Magnesium in PDB 7xd5: The Tet-S2 State of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Magnesium atom in the The Tet-S2 State of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon (pdb code 7xd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 29 binding sites of Magnesium where determined in the The Tet-S2 State of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon, PDB code: 7xd5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 29 in the The Tet-S2 State 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 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:38.9 occ:0.77 O6 N:G111 4.3 49.3 1.0 N7 N:G111 4.5 49.3 1.0 O6 N:G112 4.5 53.5 1.0 N7 N:G112 4.8 53.5 1.0 O6 N:G110 5.0 46.4 1.0

Magnesium binding site 2 out of 29 in the The Tet-S2 State 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 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:56.2 occ:1.00 OP2 N:C262 2.0 56.3 1.0 OP1 N:A207 2.3 61.3 1.0 P N:C262 3.4 56.3 1.0 P N:A207 3.7 61.3 1.0 O5' N:C262 3.7 56.3 1.0 O3' N:A206 4.1 63.7 1.0 OP2 N:A263 4.2 54.4 1.0 OP1 N:C262 4.3 56.3 1.0 O3' N:A261 4.4 45.6 1.0 C3' N:A261 4.4 45.6 1.0 OP2 N:A207 4.5 61.3 1.0 O2 N:U305 4.6 43.5 1.0 O5' N:A207 4.7 61.3 1.0 C5' N:A207 5.0 61.3 1.0

Magnesium binding site 3 out of 29 in the The Tet-S2 State 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 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:65.5 occ:0.87 O6 N:G116 3.8 76.8 1.0 O4 N:U205 4.3 69.6 1.0 N7 N:G116 4.3 76.8 1.0 O6 N:G117 4.3 77.0 1.0 OP2 N:A114 4.5 67.4 1.0 OP2 N:A115 4.5 73.3 1.0 N7 N:A115 4.6 73.3 1.0 C6 N:G116 4.6 76.8 1.0 C5 N:G116 4.9 76.8 1.0 N4 N:C204 4.9 72.9 1.0

Magnesium binding site 4 out of 29 in the The Tet-S2 State 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 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:61.5 occ:0.78 OP2 N:A187 1.9 71.8 1.0 OP1 N:A184 1.9 47.5 1.0 OP1 N:A186 2.1 64.1 1.0 P N:A184 3.3 47.5 1.0 P N:A187 3.3 71.8 1.0 P N:A186 3.4 64.1 1.0 OP2 N:G188 3.9 63.3 1.0 OP2 N:A184 3.9 47.5 1.0 O3' N:A183 4.0 51.2 1.0 OP2 N:A186 4.0 64.1 1.0 O5' N:A187 4.1 71.8 1.0 OP1 N:A187 4.1 71.8 1.0 OP1 N:G188 4.1 63.3 1.0 O5' N:A186 4.1 64.1 1.0 P N:G188 4.3 63.3 1.0 C5' N:A187 4.3 71.8 1.0 O3' N:A187 4.3 71.8 1.0 O3' N:A186 4.3 64.1 1.0 O5' N:A184 4.4 47.5 1.0 C3' N:A186 4.4 64.1 1.0 C5' N:A186 4.4 64.1 1.0 O3' N:U185 4.6 58.6 1.0 OP1 N:A183 4.8 51.2 1.0 C5' N:A184 4.8 47.5 1.0 C4' N:U185 5.0 58.6 1.0 C4' N:A186 5.0 64.1 1.0 C4' N:A187 5.0 71.8 1.0

Magnesium binding site 5 out of 29 in the The Tet-S2 State 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 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:49.3 occ:0.85 OP2 N:A184 2.1 47.5 1.0 OP1 N:A183 2.3 51.2 1.0 OP2 N:A186 2.4 64.1 1.0 P N:A184 3.6 47.5 1.0 P N:A183 3.7 51.2 1.0 P N:A186 3.9 64.1 1.0 OP2 N:A183 4.3 51.2 1.0 N7 N:A184 4.3 47.5 1.0 O5' N:A183 4.3 51.2 1.0 C3' N:A183 4.4 51.2 1.0 O5' N:A184 4.4 47.5 1.0 OP1 N:A184 4.5 47.5 1.0 O3' N:A183 4.5 51.2 1.0 N7 N:A186 4.5 64.1 1.0 OP1 N:A186 4.6 64.1 1.0 C8 N:A184 4.6 47.5 1.0 O5' N:A186 4.7 64.1 1.0 C8 N:A186 4.7 64.1 1.0 O3' N:U182 4.8 65.6 1.0 O3' N:U185 4.8 58.6 1.0 C2 N:A139 4.9 66.4 1.0 C3' N:U185 4.9 58.6 1.0 C5' N:A183 5.0 51.2 1.0 N3 N:A139 5.0 66.4 1.0

Magnesium binding site 6 out of 29 in the The Tet-S2 State 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 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:48.0 occ:0.81 N7 N:G188 3.6 63.3 1.0 OP1 N:U168 4.1 58.3 1.0 OP2 N:U168 4.1 58.3 1.0 O6 N:G188 4.3 63.3 1.0 C8 N:G188 4.4 63.3 1.0 OP1 N:C165 4.5 68.5 1.0 OP2 N:A183 4.5 51.2 1.0 C5 N:G188 4.5 63.3 1.0 N7 N:A183 4.6 51.2 1.0 P N:U168 4.7 58.3 1.0 C8 N:A183 4.7 51.2 1.0 OP2 N:C166 4.8 68.3 1.0 OP1 N:C166 4.8 68.3 1.0 C6 N:G188 4.8 63.3 1.0 OP1 N:U182 4.8 65.6 1.0

Magnesium binding site 7 out of 29 in the The Tet-S2 State 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 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:63.3 occ:0.84 O6 N:G164 2.4 70.3 1.0 N7 N:G163 3.1 73.3 1.0 C6 N:G164 3.4 70.3 1.0 C8 N:G163 3.8 73.3 1.0 C5 N:G163 4.0 73.3 1.0 OP2 N:G163 4.0 73.3 1.0 C5 N:G164 4.1 70.3 1.0 N7 N:G164 4.1 70.3 1.0 O6 N:G163 4.2 73.3 1.0 C6 N:G163 4.4 73.3 1.0 N1 N:G164 4.5 70.3 1.0 OP2 N:U162 4.6 80.3 1.0 N7 N:A178 4.6 84.0 1.0 N6 N:A178 4.7 84.0 1.0 N9 N:G163 4.9 73.3 1.0

Magnesium binding site 8 out of 29 in the The Tet-S2 State 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 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:71.0 occ:0.78 OP2 N:A140 3.0 68.8 1.0 N7 N:G141 3.4 74.8 1.0 O4 N:U142 3.9 82.1 1.0 P N:A140 4.0 68.8 1.0 O6 N:G141 4.1 74.8 1.0 C8 N:G141 4.2 74.8 1.0 C5 N:G141 4.3 74.8 1.0 O5' N:A140 4.3 68.8 1.0 OP2 N:G141 4.5 74.8 1.0 OP1 N:A140 4.5 68.8 1.0 C6 N:G141 4.6 74.8 1.0 C4 N:U142 4.7 82.1 1.0 C5 N:U142 4.9 82.1 1.0

Magnesium binding site 9 out of 29 in the The Tet-S2 State 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 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:89.0 occ:0.80 O6 N:G148 3.8 98.5 1.0 O6 N:G149 4.1 96.1 1.0 O4 N:U155 4.4 90.9 1.0 N7 N:G148 4.5 98.5 1.0 C6 N:G148 4.7 98.5 1.0 O6 N:G150 4.8 95.5 1.0 N4 N:C154 4.9 87.9 1.0 C5 N:G148 5.0 98.5 1.0

Magnesium binding site 10 out of 29 in the The Tet-S2 State 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 of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg511 b:100.6 occ:0.87 OP2 N:G150 3.9 95.5 1.0 OP2 N:A151 4.8 98.1 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