Magnesium in PDB 1y0q: Crystal Structure of An Active Group I Ribozyme-Product Complex

The structure of Crystal Structure of An Active Group I Ribozyme-Product Complex, PDB code: 1y0q was solved by B.L.Golden, H.Kim, E.Chase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 3.60
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.570, 140.970, 210.850, 90.00, 90.00, 90.00
R / Rfree (%)	27.7 / 31

The binding sites of Magnesium atom in the Crystal Structure of An Active Group I Ribozyme-Product Complex (pdb code 1y0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Active Group I Ribozyme-Product Complex, PDB code: 1y0q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of An Active Group I Ribozyme-Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Active Group I Ribozyme-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg254 b:0.2 occ:1.00 OP1 A:G117 2.7 84.3 1.0 OP2 A:A123 3.5 93.7 1.0 P A:G117 4.1 78.8 1.0 P A:A123 4.4 85.4 1.0 N7 A:A119 4.4 0.4 1.0 N6 A:A187 4.4 0.5 1.0 OP1 A:A123 4.5 93.7 1.0 N6 A:A119 4.7 0.4 1.0 N7 A:A187 4.7 0.5 1.0 O3' A:G122 4.7 99.7 1.0 O2' A:U48 4.8 96.5 1.0 OP2 A:G117 4.8 84.3 1.0 O3' A:U116 4.9 76.6 1.0 O2 A:U48 4.9 0.8 1.0 C5 A:A119 5.0 0.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of An Active Group I Ribozyme-Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Active Group I Ribozyme-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg255 b:0.5 occ:1.00 O2 A:C118 2.6 97.9 1.0 OP2 A:U186 2.6 97.6 1.0 P A:U186 3.5 0.2 1.0 O2' A:C118 3.5 87.6 1.0 OP2 A:U116 3.5 83.3 1.0 OP1 A:U186 3.5 97.6 1.0 C2 A:C118 3.6 97.9 1.0 OP1 A:U116 3.6 83.3 1.0 P A:U116 4.1 76.6 1.0 N3 A:C118 4.1 97.9 1.0 O4' A:U186 4.2 0.2 1.0 O5' A:U186 4.3 0.2 1.0 C2' A:C118 4.3 87.6 1.0 N7 A:G117 4.4 84.3 1.0 O2' A:A185 4.6 77.7 1.0 C5' A:U186 4.6 0.2 1.0 N1 A:C118 4.6 97.9 1.0 O6 A:G117 4.7 84.3 1.0 C1' A:C118 4.7 87.6 1.0 C6 A:U186 4.8 97.6 1.0 O3' A:A185 4.9 77.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of An Active Group I Ribozyme-Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of An Active Group I Ribozyme-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg256 b:0.8 occ:1.00 N7 A:G190 2.8 0.1 1.0 O6 A:G190 3.7 0.1 1.0 C5 A:G190 3.7 0.1 1.0 C8 A:G190 3.7 0.1 1.0 N7 A:A189 3.9 0.9 1.0 OP2 A:A189 3.9 0.9 1.0 C8 A:A189 4.0 0.9 1.0 C6 A:G190 4.1 0.1 1.0 O2' A:A187 4.3 0.1 1.0 OP2 A:G190 4.5 0.1 1.0 C5 A:A189 4.6 0.9 1.0 O4 A:U191 4.6 99.0 1.0 N3 A:A187 4.7 0.5 1.0 N7 A:G252 4.7 0.7 1.0 O5' A:A189 4.8 0.3 1.0 N9 A:A189 4.8 0.9 1.0 O6 A:G252 4.9 0.7 1.0 OP2 A:U188 4.9 0.8 1.0 C2 A:A187 4.9 0.5 1.0 N9 A:G190 4.9 0.1 1.0 C4 A:G190 4.9 0.1 1.0 P A:A189 5.0 0.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of An Active Group I Ribozyme-Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of An Active Group I Ribozyme-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg257 b:0.9 occ:1.00 O5' A:A187 2.6 0.1 1.0 OP1 A:U188 2.8 0.8 1.0 OP2 A:A187 2.8 0.5 1.0 OP1 A:A185 2.8 0.3 1.0 P A:A187 3.0 0.1 1.0 O3' A:A187 3.1 0.1 1.0 O3' A:G252 3.1 0.4 1.0 OP1 A:A187 3.3 0.5 1.0 P A:U188 3.5 93.5 1.0 OP1 A:U84 3.8 0.4 1.0 O5' A:U188 3.9 93.5 1.0 C5' A:A187 3.9 0.1 1.0 O3' B:U4 4.0 0.6 1.0 C5' A:U188 4.1 93.5 1.0 C3' A:A187 4.1 0.1 1.0 O2' B:U4 4.2 0.6 1.0 C4' A:A187 4.2 0.1 1.0 C3' A:G252 4.3 0.4 1.0 P A:A185 4.3 77.7 1.0 O3' A:U186 4.5 0.2 1.0 OP2 A:U84 4.8 0.4 1.0 P A:U84 4.8 0.1 1.0 C3' B:U4 4.8 0.6 1.0 O5' A:A185 4.8 77.7 1.0 C2' A:G252 4.9 0.4 1.0 O2' A:G252 4.9 0.4 1.0 OP2 A:U188 4.9 0.8 1.0 C4' B:U4 4.9 0.6 1.0

B.L.Golden, H.Kim, E.Chase. Crystal Structure of A Phage Twort Group I Ribozyme-Product Complex Nat.Struct.Mol.Biol. V. 12 82 2005.
ISSN: ISSN 1545-9993
PubMed: 15580277
DOI: 10.1038/NSMB868