Magnesium in PDB 9cby: Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Magnesium atom in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions (pdb code 9cby). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 56 binding sites of Magnesium where determined in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions, PDB code: 9cby:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:16.1 occ:1.00 OP1 N:G257 2.0 49.6 1.0 OP2 N:U258 2.3 48.4 1.0 OP2 N:U305 2.5 60.8 1.0 O N:HOH607 2.9 21.4 1.0 H5 N:U259 3.1 25.1 1.0 O N:HOH785 3.2 22.0 1.0 O N:HOH767 3.3 19.8 1.0 P N:G257 3.4 10.3 1.0 O4 N:U259 3.6 14.7 1.0 O2 N:C260 3.6 15.6 1.0 P N:U258 3.7 22.0 1.0 P N:U305 3.8 9.9 1.0 H3' N:G257 3.9 27.6 1.0 C5 N:U259 4.0 25.1 1.0 O5' N:U305 4.0 46.0 1.0 H5'' N:G257 4.0 23.7 1.0 OP2 N:G257 4.1 51.5 1.0 C4 N:U259 4.2 10.9 1.0 O5' N:G257 4.2 29.8 1.0 O2' N:C260 4.2 20.6 1.0 C2 N:C260 4.3 22.8 1.0 O3' N:G257 4.3 48.1 1.0 O3' N:A256 4.3 59.9 1.0 O3' N:A304 4.5 33.0 1.0 OP1 N:U258 4.5 112.7 1.0 H5 N:U258 4.5 28.1 1.0 O N:HOH710 4.5 23.4 1.0 C3' N:G257 4.5 27.6 1.0 C5' N:G257 4.6 23.7 1.0 O N:HOH762 4.6 16.3 1.0 H1' N:C260 4.6 27.1 1.0 O5' N:U258 4.7 27.0 1.0 H6 N:U258 4.8 27.1 1.0 HO2' N:C260 4.8 20.6 1.0 N3 N:C260 4.9 26.4 1.0 OP1 N:U305 5.0 95.5 1.0

Magnesium binding site 2 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:18.9 occ:1.00 OP2 N:A186 2.0 65.0 1.0 OP1 N:A183 2.0 25.1 1.0 OP2 N:A184 2.3 51.1 1.0 P N:A186 3.4 12.7 1.0 P N:A183 3.4 14.8 1.0 H8 N:A186 3.4 21.2 1.0 H3' N:A183 3.5 33.2 1.0 P N:A184 3.6 11.0 1.0 H3' N:U185 3.7 41.0 1.0 O N:HOH903 3.9 20.4 1.0 O N:HOH744 4.0 16.9 1.0 H8 N:A184 4.0 28.6 1.0 O N:HOH634 4.0 19.2 1.0 OP2 N:A183 4.1 71.1 1.0 N7 N:A186 4.1 25.6 1.0 OP1 N:A186 4.1 42.5 1.0 C8 N:A186 4.1 21.2 1.0 N7 N:A184 4.2 32.6 1.0 O3' N:U185 4.2 80.5 1.0 O3' N:A183 4.3 31.2 1.0 O5' N:A183 4.3 38.8 1.0 O5' N:A186 4.3 38.1 1.0 C3' N:A183 4.4 33.2 1.0 C3' N:U185 4.4 41.0 1.0 O3' N:U182 4.4 64.2 1.0 OP1 N:A184 4.4 74.3 1.0 C8 N:A184 4.5 28.6 1.0 O N:HOH621 4.6 29.2 1.0 HO2' N:U185 4.6 65.7 1.0 H5'' N:A183 4.6 15.2 1.0 O5' N:A184 4.6 63.2 1.0 O N:HOH605 4.8 25.0 1.0 N3 N:A139 4.8 35.8 1.0 H2 N:A139 4.9 22.4 1.0 C5' N:A183 4.9 15.2 1.0 C2 N:A139 5.0 22.4 1.0

Magnesium binding site 3 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:16.2 occ:1.00 OP1 N:A184 2.1 74.3 1.0 OP2 N:A187 2.2 53.5 1.0 OP1 N:A186 2.3 42.5 1.0 O N:HOH744 2.8 16.9 1.0 OP2 N:G188 3.1 76.2 1.0 P N:A184 3.3 11.0 1.0 H3' N:A186 3.3 39.3 1.0 H5' N:A187 3.6 20.9 1.0 P N:A187 3.6 13.9 1.0 P N:A186 3.6 12.7 1.0 P N:G188 3.8 19.2 1.0 OP1 N:G188 3.8 27.4 1.0 H4' N:U185 3.8 35.7 1.0 O3' N:A183 3.9 31.2 1.0 H4' N:A187 3.9 24.7 1.0 OP2 N:A184 3.9 51.1 1.0 O N:HOH805 4.0 15.5 1.0 O N:HOH866 4.0 16.2 1.0 O N:HOH680 4.0 14.2 1.0 H5'' N:U185 4.1 33.5 1.0 H5'' N:A186 4.1 22.5 1.0 O3' N:A187 4.2 47.3 1.0 C3' N:A186 4.2 39.3 1.0 OP2 N:A186 4.2 65.0 1.0 O3' N:A186 4.3 73.7 1.0 C5' N:A187 4.3 20.9 1.0 H5'' N:A183 4.3 15.2 1.0 O5' N:A187 4.4 73.2 1.0 O5' N:A186 4.4 38.1 1.0 C4' N:A187 4.5 24.7 1.0 O5' N:A184 4.5 63.2 1.0 OP1 N:A187 4.6 48.6 1.0 H5'' N:A184 4.6 24.2 1.0 C4' N:U185 4.7 35.7 1.0 C5' N:A186 4.7 22.5 1.0 O3' N:U185 4.7 80.5 1.0 H3' N:U185 4.8 41.0 1.0 C3' N:A187 4.8 48.7 1.0 C5' N:U185 4.8 33.5 1.0 OP1 N:A183 4.8 25.1 1.0 C3' N:U185 4.9 41.0 1.0 H2' N:A186 5.0 25.7 1.0 C5' N:A184 5.0 24.2 1.0 HO2' N:U182 5.0 15.3 1.0

Magnesium binding site 4 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:39.0 occ:1.00 N7 N:G96 2.4 27.3 1.0 C8 N:G96 3.2 17.9 1.0 C6 N:U300 3.2 22.3 1.0 H8 N:G96 3.2 17.9 1.0 H5' N:U300 3.3 37.0 1.0 N1 N:A299 3.3 25.7 1.0 C5 N:U300 3.3 21.2 1.0 C2 N:A299 3.4 16.6 1.0 N1 N:U300 3.5 26.1 1.0 C6 N:A299 3.5 22.5 1.0 H6 N:U300 3.5 22.3 1.0 C5 N:G96 3.5 23.9 1.0 C4 N:U300 3.7 13.6 1.0 H5 N:U300 3.7 21.2 1.0 N3 N:A299 3.7 20.0 1.0 C5 N:A299 3.7 25.2 1.0 C2 N:U300 3.8 20.3 1.0 C4 N:A299 3.8 21.9 1.0 O4' N:U300 3.8 51.8 1.0 H2 N:A299 3.8 16.6 1.0 N3 N:U300 3.9 20.6 1.0 H2' N:A299 3.9 20.1 1.0 H5'' N:U300 3.9 37.0 1.0 H1 N:G279 3.9 27.2 1.0 O6 N:G96 4.0 28.7 1.0 N6 N:A299 4.0 18.3 1.0 C5' N:U300 4.1 37.0 1.0 C6 N:G96 4.1 16.2 1.0 H21 N:G279 4.2 16.1 1.0 C1' N:U300 4.3 37.5 1.0 H62 N:A299 4.3 18.3 1.0 O4 N:U300 4.4 25.1 1.0 N9 N:G96 4.5 30.1 1.0 O2 N:U300 4.5 21.8 1.0 H3 N:U300 4.6 20.6 1.0 H61 N:A299 4.6 18.3 1.0 N7 N:A299 4.6 18.1 1.0 C4' N:U300 4.6 24.5 1.0 N9 N:A299 4.6 20.9 1.0 C4 N:G96 4.6 21.0 1.0 N1 N:G279 4.7 27.2 1.0 H2' N:U300 4.8 21.9 1.0 MG N:MG530 4.8 18.9 1.0 OP2 N:U300 4.9 36.8 1.0 H3' N:A299 4.9 42.9 1.0 C2' N:A299 4.9 20.1 1.0 N2 N:G279 5.0 16.1 1.0 OP2 N:G96 5.0 94.8 1.0 C8 N:A299 5.0 19.0 1.0

Magnesium binding site 5 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:18.9 occ:1.00 OP2 N:A302 2.0 45.6 1.0 OP1 N:A301 2.1 77.5 1.0 O N:HOH618 2.8 12.9 1.0 H21 N:G303 2.8 12.2 1.0 H62 N:A256 3.2 15.5 1.0 H1 N:G303 3.3 30.1 1.0 HO2' N:U300 3.3 22.3 1.0 P N:A302 3.4 12.0 1.0 H4' N:U271 3.5 20.1 1.0 P N:A301 3.5 14.2 1.0 H3' N:A301 3.6 38.6 1.0 H5'' N:A301 3.8 50.2 1.0 H3' N:U300 3.8 27.1 1.0 N2 N:G303 3.8 12.2 1.0 O N:HOH861 3.9 17.5 1.0 O5' N:A301 4.0 41.1 1.0 N1 N:G303 4.1 30.1 1.0 O3' N:A301 4.1 75.5 1.0 N6 N:A256 4.2 15.5 1.0 OP1 N:A302 4.2 49.7 1.0 OP1 N:G272 4.2 74.2 1.0 N1 N:A256 4.2 41.9 1.0 O2' N:U300 4.3 22.3 1.0 C3' N:A301 4.3 38.6 1.0 OP2 N:A301 4.4 38.1 1.0 O5' N:A302 4.4 45.6 1.0 O4' N:U271 4.4 31.7 1.0 C5' N:A301 4.4 50.2 1.0 C4' N:U271 4.4 20.1 1.0 H8 N:A302 4.4 20.0 1.0 C3' N:U300 4.5 27.1 1.0 C2 N:G303 4.5 18.4 1.0 O3' N:U300 4.5 72.2 1.0 H22 N:G303 4.5 12.2 1.0 O3' N:U271 4.7 90.8 1.0 C6 N:A256 4.7 19.8 1.0 C2' N:U300 4.8 21.9 1.0 O N:HOH666 4.9 21.6 1.0 H61 N:A256 4.9 15.5 1.0 H5' N:U271 4.9 17.6 1.0 OP1 N:U300 4.9 90.0 1.0 H1' N:U271 4.9 22.3 1.0 H2' N:U300 4.9 21.9 1.0

Magnesium binding site 6 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:25.4 occ:1.00 OP2 N:U259 2.4 25.4 1.0 OP1 N:U258 2.6 112.7 1.0 H5'' N:U258 2.7 20.5 1.0 OP2 N:A261 3.0 29.4 1.0 HO2' N:C260 3.1 20.6 1.0 O N:HOH824 3.1 27.4 1.0 P N:U258 3.5 22.0 1.0 C5' N:U258 3.6 20.5 1.0 O5' N:U258 3.6 27.0 1.0 P N:U259 3.7 14.5 1.0 O3' N:C260 3.7 51.2 1.0 P N:A261 3.8 12.6 1.0 O2' N:C260 3.8 20.6 1.0 O N:HOH607 3.8 21.4 1.0 N7 N:A306 3.9 20.4 1.0 H8 N:A306 4.1 12.3 1.0 OP1 N:U259 4.1 99.6 1.0 C8 N:A306 4.2 12.3 1.0 OP1 N:A261 4.2 49.2 1.0 OP2 N:U258 4.2 48.4 1.0 H5' N:U258 4.2 20.5 1.0 MG N:MG510 4.3 40.2 1.0 H3' N:U258 4.3 39.7 1.0 H3' N:C260 4.4 46.3 1.0 O3' N:U258 4.4 39.1 1.0 C3' N:C260 4.5 46.3 1.0 C3' N:U258 4.6 39.7 1.0 C4' N:U258 4.7 36.5 1.0 C2' N:C260 4.7 32.2 1.0 C5 N:A306 4.8 33.0 1.0 H5'' N:A306 4.8 28.2 1.0 O3' N:G257 4.9 48.1 1.0 O5' N:U259 4.9 44.6 1.0 O N:HOH635 4.9 14.4 1.0

Magnesium binding site 7 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:27.0 occ:1.00 OP1 N:U273 1.9 60.2 1.0 OP1 N:A256 2.4 60.6 1.0 P N:U273 3.3 13.2 1.0 H8 N:A256 3.5 15.2 1.0 H5'' N:U273 3.6 17.1 1.0 P N:A256 3.7 11.4 1.0 O3' N:C255 4.0 76.4 1.0 O N:HOH888 4.0 33.7 1.0 H4' N:C255 4.1 21.4 1.0 OP2 N:U273 4.1 54.1 1.0 O5' N:U273 4.1 49.7 1.0 MG N:MG527 4.1 25.2 1.0 OP2 N:C274 4.1 39.0 1.0 N7 N:A256 4.2 24.6 1.0 C8 N:A256 4.2 15.2 1.0 O3' N:G272 4.3 55.5 1.0 C5' N:U273 4.3 17.1 1.0 O N:HOH836 4.3 17.7 1.0 O N:HOH811 4.5 25.7 1.0 O N:HOH834 4.5 22.0 1.0 O5' N:A256 4.6 48.0 1.0 MG N:MG515 4.6 17.3 1.0 O N:HOH796 4.7 29.7 1.0 H5' N:U273 4.7 17.1 1.0 OP2 N:A256 4.8 60.9 1.0 O N:HOH833 4.9 25.8 1.0

Magnesium binding site 8 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:16.7 occ:1.00 OP1 N:A304 1.9 42.1 1.0 OP1 N:A306 2.0 37.7 1.0 P N:A304 3.3 8.0 1.0 P N:A306 3.4 13.1 1.0 H3' N:U305 3.5 51.1 1.0 H5'' N:A304 3.7 35.5 1.0 OP1 N:C208 3.9 128.6 1.0 O5' N:A304 4.0 37.4 1.0 O3' N:U305 4.1 78.4 1.0 O N:HOH814 4.2 23.5 1.0 OP2 N:A304 4.2 61.7 1.0 OP2 N:A306 4.2 54.5 1.0 C3' N:U305 4.2 51.1 1.0 O N:HOH664 4.3 22.9 1.0 O3' N:G303 4.3 60.6 1.0 O5' N:A306 4.4 33.1 1.0 OP1 N:U307 4.4 59.4 1.0 C5' N:A304 4.4 35.5 1.0 HO2' N:U305 4.5 18.8 1.0 O N:HOH715 4.6 19.5 1.0 H5' N:A304 4.9 35.5 1.0 O N:HOH627 4.9 15.4 1.0 O2' N:U305 4.9 18.8 1.0

Magnesium binding site 9 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:15.1 occ:1.00 OP2 N:A308 2.3 36.2 1.0 OP2 N:U307 2.4 50.9 1.0 MG N:MG512 2.7 25.0 1.0 H3' N:U307 3.4 35.6 1.0 P N:U307 3.7 12.3 1.0 O3' N:A306 3.8 49.5 1.0 P N:A308 3.8 16.4 1.0 O N:HOH693 3.8 12.0 1.0 H8 N:A308 3.9 20.2 1.0 O N:HOH670 4.0 14.6 1.0 N7 N:A308 4.2 27.1 1.0 C3' N:U307 4.3 35.6 1.0 O N:HOH691 4.3 19.8 1.0 C8 N:A308 4.4 20.2 1.0 O3' N:U307 4.4 65.8 1.0 O5' N:A308 4.5 47.5 1.0 O5' N:U307 4.5 29.6 1.0 O2' N:A306 4.7 23.1 1.0 OP1 N:A308 4.8 110.4 1.0 OP1 N:U307 4.8 59.4 1.0 N7 N:G309 4.9 16.3 1.0 H1' N:A306 4.9 19.9 1.0 H5'' N:U307 5.0 32.9 1.0 H2' N:U307 5.0 26.8 1.0

Magnesium binding site 10 out of 56 in the Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tetrahymena Ribozyme with Automatically Identified Water and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:40.2 occ:1.00 OP1 N:U259 2.0 99.6 1.0 H61 N:A306 3.2 13.9 1.0 P N:U259 3.3 14.5 1.0 OP1 N:A261 3.7 49.2 1.0 N7 N:A261 3.7 20.9 1.0 OP2 N:U259 3.7 25.4 1.0 H8 N:A261 3.8 25.4 1.0 O N:HOH824 3.8 27.4 1.0 N7 N:A306 3.8 20.4 1.0 C8 N:A261 4.0 25.4 1.0 H5' N:G264 4.2 28.0 1.0 O3' N:U258 4.2 39.1 1.0 N6 N:A306 4.2 13.9 1.0 H3' N:C260 4.2 46.3 1.0 MG N:MG506 4.3 25.4 1.0 O5' N:U259 4.3 44.6 1.0 OP2 N:A265 4.5 37.0 1.0 O N:HOH662 4.5 14.0 1.0 H5'' N:U259 4.6 20.0 1.0 C5 N:A306 4.7 33.0 1.0 H2' N:U106 4.7 24.2 1.0 H5'' N:G264 4.7 28.0 1.0 P N:A261 4.7 12.6 1.0 C5 N:A261 4.8 34.4 1.0 H5' N:U259 4.8 20.0 1.0 C5' N:U259 4.8 20.0 1.0 C8 N:A306 4.8 12.3 1.0 H61 N:A261 4.8 17.7 1.0 O2' N:U106 4.9 18.2 1.0 HO2' N:U106 4.9 18.2 1.0 C6 N:A306 4.9 18.8 1.0 H62 N:A306 4.9 13.9 1.0 H8 N:A306 5.0 12.3 1.0 C5' N:G264 5.0 28.0 1.0

R.C.Kretsch, S.Li, G.Pintilie, M.Z.Palo, D.A.Case, R.Das, W.Chiu. Complex Water Networks Visualized Through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of Rna To Be Published.