Magnesium in PDB 7xd4: The Intermediate Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon

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>>> 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 Intermediate Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon (pdb code 7xd4). 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 Intermediate Pre-Tet-S1 State of Wild-Type Tetrahymena Group I Intron with 6NT 3'/5'-Exon, PDB code: 7xd4:
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 Intermediate 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 Intermediate 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:44.9 occ:0.77 O6 N:G111 4.8 56.8 1.0 N7 N:G111 4.9 56.8 1.0

Magnesium binding site 2 out of 28 in the The Intermediate 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 Intermediate 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:73.6 occ:1.00 OP2 N:C262 2.2 74.8 1.0 OP1 N:A207 2.9 75.4 1.0 P N:C262 3.5 74.8 1.0 O2 N:U305 3.6 51.3 1.0 OP1 N:C262 4.0 74.8 1.0 P N:A207 4.2 75.4 1.0 O3' N:A261 4.5 58.3 1.0 C3' N:A261 4.6 58.3 1.0 O2' N:U305 4.6 51.3 1.0 O5' N:C262 4.6 74.8 1.0 C2 N:U305 4.7 51.3 1.0 O3' N:A206 4.8 72.0 1.0 C5' N:C262 4.8 74.8 1.0 OP2 N:A207 4.9 75.4 1.0 OP2 N:A263 5.0 71.0 1.0

Magnesium binding site 3 out of 28 in the The Intermediate 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 Intermediate 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:63.0 occ:0.87 OP2 N:A114 2.5 79.7 1.0 P N:A114 3.5 79.7 1.0 OP1 N:A114 3.7 79.7 1.0 O6 N:G116 4.1 86.8 1.0 C2 N:A206 4.2 72.0 1.0 O4 N:U205 4.3 81.0 1.0 O5' N:A114 4.5 79.7 1.0 N1 N:A206 4.6 72.0 1.0 O3' N:A113 4.7 72.2 1.0 N7 N:G116 4.8 86.8 1.0 O6 N:G117 5.0 89.4 1.0

Magnesium binding site 4 out of 28 in the The Intermediate 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 Intermediate 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:97.4 occ:0.85 OP1 N:A183 2.1 54.2 1.0 OP2 N:A186 2.1 68.3 1.0 OP2 N:A184 2.1 48.3 1.0 C5' N:A183 2.4 54.2 1.0 P N:A186 3.1 68.3 1.0 P N:A183 3.2 54.2 1.0 O5' N:A183 3.2 54.2 1.0 P N:A184 3.3 48.3 1.0 OP1 N:A186 3.5 68.3 1.0 C4' N:A183 3.6 54.2 1.0 OP1 N:A184 3.7 48.3 1.0 O5' N:A186 3.8 68.3 1.0 C3' N:A183 4.0 54.2 1.0 O3' N:U182 4.1 75.7 1.0 O3' N:A183 4.1 54.2 1.0 OP2 N:A183 4.3 54.2 1.0 N7 N:A184 4.4 48.3 1.0 O3' N:U185 4.5 49.6 1.0 O5' N:A184 4.5 48.3 1.0 N7 N:A186 4.5 68.3 1.0 C8 N:A186 4.6 68.3 1.0 C8 N:A184 4.6 48.3 1.0 O4' N:A183 4.7 54.2 1.0 OP2 N:A187 4.8 82.9 1.0

Magnesium binding site 5 out of 28 in the The Intermediate 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 Intermediate 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:97.4 occ:0.81 N7 N:G188 3.2 66.7 1.0 C8 N:G188 3.9 66.7 1.0 OP1 N:C166 4.2 90.0 1.0 N7 N:A183 4.2 54.2 1.0 C5 N:G188 4.2 66.7 1.0 C8 N:A183 4.2 54.2 1.0 O6 N:G188 4.4 66.7 1.0 OP1 N:C165 4.5 89.0 1.0 OP1 N:U168 4.5 65.4 1.0 OP2 N:A183 4.6 54.2 1.0 OP2 N:U168 4.6 65.4 1.0 C6 N:G188 4.7 66.7 1.0 O3' N:C165 4.7 89.0 1.0 P N:C166 4.8 90.0 1.0 OP2 N:C166 5.0 90.0 1.0

Magnesium binding site 6 out of 28 in the The Intermediate 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 Intermediate 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:91.7 occ:0.84 O6 N:G164 2.0 90.6 1.0 OP2 N:A178 2.1 102.2 1.0 N7 N:G164 2.7 90.6 1.0 C6 N:G164 2.7 90.6 1.0 C5 N:G164 3.0 90.6 1.0 N7 N:G163 3.3 97.8 1.0 P N:A178 3.5 102.2 1.0 C8 N:G163 3.9 97.8 1.0 C5 N:G163 3.9 97.8 1.0 O3' N:U177 3.9 106.2 1.0 C8 N:G164 4.0 90.6 1.0 N1 N:G164 4.0 90.6 1.0 O6 N:G163 4.3 97.8 1.0 C4 N:G164 4.3 90.6 1.0 C6 N:G163 4.3 97.8 1.0 O5' N:A178 4.4 102.2 1.0 OP1 N:A178 4.5 102.2 1.0 C8 N:A178 4.7 102.2 1.0 N9 N:G163 4.8 97.8 1.0 C4 N:G163 4.8 97.8 1.0 N7 N:A178 4.8 102.2 1.0 N9 N:G164 4.8 90.6 1.0 OP2 N:G163 4.8 97.8 1.0 C3' N:U177 4.9 106.2 1.0

Magnesium binding site 7 out of 28 in the The Intermediate 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 Intermediate 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:66.0 occ:0.78 OP2 N:A140 3.3 90.4 1.0 OP2 N:G141 3.7 98.7 1.0 O4 N:U142 3.8 106.3 1.0 N7 N:G141 3.8 98.7 1.0 P N:A140 4.1 90.4 1.0 O5' N:A140 4.2 90.4 1.0 C5 N:U142 4.2 106.3 1.0 C4 N:U142 4.4 106.3 1.0 OP1 N:A140 4.5 90.4 1.0 C8 N:G141 4.5 98.7 1.0 C5 N:G141 4.9 98.7 1.0 O6 N:G141 4.9 98.7 1.0

Magnesium binding site 8 out of 28 in the The Intermediate 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 Intermediate 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:122.3 occ:0.80 N7 N:G148 2.2 119.6 1.0 O6 N:G148 2.4 119.6 1.0 C5 N:G148 2.6 119.6 1.0 C6 N:G148 2.7 119.6 1.0 C8 N:G148 3.4 119.6 1.0 O6 N:G149 3.7 118.5 1.0 N7 N:G149 3.8 118.5 1.0 C6 N:G147 3.9 122.1 1.0 C4 N:G148 3.9 119.6 1.0 O6 N:G147 3.9 122.1 1.0 N1 N:G148 4.0 119.6 1.0 N1 N:G147 4.2 122.1 1.0 N9 N:G148 4.3 119.6 1.0 C5 N:G147 4.3 122.1 1.0 C6 N:G149 4.4 118.5 1.0 C5 N:G149 4.4 118.5 1.0 O4 N:U155 4.5 110.3 1.0 O6 N:G150 4.6 117.6 1.0 N7 N:G147 4.7 122.1 1.0 C4 N:G147 4.9 122.1 1.0 C2 N:G147 4.9 122.1 1.0 C8 N:G149 4.9 118.5 1.0 C2 N:G148 5.0 119.6 1.0 N3 N:G148 5.0 119.6 1.0

Magnesium binding site 9 out of 28 in the The Intermediate 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 Intermediate 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:33.5 occ:0.88 OP1 N:U273 2.6 38.0 1.0 OP1 N:A256 2.8 34.6 1.0 P N:U273 3.9 38.0 1.0 C5' N:U273 4.0 38.0 1.0 P N:A256 4.1 34.6 1.0 O5' N:U273 4.2 38.0 1.0 O3' N:C255 4.3 36.7 1.0 N7 N:A256 4.3 34.6 1.0 C8 N:A256 4.4 34.6 1.0 OP2 N:C274 4.4 43.1 1.0 O3' N:G272 4.6 36.8 1.0 O3' N:U273 4.8 38.0 1.0

Magnesium binding site 10 out of 28 in the The Intermediate 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 Intermediate 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:97.4 occ:1.00 O6 N:G276 4.8 60.6 1.0 O4 N:U300 4.8 61.4 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