2 occ:1.00 O3P A:GLP201 3.0 50.3 1.0 O2P A:GLP201 3.0 49.4 1.0 O6 B:G64 3.5 29.0 1.0 P A:GLP201 3.6 49.5 1.0 C6 A:GLP201 3.8 46.9 1.0 N4 B:C63 3.8 26.5 1.0 N7 B:G64 4.0 27.4 1.0 O B:HOH402 4.2 26.6 1.0 O6 A:GLP201 4.2 49.0 1.0 O6 B:G65 4.3 26.1 1.0 C6 B:G64 4.4 27.3 1.0 C4 B:C63 4.5 28.2 1.0 C5 B:G64 4.6 27.4 1.0 C5 B:C63 4.6 27.0 1.0 O1P A:GLP201 4.9 49.0 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