Magnesium in PDB 8i7n: The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside (pdb code 8i7n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside, PDB code: 8i7n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:27.4 occ:0.77 N7 N:G112 3.9 28.6 1.0 N7 N:G111 4.1 28.6 1.0 O6 N:G112 4.3 28.6 1.0 O6 N:G111 4.4 28.6 1.0 N6 N:A113 4.7 28.6 1.0 C5 N:G111 4.8 28.6 1.0 C5 N:G112 4.8 28.6 1.0 C8 N:G112 4.9 28.6 1.0 C6 N:G111 4.9 28.6 1.0 C6 N:G112 4.9 28.6 1.0 C8 N:G111 5.0 28.6 1.0

Magnesium binding site 2 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:22.2 occ:1.00 OP1 N:A207 2.1 21.1 1.0 OP2 N:C262 2.3 30.0 1.0 P N:A207 3.4 21.1 1.0 P N:C262 3.6 30.0 1.0 OP2 N:A207 4.0 21.1 1.0 OP1 N:C262 4.1 30.0 1.0 O2 N:U305 4.2 28.6 1.0 O3' N:A206 4.3 28.6 1.0 C3' N:A261 4.4 28.6 1.0 O3' N:A261 4.4 28.6 1.0 O2' N:U305 4.4 28.6 1.0 O5' N:A207 4.5 21.1 1.0 O5' N:C262 4.7 30.0 1.0 C5' N:A207 4.8 21.1 1.0 C5' N:C262 5.0 30.0 1.0

Magnesium binding site 3 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:18.2 occ:0.87 O6 N:G116 3.7 28.6 1.0 N7 N:G116 3.9 28.6 1.0 N7 N:A115 4.1 28.6 1.0 O6 N:G117 4.1 24.3 1.0 C6 N:G116 4.5 28.6 1.0 C5 N:G116 4.6 28.6 1.0 O4 N:U205 4.6 28.6 1.0 C8 N:A115 4.8 28.6 1.0 OP2 N:A115 4.9 28.6 1.0 C5 N:A115 4.9 28.6 1.0 N4 N:C204 4.9 28.6 1.0 C8 N:G116 5.0 28.6 1.0

Magnesium binding site 4 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:19.3 occ:0.78 OP1 N:A184 2.0 28.6 1.0 OP2 N:A187 2.0 28.6 1.0 OP1 N:A186 2.0 28.6 1.0 P N:A184 3.4 28.6 1.0 P N:A187 3.5 28.6 1.0 P N:A186 3.5 28.6 1.0 OP1 N:G188 3.7 28.6 1.0 OP2 N:G188 4.0 28.6 1.0 C5' N:A187 4.1 28.6 1.0 OP2 N:A184 4.1 28.6 1.0 OP2 N:A186 4.2 28.6 1.0 OP1 N:A187 4.2 28.6 1.0 O3' N:A183 4.3 28.6 1.0 P N:G188 4.3 28.6 1.0 O5' N:A187 4.3 28.6 1.0 O5' N:A186 4.3 28.6 1.0 O5' N:A184 4.3 28.6 1.0 O3' N:U185 4.4 25.5 1.0 C3' N:A186 4.4 28.6 1.0 O3' N:A186 4.4 28.6 1.0 C5' N:A186 4.5 28.6 1.0 C4' N:U185 4.7 25.5 1.0 O3' N:A187 4.7 28.6 1.0 C3' N:U185 4.8 25.5 1.0 C4' N:A187 4.8 28.6 1.0 OP1 N:A183 4.9 28.6 1.0 C5' N:U185 5.0 25.5 1.0

Magnesium binding site 5 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:19.5 occ:0.85 OP1 N:A183 2.2 28.6 1.0 OP2 N:A184 2.4 28.6 1.0 OP2 N:A186 2.5 28.6 1.0 P N:A183 3.6 28.6 1.0 P N:A184 3.9 28.6 1.0 P N:A186 3.9 28.6 1.0 OP2 N:A183 4.1 28.6 1.0 N7 N:A184 4.2 28.6 1.0 O5' N:A183 4.4 28.6 1.0 C3' N:A183 4.5 28.6 1.0 C8 N:A184 4.5 28.6 1.0 OP1 N:A186 4.5 28.6 1.0 OP1 N:A184 4.6 28.6 1.0 N7 N:A186 4.6 28.6 1.0 O3' N:U182 4.7 28.6 1.0 O3' N:A183 4.7 28.6 1.0 O5' N:A184 4.7 28.6 1.0 C8 N:A186 4.8 28.6 1.0 O3' N:U185 4.8 25.5 1.0 C3' N:U185 4.8 25.5 1.0 O5' N:A186 4.8 28.6 1.0 C5' N:A183 4.9 28.6 1.0

Magnesium binding site 6 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:17.3 occ:0.81 O6 N:G188 2.2 28.6 1.0 C6 N:G188 3.2 28.6 1.0 N7 N:G188 3.8 28.6 1.0 C5 N:G188 3.9 28.6 1.0 OP1 N:C165 4.2 28.6 1.0 OP2 N:C166 4.4 28.6 1.0 N1 N:G188 4.4 28.6 1.0 OP2 N:A183 4.4 28.6 1.0 OP2 N:U168 4.5 28.6 1.0 OP1 N:U168 4.5 28.6 1.0 OP1 N:C166 4.6 28.6 1.0 N7 N:A183 4.7 28.6 1.0 OP1 N:U182 4.7 28.6 1.0 C8 N:A183 4.8 28.6 1.0 P N:C166 4.8 28.6 1.0 P N:U168 5.0 28.6 1.0

Magnesium binding site 7 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:25.7 occ:0.84 O6 N:G164 2.8 28.6 1.0 N7 N:G163 3.1 28.6 1.0 C6 N:G164 3.8 28.6 1.0 C8 N:G163 3.8 28.6 1.0 C5 N:G163 4.1 28.6 1.0 OP2 N:U162 4.3 34.2 1.0 OP2 N:G163 4.3 28.6 1.0 O6 N:G163 4.3 28.6 1.0 C5 N:G164 4.6 28.6 1.0 C6 N:G163 4.6 28.6 1.0 N7 N:G164 4.6 28.6 1.0 N6 N:A178 4.7 42.4 1.0 N7 N:A178 4.7 42.4 1.0 O5' N:U162 4.8 34.2 1.0 N1 N:G164 4.8 28.6 1.0 C5 N:U162 4.9 34.2 1.0

Magnesium binding site 8 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:25.0 occ:0.78 OP2 N:A140 3.1 28.6 1.0 N7 N:G141 3.4 28.6 1.0 O4 N:U142 3.7 32.4 1.0 O6 N:G141 4.0 28.6 1.0 C5 N:G141 4.2 28.6 1.0 P N:A140 4.3 28.6 1.0 C8 N:G141 4.3 28.6 1.0 C6 N:G141 4.5 28.6 1.0 O5' N:A140 4.5 28.6 1.0 C4 N:U142 4.6 32.4 1.0 OP1 N:A140 4.8 28.6 1.0 C5 N:U142 4.9 32.4 1.0 N6 N:A161 4.9 41.0 1.0

Magnesium binding site 9 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:31.9 occ:0.80 O6 N:G148 2.9 51.4 1.0 O6 N:G149 3.5 45.6 1.0 C6 N:G148 3.8 51.4 1.0 N7 N:G148 3.8 51.4 1.0 O4 N:U155 4.1 36.4 1.0 C5 N:G148 4.1 51.4 1.0 O6 N:G147 4.3 56.5 1.0 C6 N:G149 4.5 45.6 1.0 N7 N:G149 4.7 45.6 1.0 N3 N:U155 4.7 36.4 1.0 N4 N:C154 4.7 35.1 1.0 C4 N:U155 4.8 36.4 1.0 C6 N:G147 4.8 56.5 1.0 C5 N:G149 4.9 45.6 1.0 N1 N:G148 5.0 51.4 1.0

Magnesium binding site 10 out of 27 in the The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:32.4 occ:1.00 N7 N:G150 4.0 40.7 1.0 OP2 N:A151 4.2 37.7 1.0 C8 N:G150 4.4 40.7 1.0 OP2 N:G150 4.5 40.7 1.0 C5' N:A151 4.5 37.7 1.0 OP2 N:A152 4.7 36.1 1.0 O5' N:A151 4.7 37.7 1.0 C5 N:G150 4.8 40.7 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