Magnesium in PDB 2z74: T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate

The structure of T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate, PDB code: 2z74 was solved by D.J.Klein, S.R.Wilkinson, M.D.Been, 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 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.110, 40.060, 70.280, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.5

The binding sites of Magnesium atom in the T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate (pdb code 2z74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate, PDB code: 2z74:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:62.1 occ:1.00 O B:HOH402 1.7 37.7 1.0 O B:HOH401 2.1 26.0 1.0 OP2 A:C2 2.5 34.5 1.0 OP2 B:C36 2.7 42.1 1.0 O3' B:A35 3.0 36.5 1.0 OP2 B:G37 3.2 30.4 1.0 O3' A:G1 3.4 30.9 1.0 P B:C36 3.5 38.5 1.0 P A:C2 3.5 32.5 1.0 O2' B:A35 3.6 33.7 1.0 C5' A:C2 3.8 36.6 1.0 C3' B:A35 4.1 32.1 1.0 O5' A:C2 4.1 33.0 1.0 O5' B:C36 4.3 38.0 1.0 P B:G37 4.3 27.2 1.0 O2' A:G1 4.4 34.9 1.0 C2' B:A35 4.4 31.5 1.0 OP1 B:G37 4.5 26.4 1.0 C3' A:G1 4.7 29.8 1.0 OP1 B:C36 4.8 41.1 1.0 OP2 A:G3 4.8 41.4 1.0 OP1 A:C2 4.8 31.3 1.0 C3' B:C36 5.0 30.1 1.0

Magnesium binding site 2 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:37.4 occ:1.00 C4' B:C57 3.1 54.0 1.0 O2' B:A56 3.2 42.9 1.0 C5' B:C57 3.3 52.7 1.0 O4' B:C57 3.3 54.0 1.0 O B:HOH461 3.4 34.7 1.0 C6 B:U59 3.5 32.2 1.0 C2' B:U59 3.8 35.1 1.0 C5 B:U59 3.9 29.2 1.0 OP1 B:U59 3.9 36.7 1.0 N1 B:U59 4.0 32.5 1.0 C5' B:A58 4.0 41.2 1.0 C3' B:A58 4.0 37.0 1.0 O2' B:U59 4.2 37.3 1.0 O5' B:A58 4.2 49.8 1.0 C2' B:A56 4.2 41.9 1.0 O5' B:U59 4.3 34.2 1.0 C1' B:U59 4.4 34.5 1.0 C3' B:C57 4.5 54.1 1.0 C4' B:A58 4.5 39.4 1.0 P B:U59 4.5 38.9 1.0 O3' B:A58 4.6 36.2 1.0 O5' B:C57 4.6 47.4 1.0 C4 B:U59 4.6 27.4 1.0 C2 B:U59 4.7 30.1 1.0 C1' B:C57 4.7 53.3 1.0 N3 B:U59 4.9 31.0 1.0 C3' B:U59 4.9 34.8 1.0

Magnesium binding site 3 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:28.9 occ:1.00 O2 B:U79 2.9 53.8 1.0 C2 B:U79 3.0 55.2 1.0 O2' B:U79 3.2 50.6 1.0 N3 B:U79 3.3 56.5 1.0 N4 B:C82 3.3 44.1 1.0 N1 B:U79 3.5 53.7 1.0 C5 B:C81 3.7 40.5 1.0 C2' B:U79 3.8 50.0 1.0 N4 B:C81 3.9 39.3 1.0 C1' B:U79 4.0 51.2 1.0 C4 B:C81 4.0 41.1 1.0 C4 B:U79 4.1 58.7 1.0 C5 B:C82 4.1 41.7 1.0 C4 B:C82 4.2 42.9 1.0 C6 B:U79 4.3 55.4 1.0 C5 B:U79 4.5 57.9 1.0 C6 B:C81 4.6 42.8 1.0 O4 B:U79 4.8 59.3 1.0

Magnesium binding site 4 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:57.2 occ:1.00 O B:HOH455 2.1 35.2 1.0 O B:HOH439 2.3 36.8 1.0 O4 B:U100 3.6 60.4 1.0 O6 B:G101 4.2 44.2 1.0 C4 B:U100 4.2 58.9 1.0 N7 B:G101 4.2 48.6 1.0 C5 B:U100 4.3 60.0 1.0 O6 B:G102 4.3 47.4 1.0 OP2 B:A129 4.6 29.0 1.0 OP1 B:A129 4.6 35.8 1.0 N1 B:G102 4.8 42.5 1.0 C6 B:G102 4.8 46.5 1.0 C6 B:G101 4.9 45.3 1.0 C5 B:G101 5.0 45.7 1.0

Magnesium binding site 5 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:36.4 occ:1.00 N2 B:G122 3.5 25.6 1.0 C1' B:A110 4.5 34.5 1.0 O2' B:A110 4.5 30.0 1.0 C2 B:G122 4.6 29.6 1.0 N3 B:G122 4.6 22.9 1.0 O4' B:A110 4.8 34.5 1.0 C1' B:G123 4.8 30.5 1.0 O4' B:G123 4.9 30.3 1.0

Magnesium binding site 6 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-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 Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg306 b:47.7 occ:1.00 O A:HOH422 2.5 25.3 1.0 O3P A:G6P201 2.6 55.6 1.0 O2P A:G6P201 2.6 54.8 1.0 P A:G6P201 3.1 52.0 1.0 C6 A:G6P201 3.5 50.4 1.0 O6 B:G64 3.6 34.1 1.0 N4 B:C63 3.8 39.5 1.0 O6 A:G6P201 3.9 53.7 1.0 O1P A:G6P201 4.4 55.5 1.0 O6 B:G65 4.4 27.0 1.0 C6 B:G64 4.6 30.9 1.0 N7 B:G64 4.6 29.8 1.0 C4 B:C63 4.7 44.5 1.0 C5 A:G6P201 4.9 49.4 1.0 C5 B:C63 5.0 44.6 1.0

Magnesium binding site 7 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg307 b:40.4 occ:1.00 N2 B:G86 3.4 32.3 1.0 O4' B:G139 3.4 59.5 1.0 C1' B:G139 3.8 57.3 1.0 C1' B:A87 4.3 43.5 1.0 O4' B:A87 4.3 46.0 1.0 N9 B:G139 4.4 50.1 1.0 C2 B:G86 4.4 35.2 1.0 N3 B:G86 4.5 32.9 1.0 C4' B:G139 4.7 62.4 1.0 C4 B:G139 4.9 46.3 1.0 O2' B:A87 4.9 46.2 1.0 O2 B:C78 4.9 36.8 1.0

Magnesium binding site 8 out of 8 in the T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of T. Tengcongensis Glms Ribozyme Bound to Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg308 b:48.5 occ:1.00 N2 B:G142 4.1 41.9 1.0 C1' B:U83 4.6 51.7 1.0 O4' B:U83 4.9 52.3 1.0 O2 B:U83 4.9 47.6 1.0 N3 B:G142 4.9 40.4 1.0 O2' B:U83 5.0 51.3 1.0

D.J.Klein, S.R.Wilkinson, M.D.Been, A.R.Ferre-D'amare. Requirement of Helix P2.2 and Nucleotide G1 For Positioning the Cleavage Site and Cofactor of the Glms Ribozyme J.Mol.Biol. V. 373 178 2007.
ISSN: ISSN 0022-2836
PubMed: 17804015
DOI: 10.1016/J.JMB.2007.07.062