Magnesium in PDB 1x8w: Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site

The structure of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site, PDB code: 1x8w was solved by F.Guo, A.R.Gooding, T.R.Cech, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	175.400, 175.400, 304.800, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 32

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site (pdb code 1x8w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 38 binding sites of Magnesium where determined in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site, PDB code: 1x8w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1 b:25.9 occ:1.00 OP2 C:G188 2.1 58.4 1.0 OP2 C:A187 2.1 73.0 1.0 OP1 C:A184 2.1 38.3 1.0 OP1 C:A186 2.3 45.5 1.0 P C:A187 3.2 73.0 1.0 P C:A186 3.2 45.5 1.0 O5' C:A186 3.2 45.5 1.0 O5' C:A187 3.2 73.0 1.0 P C:A184 3.2 38.3 1.0 P C:G188 3.5 58.4 1.0 OP2 C:A184 3.7 38.3 1.0 OP1 C:A183 3.8 54.5 1.0 C5' C:A186 3.9 45.5 1.0 O3' C:A183 3.9 54.5 1.0 OP2 C:A186 4.0 45.5 1.0 O3' C:A187 4.2 73.0 1.0 OP1 C:A187 4.2 73.0 1.0 O3' C:A186 4.2 45.5 1.0 C3' C:A186 4.2 45.5 1.0 OP1 C:G188 4.3 58.4 1.0 O2' C:U182 4.4 64.0 1.0 O5' C:G188 4.5 58.4 1.0 O5' C:A184 4.5 38.3 1.0 O3' C:U185 4.6 99.7 1.0 C5' C:A187 4.6 73.0 1.0 C4' C:A186 4.7 45.5 1.0 C5' C:U185 4.8 99.7 1.0 C4' C:U185 4.9 99.7 1.0 C4' C:A183 5.0 54.5 1.0 C3' C:A187 5.0 73.0 1.0

Magnesium binding site 2 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:49.9 occ:1.00 OP1 B:A184 1.7 49.3 1.0 OP2 B:A187 2.1 80.4 1.0 OP1 B:A186 2.2 44.4 1.0 OP2 B:G188 2.3 62.3 1.0 P B:A184 2.9 49.3 1.0 P B:A187 2.9 80.4 1.0 OP1 B:A187 3.0 80.4 1.0 P B:G188 3.1 62.3 1.0 P B:A186 3.1 44.4 1.0 O3' B:A183 3.2 50.8 1.0 OP2 B:A186 3.3 44.4 1.0 O3' B:A187 3.3 80.4 1.0 OP1 B:G188 3.7 62.3 1.0 OP2 B:A184 3.7 49.3 1.0 O5' B:A184 4.0 49.3 1.0 C4' B:U185 4.0 80.3 1.0 O3' B:A186 4.0 44.4 1.0 C5' B:A184 4.1 49.3 1.0 O5' B:A187 4.1 80.4 1.0 O3' B:U185 4.1 80.3 1.0 C3' B:A186 4.2 44.4 1.0 C5' B:U185 4.2 80.3 1.0 O5' B:A186 4.3 44.4 1.0 C3' B:A187 4.4 80.4 1.0 O5' B:A183 4.4 50.8 1.0 O5' B:G188 4.5 62.3 1.0 OP1 B:A183 4.5 50.8 1.0 C3' B:A183 4.6 50.8 1.0 C5' B:A186 4.6 44.4 1.0 C3' B:U185 4.7 80.3 1.0 C5' B:A187 4.9 80.4 1.0 C4' B:A187 5.0 80.4 1.0 C4' B:A186 5.0 44.4 1.0

Magnesium binding site 3 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:10.0 occ:1.00 OP2 A:A187 2.1 99.4 1.0 OP1 A:A184 2.2 65.9 1.0 OP1 A:A186 2.3 47.8 1.0 OP2 A:G188 3.1 94.1 1.0 P A:A187 3.1 99.4 1.0 P A:A184 3.2 65.9 1.0 P A:A186 3.2 47.8 1.0 O3' A:A183 3.5 61.6 1.0 O3' A:A186 3.5 47.8 1.0 C3' A:A186 3.5 47.8 1.0 O5' A:A186 3.6 47.8 1.0 O5' A:A184 3.6 65.9 1.0 OP2 A:A186 3.6 47.8 1.0 O5' A:A187 3.6 99.4 1.0 C5' A:A184 3.8 65.9 1.0 C5' A:A187 3.9 99.4 1.0 OP1 A:A183 4.0 61.6 1.0 OP1 A:A187 4.5 99.4 1.0 P A:G188 4.5 94.1 1.0 C5' A:A186 4.5 47.8 1.0 C2' A:A186 4.6 47.8 1.0 C4' A:A186 4.6 47.8 1.0 OP2 A:A184 4.6 65.9 1.0 C8 A:A186 4.6 47.8 1.0 O3' A:U185 4.6 91.9 1.0 O3' A:U182 4.7 70.2 1.0 C3' A:A183 4.8 61.6 1.0 O2' A:U182 4.8 70.2 1.0 O5' A:G188 4.9 94.1 1.0 P A:A183 5.0 61.6 1.0

Magnesium binding site 4 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4 b:65.8 occ:1.00 OP1 D:A184 2.1 0.9 1.0 OP2 D:A187 2.2 92.3 1.0 OP2 D:G188 2.5 0.5 1.0 OP1 D:A186 2.7 98.3 1.0 OP2 D:A186 2.8 98.3 1.0 O3' D:A187 2.9 92.3 1.0 P D:A186 3.2 98.3 1.0 P D:A184 3.3 0.9 1.0 P D:G188 3.3 0.5 1.0 P D:A187 3.4 92.3 1.0 O5' D:A187 3.6 92.3 1.0 O5' D:A184 3.6 0.9 1.0 O3' D:A186 4.0 98.3 1.0 C3' D:A187 4.1 92.3 1.0 OP2 D:A184 4.1 0.9 1.0 C5' D:A184 4.2 0.9 1.0 O5' D:A186 4.3 98.3 1.0 C3' D:A186 4.3 98.3 1.0 O5' D:G188 4.3 0.5 1.0 C5' D:A183 4.4 0.7 1.0 OP1 D:G188 4.4 0.5 1.0 O3' D:A183 4.4 0.7 1.0 O5' D:A183 4.4 0.7 1.0 O3' D:U185 4.5 0.3 1.0 O2' D:U182 4.5 0.2 1.0 C5' D:A187 4.5 92.3 1.0 C5' D:A186 4.6 98.3 1.0 C4' D:A187 4.6 92.3 1.0 OP1 D:A187 4.6 92.3 1.0 OP1 D:A183 4.7 0.7 1.0 C4' D:A183 4.7 0.7 1.0 C4' D:U185 4.8 0.3 1.0

Magnesium binding site 5 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg5 b:53.7 occ:1.00 N6 B:A256 2.5 0.8 1.0 C6 B:A256 2.8 0.8 1.0 OP1 B:U273 3.0 10.0 1.0 N1 B:A256 3.2 0.8 1.0 OP2 B:C274 3.4 30.3 1.0 C5 B:A256 3.6 0.8 1.0 OP1 B:A256 3.7 0.8 1.0 O2' B:C255 3.9 55.5 1.0 C2 B:A256 4.1 0.8 1.0 P B:C274 4.1 30.3 1.0 P B:U273 4.1 10.0 1.0 O5' B:U273 4.2 10.0 1.0 O3' B:C255 4.2 55.5 1.0 N7 B:A256 4.2 0.8 1.0 OP1 B:C274 4.3 30.3 1.0 O3' B:U273 4.4 10.0 1.0 C4 B:A256 4.5 0.8 1.0 P B:A256 4.5 0.8 1.0 C4' B:C255 4.5 55.5 1.0 C5' B:U273 4.6 10.0 1.0 N3 B:A256 4.8 0.8 1.0 C3' B:C255 4.8 55.5 1.0 C2' B:C255 4.9 55.5 1.0 OP2 B:A256 4.9 0.8 1.0

Magnesium binding site 6 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6 b:10.0 occ:1.00 OP2 B:G210 2.4 50.7 1.0 OP1 B:C209 2.5 47.9 1.0 P B:G210 3.6 50.7 1.0 P B:C209 3.7 47.9 1.0 C5' B:C209 3.8 47.9 1.0 O5' B:C209 4.0 47.9 1.0 OP1 B:G210 4.0 50.7 1.0 O4' B:G210 4.2 50.7 1.0 O5' B:G210 4.4 50.7 1.0 C5' B:G210 4.5 50.7 1.0 O3' B:C209 4.7 47.9 1.0 O3' B:C208 4.8 58.9 1.0 OP2 B:C209 4.8 47.9 1.0 C4' B:C209 4.9 47.9 1.0 C8 B:G210 4.9 50.7 1.0 C4' B:G210 5.0 50.7 1.0

Magnesium binding site 7 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg7 b:83.5 occ:1.00 OP2 C:A306 2.0 0.3 1.0 O2' C:G414 2.1 59.7 1.0 OP2 C:C262 2.5 40.5 1.0 OP1 C:C262 2.7 40.5 1.0 P C:C262 2.9 40.5 1.0 O3' C:G414 3.3 59.7 1.0 P C:A306 3.4 0.3 1.0 C2' C:G414 3.4 59.7 1.0 OP2 C:C208 3.5 93.6 1.0 O5' C:C262 3.6 40.5 1.0 C3' C:G414 3.8 59.7 1.0 OP1 C:C208 3.8 93.6 1.0 OP1 C:A306 3.9 0.3 1.0 C4' C:G414 4.1 59.7 1.0 P C:C208 4.2 93.6 1.0 C5' C:C262 4.2 40.5 1.0 C3' C:U305 4.3 1.0 1.0 O5' C:A306 4.3 0.3 1.0 O3' C:U305 4.3 1.0 1.0 O3' C:A261 4.4 56.2 1.0 C1' C:G414 4.4 59.7 1.0 O2 C:U305 4.5 1.0 1.0 O4' C:G414 4.7 59.7 1.0 O2' C:A261 4.8 56.2 1.0 C5' C:A306 5.0 0.3 1.0

Magnesium binding site 8 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg8 b:0.8 occ:1.00 OP1 D:U273 2.5 86.8 1.0 OP2 D:C274 2.6 69.0 1.0 N6 D:A256 2.6 0.7 1.0 C6 D:A256 3.2 0.7 1.0 O3' D:U273 3.3 86.8 1.0 P D:C274 3.4 69.0 1.0 P D:U273 3.6 86.8 1.0 O5' D:U273 3.6 86.8 1.0 C5' D:U273 3.6 86.8 1.0 C5 D:A256 3.8 0.7 1.0 N1 D:A256 3.8 0.7 1.0 C3' D:U273 3.9 86.8 1.0 OP1 D:C274 4.1 69.0 1.0 N7 D:A256 4.2 0.7 1.0 OP1 D:A256 4.2 0.7 1.0 C4' D:U273 4.2 86.8 1.0 O2' D:C255 4.3 82.5 1.0 O3' D:C255 4.5 82.5 1.0 OP2 D:U273 4.5 86.8 1.0 O3' D:G272 4.8 0.3 1.0 O5' D:C274 4.8 69.0 1.0 C2 D:A256 4.8 0.7 1.0 C4 D:A256 4.8 0.7 1.0 P D:A256 4.9 0.7 1.0 C4' D:C255 5.0 82.5 1.0

Magnesium binding site 9 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9 b:0.5 occ:1.00 OP1 A:C209 2.2 78.8 1.0 OP2 A:G210 2.8 90.8 1.0 OP2 A:G303 3.0 0.2 1.0 P A:C209 3.3 78.8 1.0 O4' A:G210 3.6 90.8 1.0 OP2 A:C209 3.6 78.8 1.0 OP1 A:G303 3.6 0.2 1.0 P A:G303 3.7 0.2 1.0 P A:G210 4.0 90.8 1.0 O3' A:A302 4.2 0.1 1.0 O5' A:C209 4.2 78.8 1.0 C1' A:G210 4.2 90.8 1.0 OP1 A:G210 4.3 90.8 1.0 N3 A:G210 4.5 90.8 1.0 N9 A:G210 4.5 90.8 1.0 O3' A:C208 4.5 69.8 1.0 C4 A:G210 4.6 90.8 1.0 C5' A:C209 4.6 78.8 1.0 O5' A:G210 4.7 90.8 1.0 C4' A:G210 4.8 90.8 1.0 OP1 A:G304 4.9 79.9 1.0

Magnesium binding site 10 out of 38 in the Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg10 b:16.6 occ:1.00 OP1 C:U273 2.2 23.8 1.0 OP1 C:A256 2.4 60.7 1.0 N1 C:A256 2.7 60.7 1.0 C2 C:A256 2.8 60.7 1.0 P C:U273 3.4 23.8 1.0 C6 C:A256 3.5 60.7 1.0 N3 C:A256 3.6 60.7 1.0 P C:A256 3.8 60.7 1.0 C5' C:U273 3.8 23.8 1.0 OP2 C:C274 3.8 32.5 1.0 OP2 C:U273 3.9 23.8 1.0 O5' C:U273 4.0 23.8 1.0 O3' C:U273 4.1 23.8 1.0 N6 C:A256 4.2 60.7 1.0 C4 C:A256 4.2 60.7 1.0 C5 C:A256 4.2 60.7 1.0 P C:C274 4.4 32.5 1.0 OP2 C:A256 4.4 60.7 1.0 C4' C:C255 4.5 45.5 1.0 C3' C:U273 4.5 23.8 1.0 O5' C:A256 4.5 60.7 1.0 O3' C:G272 4.6 23.1 1.0 C4' C:U273 4.6 23.8 1.0 OP1 C:C274 4.7 32.5 1.0 O3' C:C255 4.8 45.5 1.0

F.Guo, A.R.Gooding, T.R.Cech. Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site. Mol.Cell V. 16 351 2004.
ISSN: ISSN 1097-2765
PubMed: 15525509
DOI: 10.1016/J.MOLCEL.2004.10.003