Magnesium in PDB 3b4a: T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate

The structure of T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate, PDB code: 3b4a 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 (°)	177.154, 41.692, 77.699, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 27.5

The binding sites of Magnesium atom in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate (pdb code 3b4a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate, PDB code: 3b4a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:55.7 occ:1.00 OP1 A:A15 3.2 74.9 1.0 C5' A:A15 3.8 77.7 1.0 O5' A:A15 4.2 75.4 1.0 P A:A15 4.3 74.7 1.0 O3' A:A15 4.5 82.5 1.0 OP1 A:G16 4.7 85.7 1.0 C4' A:A15 4.8 79.0 1.0 OP2 A:G16 4.8 84.3 1.0 P A:G16 4.9 84.9 1.0

Magnesium binding site 2 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:31.9 occ:1.00 O A:HOH302 1.8 43.8 1.0 O A:HOH301 2.0 29.2 1.0 OP2 A:C2 2.4 38.5 1.0 OP2 B:C36 2.4 27.7 1.0 O B:HOH303 2.5 26.4 1.0 OP2 B:G37 2.6 26.1 1.0 O3' B:A35 3.0 30.6 1.0 P B:C36 3.3 29.7 1.0 O3' A:G1 3.5 37.6 1.0 P A:C2 3.5 37.5 1.0 P B:G37 3.5 23.9 1.0 OP1 B:G37 3.7 24.8 1.0 O2' B:A35 4.0 33.8 1.0 C5' A:C2 4.1 43.0 1.0 O5' B:C36 4.2 29.4 1.0 O3' B:C36 4.3 24.2 1.0 C3' B:A35 4.3 30.0 1.0 C3' B:C36 4.3 23.8 1.0 O5' A:C2 4.3 40.9 1.0 O2' A:G1 4.3 34.8 1.0 OP1 B:C36 4.5 31.3 1.0 OP1 A:C2 4.7 39.1 1.0 C2' B:A35 4.8 31.6 1.0 C3' A:G1 4.8 36.7 1.0 O5' B:G37 4.9 24.2 1.0 C5' B:C36 5.0 27.7 1.0

Magnesium binding site 3 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:57.1 occ:1.00 OP2 B:A38 2.6 27.6 1.0 N7 B:G39 3.2 25.4 1.0 O6 B:G39 3.3 24.5 1.0 N7 B:A38 3.7 19.1 1.0 OP1 A:C2 3.8 39.1 1.0 C5 B:G39 3.9 22.3 1.0 P B:A38 3.9 26.6 1.0 C6 B:G39 3.9 23.0 1.0 C8 B:A38 4.0 21.3 1.0 O5' B:A38 4.1 25.0 1.0 C8 B:G39 4.3 26.4 1.0 OP1 A:A-1 4.7 67.3 1.0 C5 B:A38 4.7 18.2 1.0 C3' B:G37 4.8 20.3 1.0 O3' B:G37 4.9 22.8 1.0 OP1 B:A38 5.0 24.7 1.0

Magnesium binding site 4 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


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 with G40A Mutation, Bound to Glucosamine-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:38.1 occ:1.00 C4' B:C57 2.8 48.8 1.0 C5' B:C57 2.9 46.5 1.0 O2' B:A56 3.0 29.0 1.0 O4' B:C57 3.1 49.6 1.0 C6 B:U59 3.6 24.9 1.0 C5' B:A58 3.8 46.8 1.0 C2' B:A56 3.9 29.7 1.0 C5 B:U59 3.9 20.5 1.0 C2' B:U59 4.0 34.5 1.0 C3' B:A58 4.1 43.2 1.0 OP1 B:U59 4.1 39.3 1.0 N1 B:U59 4.2 27.5 1.0 C3' B:C57 4.3 49.6 1.0 O5' B:C57 4.3 42.4 1.0 O5' B:A58 4.3 49.6 1.0 O2' B:U59 4.3 36.3 1.0 C4' B:A58 4.4 44.7 1.0 O5' B:U59 4.5 38.1 1.0 C1' B:C57 4.5 48.5 1.0 C1' B:U59 4.6 32.2 1.0 O3' B:A58 4.7 40.8 1.0 O3' B:A56 4.7 36.5 1.0 C4 B:U59 4.7 22.4 1.0 P B:U59 4.8 37.7 1.0 O3' B:C57 4.9 51.8 1.0 C3' B:A56 4.9 31.7 1.0 C2 B:U59 4.9 25.7 1.0 C1' B:A56 5.0 27.2 1.0

Magnesium binding site 5 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:44.6 occ:1.00 O3' B:A107 3.8 25.3 1.0 OP1 B:C108 3.9 26.9 1.0 P B:C108 4.2 24.9 1.0 OP2 B:C108 4.2 27.5 1.0 C5' B:A107 4.3 21.3 1.0 C4' B:A107 4.3 23.7 1.0 O3' B:A56 4.6 36.5 1.0 C3' B:A107 4.7 24.2 1.0 C4' B:A56 4.7 31.0 1.0 C5' B:A56 4.8 30.7 1.0 OP1 B:C57 4.8 40.9 1.0

Magnesium binding site 6 out of 6 in the T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of T. Tengcongensis Glms Ribozyme with G40A Mutation, Bound to Glucosamine-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:70.3 occ:1.00 N7 B:G114 2.6 27.0 1.0 O6 B:G114 3.4 27.1 1.0 C5 B:G114 3.4 26.5 1.0 C8 B:G114 3.6 30.1 1.0 C6 B:G114 3.7 25.1 1.0 OP2 B:G116 4.1 43.9 1.0 OP1 B:G116 4.2 43.6 1.0 C4 B:G114 4.6 28.7 1.0 N7 B:G113 4.6 15.2 1.0 N9 B:G114 4.7 31.6 1.0 P B:G116 4.7 45.2 1.0 O6 B:G113 4.7 14.2 1.0 C5 B:G113 5.0 12.7 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