Magnesium in PDB 7xd6: The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon (pdb code 7xd6). 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon, PDB code: 7xd6:
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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:20.7 occ:0.77 N7 N:G111 4.3 27.1 1.0 O6 N:G111 4.3 27.1 1.0 O6 N:G112 4.5 28.7 1.0 N7 N:G112 4.6 28.7 1.0 O6 N:G110 4.9 25.9 1.0 N7 N:G110 5.0 25.9 1.0 C6 N:G111 5.0 27.1 1.0 C5 N:G111 5.0 27.1 1.0

Magnesium binding site 2 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:29.4 occ:1.00 OP2 N:C262 2.0 33.0 1.0 OP1 N:A207 2.2 31.0 1.0 P N:C262 3.4 33.0 1.0 P N:A207 3.6 31.0 1.0 O5' N:C262 3.7 33.0 1.0 O3' N:A206 4.2 34.3 1.0 OP2 N:A263 4.2 32.2 1.0 OP1 N:C262 4.3 33.0 1.0 OP2 N:A207 4.3 31.0 1.0 O3' N:A261 4.5 24.8 1.0 C3' N:A261 4.5 24.8 1.0 O5' N:A207 4.7 31.0 1.0 O2 N:U305 4.8 21.6 1.0 C5' N:A207 4.9 31.0 1.0 C5' N:C262 5.0 33.0 1.0

Magnesium binding site 3 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:40.4 occ:0.87 O6 N:G116 4.0 45.3 1.0 O4 N:U205 4.3 40.5 1.0 N7 N:G116 4.4 45.3 1.0 OP2 N:A114 4.4 37.0 1.0 O6 N:G117 4.5 47.4 1.0 OP2 N:A115 4.5 41.8 1.0 N7 N:A115 4.5 41.8 1.0 C6 N:G116 4.9 45.3 1.0 N4 N:C204 4.9 45.0 1.0

Magnesium binding site 4 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:37.6 occ:0.78 OP2 N:A187 2.0 49.2 1.0 OP1 N:A184 2.0 27.5 1.0 OP1 N:A186 2.3 42.0 1.0 OP2 N:G188 3.1 39.9 1.0 P N:A184 3.4 27.5 1.0 P N:A187 3.4 49.2 1.0 P N:G188 3.7 39.9 1.0 P N:A186 3.8 42.0 1.0 OP1 N:G188 3.8 39.9 1.0 O3' N:A187 3.9 49.2 1.0 O3' N:A183 4.0 30.7 1.0 O5' N:A187 4.0 49.2 1.0 OP2 N:A184 4.1 27.5 1.0 C5' N:A187 4.2 49.2 1.0 OP1 N:A187 4.2 49.2 1.0 O5' N:A184 4.4 27.5 1.0 O3' N:A186 4.5 42.0 1.0 OP2 N:A186 4.5 42.0 1.0 O5' N:A186 4.5 42.0 1.0 C3' N:A186 4.6 42.0 1.0 C5' N:A186 4.7 42.0 1.0 C3' N:A187 4.7 49.2 1.0 C4' N:A187 4.8 49.2 1.0 O3' N:U185 4.8 36.2 1.0 C5' N:A184 4.8 27.5 1.0

Magnesium binding site 5 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:30.2 occ:0.85 OP2 N:A184 2.1 27.5 1.0 OP2 N:A186 2.2 42.0 1.0 OP1 N:A183 2.2 30.7 1.0 P N:A186 3.6 42.0 1.0 P N:A184 3.6 27.5 1.0 P N:A183 3.6 30.7 1.0 O5' N:A183 4.2 30.7 1.0 OP1 N:A186 4.3 42.0 1.0 C3' N:A183 4.4 30.7 1.0 N7 N:A184 4.4 27.5 1.0 OP2 N:A183 4.4 30.7 1.0 O5' N:A186 4.4 42.0 1.0 O5' N:A184 4.4 27.5 1.0 OP1 N:A184 4.5 27.5 1.0 O3' N:A183 4.5 30.7 1.0 N7 N:A186 4.6 42.0 1.0 C8 N:A186 4.6 42.0 1.0 C8 N:A184 4.6 27.5 1.0 O3' N:U185 4.6 36.2 1.0 O3' N:U182 4.7 42.8 1.0 C5' N:A183 4.8 30.7 1.0 C3' N:U185 4.8 36.2 1.0 C2 N:A139 4.9 45.2 1.0

Magnesium binding site 6 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:25.9 occ:0.81 N7 N:G188 3.5 39.9 1.0 O6 N:G188 4.0 39.9 1.0 OP2 N:U168 4.2 35.6 1.0 OP1 N:U168 4.3 35.6 1.0 C5 N:G188 4.4 39.9 1.0 OP1 N:C165 4.4 44.7 1.0 OP2 N:A183 4.4 30.7 1.0 C8 N:G188 4.5 39.9 1.0 C6 N:G188 4.6 39.9 1.0 C8 N:A183 4.6 30.7 1.0 N7 N:A183 4.6 30.7 1.0 P N:U168 4.8 35.6 1.0 OP2 N:C166 4.8 44.3 1.0 OP1 N:U182 4.9 42.8 1.0 OP1 N:C166 4.9 44.3 1.0

Magnesium binding site 7 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:41.1 occ:0.84 O6 N:G164 2.2 46.9 1.0 N7 N:G163 2.7 50.3 1.0 C6 N:G164 3.2 46.9 1.0 C8 N:G163 3.6 50.3 1.0 C5 N:G163 3.7 50.3 1.0 O6 N:G163 3.9 50.3 1.0 C5 N:G164 4.0 46.9 1.0 N7 N:G164 4.1 46.9 1.0 C6 N:G163 4.1 50.3 1.0 OP2 N:G163 4.2 50.3 1.0 N1 N:G164 4.3 46.9 1.0 N7 N:A178 4.5 59.0 1.0 OP2 N:U162 4.5 57.4 1.0 N6 N:A178 4.6 59.0 1.0 N9 N:G163 4.7 50.3 1.0 C4 N:G163 4.8 50.3 1.0

Magnesium binding site 8 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:47.7 occ:0.78 OP2 N:A140 3.1 46.8 1.0 N7 N:G141 3.4 52.1 1.0 O4 N:U142 3.9 58.6 1.0 P N:A140 4.1 46.8 1.0 O6 N:G141 4.2 52.1 1.0 C8 N:G141 4.2 52.1 1.0 C5 N:G141 4.3 52.1 1.0 O5' N:A140 4.3 46.8 1.0 OP1 N:A140 4.5 46.8 1.0 C6 N:G141 4.6 52.1 1.0 OP2 N:G141 4.6 52.1 1.0 C4 N:U142 4.7 58.6 1.0 C5 N:U142 4.9 58.6 1.0

Magnesium binding site 9 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:80.3 occ:0.80 O6 N:G148 3.0 78.3 1.0 N7 N:G148 3.3 78.3 1.0 C6 N:G148 3.7 78.3 1.0 C5 N:G148 3.8 78.3 1.0 O6 N:G149 3.9 75.0 1.0 O4 N:U155 4.3 69.0 1.0 O6 N:G147 4.4 80.5 1.0 C8 N:G148 4.5 78.3 1.0 C6 N:G147 4.7 80.5 1.0 N7 N:G149 4.7 75.0 1.0 C6 N:G149 4.8 75.0 1.0 N1 N:G148 5.0 78.3 1.0 N7 N:G147 5.0 80.5 1.0 C5 N:G147 5.0 80.5 1.0

Magnesium binding site 10 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 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 Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:74.3 occ:0.87 OP2 N:G150 2.0 73.9 1.0 P N:G150 3.2 73.9 1.0 O5' N:G150 3.5 73.9 1.0 OP1 N:G150 4.0 73.9 1.0 C8 N:G150 4.2 73.9 1.0 N7 N:G150 4.3 73.9 1.0 OP2 N:A151 4.3 75.4 1.0 O3' N:G149 4.4 75.0 1.0 C3' N:G149 4.7 75.0 1.0 OP2 N:G149 4.8 75.0 1.0 C5' N:G150 4.9 73.9 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