Magnesium in PDB 7xd3: The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Magnesium atom in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon (pdb code 7xd3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon, PDB code: 7xd3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:22.9 occ:0.77 O6 N:G110 4.3 21.2 1.0 O6 N:G111 4.6 26.6 1.0 C6 N:G110 5.0 21.2 1.0

Magnesium binding site 2 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:40.7 occ:1.00 OP2 N:C262 2.0 48.7 1.0 P N:C262 3.3 48.7 1.0 OP2 N:A263 3.5 50.6 1.0 C5' N:C262 3.6 48.7 1.0 O5' N:C262 3.7 48.7 1.0 OP1 N:A207 3.8 52.4 1.0 OP1 N:C262 4.1 48.7 1.0 C4' N:C262 4.5 48.7 1.0 O3' N:A261 4.5 31.4 1.0 C3' N:C262 4.6 48.7 1.0 C3' N:A261 4.7 31.4 1.0 O3' N:A206 4.8 46.8 1.0 P N:A263 4.9 50.6 1.0 O2 N:U305 4.9 28.2 1.0 P N:A207 5.0 52.4 1.0

Magnesium binding site 3 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:39.2 occ:0.87 O6 N:G116 3.8 56.2 1.0 N7 N:G116 3.9 56.2 1.0 OP2 N:A115 3.9 56.0 1.0 OP2 N:A114 4.1 54.6 1.0 OP1 N:A114 4.3 54.6 1.0 O6 N:G117 4.5 55.9 1.0 C6 N:G116 4.6 56.2 1.0 O4 N:U205 4.6 51.9 1.0 C5 N:G116 4.6 56.2 1.0 P N:A114 4.6 54.6 1.0 N7 N:A115 4.7 56.0 1.0 C8 N:G116 5.0 56.2 1.0

Magnesium binding site 4 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:13.4 occ:0.81 OP2 N:A184 2.4 30.2 1.0 OP2 N:A186 2.6 43.6 1.0 OP1 N:A183 2.6 29.4 1.0 C5' N:A183 2.9 29.4 1.0 P N:A183 3.7 29.4 1.0 O5' N:A183 3.7 29.4 1.0 P N:A184 3.8 30.2 1.0 P N:A186 4.0 43.6 1.0 N7 N:A184 4.0 30.2 1.0 C4' N:A183 4.0 29.4 1.0 C3' N:A183 4.0 29.4 1.0 O3' N:A183 4.3 29.4 1.0 C8 N:A184 4.4 30.2 1.0 OP1 N:A184 4.5 30.2 1.0 OP2 N:A183 4.5 29.4 1.0 OP1 N:A186 4.5 43.6 1.0 O5' N:A186 4.9 43.6 1.0 O4' N:A183 4.9 29.4 1.0 N7 N:A186 4.9 43.6 1.0 O5' N:A184 4.9 30.2 1.0 O3' N:U185 4.9 32.1 1.0 O3' N:U182 5.0 52.1 1.0

Magnesium binding site 5 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:13.4 occ:0.81 N7 N:G188 3.1 46.7 1.0 C8 N:G188 3.4 46.7 1.0 N7 N:A183 4.2 29.4 1.0 C8 N:A183 4.2 29.4 1.0 C5 N:G188 4.3 46.7 1.0 OP1 N:C166 4.4 69.3 1.0 OP2 N:A183 4.4 29.4 1.0 OP1 N:C165 4.4 65.6 1.0 OP1 N:U168 4.5 37.2 1.0 OP2 N:U168 4.7 37.2 1.0 N9 N:G188 4.7 46.7 1.0

Magnesium binding site 6 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:48.7 occ:0.78 OP2 N:A178 2.0 88.1 1.0 O6 N:G164 2.0 67.4 1.0 C6 N:G164 3.1 67.4 1.0 P N:A178 3.4 88.1 1.0 N7 N:G164 3.7 67.4 1.0 N7 N:G163 3.7 68.2 1.0 C5 N:G164 3.7 67.4 1.0 O3' N:U177 4.0 96.9 1.0 N7 N:A178 4.2 88.1 1.0 N1 N:G164 4.2 67.4 1.0 C8 N:A178 4.3 88.1 1.0 OP1 N:A178 4.3 88.1 1.0 O6 N:G163 4.3 68.2 1.0 O5' N:A178 4.4 88.1 1.0 C5 N:G163 4.4 68.2 1.0 C8 N:G163 4.5 68.2 1.0 C6 N:G163 4.7 68.2 1.0 OP2 N:U162 4.8 76.4 1.0 C3' N:U177 4.9 96.9 1.0

Magnesium binding site 7 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:48.7 occ:0.78 N7 N:G141 2.6 63.6 1.0 OP2 N:A140 3.3 53.8 1.0 O6 N:G141 3.4 63.6 1.0 O4 N:U142 3.5 75.9 1.0 C5 N:G141 3.5 63.6 1.0 C8 N:G141 3.6 63.6 1.0 C6 N:G141 3.8 63.6 1.0 N2 N:G163 3.9 68.2 1.0 C5 N:U142 3.9 75.9 1.0 C4 N:U142 4.0 75.9 1.0 P N:A140 4.3 53.8 1.0 O5' N:A140 4.4 53.8 1.0 N7 N:A140 4.4 53.8 1.0 C8 N:A140 4.5 53.8 1.0 O4 N:U162 4.5 76.4 1.0 C4 N:G141 4.7 63.6 1.0 OP2 N:G141 4.7 63.6 1.0 N9 N:G141 4.8 63.6 1.0 C2 N:G163 4.9 68.2 1.0

Magnesium binding site 8 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:68.9 occ:0.80 O4 N:U156 3.6 102.9 1.0 O4 N:U155 3.8 93.1 1.0 O6 N:G147 3.9 111.3 1.0 C4 N:U156 4.7 102.9 1.0 C4 N:U155 4.9 93.1 1.0 O6 N:G148 5.0 106.9 1.0

Magnesium binding site 9 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:75.3 occ:0.87 OP2 N:G150 2.1 97.5 1.0 P N:G150 3.5 97.5 1.0 OP2 N:G149 3.8 101.2 1.0 OP1 N:G149 3.9 101.2 1.0 O5' N:G150 4.0 97.5 1.0 P N:G149 4.1 101.2 1.0 O5' N:G149 4.2 101.2 1.0 OP1 N:G150 4.3 97.5 1.0 N7 N:G150 4.5 97.5 1.0 O3' N:G149 4.5 101.2 1.0 C8 N:G150 4.7 97.5 1.0 C3' N:G149 4.7 101.2 1.0

Magnesium binding site 10 out of 28 in the The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Relaxed Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:73.3 occ:0.88 OP1 N:A256 2.3 25.3 1.0 OP1 N:U273 2.7 14.9 1.0 P N:A256 3.7 25.3 1.0 P N:U273 4.1 14.9 1.0 O3' N:C255 4.2 18.4 1.0 C5' N:U273 4.4 14.9 1.0 O5' N:U273 4.6 14.9 1.0 O5' N:A256 4.6 25.3 1.0 OP2 N:A256 4.7 25.3 1.0 O3' N:G272 4.7 18.9 1.0 OP2 N:C274 4.7 18.8 1.0 C8 N:A256 5.0 25.3 1.0

B.Luo, C.Zhang, X.Ling, S.Mukherjee, G.Jia, J.Xie, X.Jia, L.Liu, E.F.Baulin, Y.Luo, L.Jiang, H.Dong, X.Wei, J.M.Bujnicki, Z.Su. Cryo-Em Reveals Dynamics of Tetrahymena Group I Intron Self-Splicing Nat Catal 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-00934-3