Magnesium in PDB 7xd7: The Pre-Tet-C 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 Pre-Tet-C State of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon (pdb code 7xd7). 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 Pre-Tet-C State of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon, PDB code: 7xd7:
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 Pre-Tet-C 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 Pre-Tet-C 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:Mg501 b:22.5 occ:0.77 O6 N:G111 4.2 48.3 1.0 N7 N:G111 4.5 48.3 1.0 O6 N:G112 4.5 56.6 1.0 O6 N:G110 4.9 43.4 1.0 C6 N:G111 4.9 48.3 1.0

Magnesium binding site 2 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:61.5 occ:1.00 OP2 N:C262 1.7 53.5 1.0 P N:C262 3.1 53.5 1.0 OP1 N:A207 3.2 71.3 1.0 O5' N:C262 3.4 53.5 1.0 OP1 N:C262 4.1 53.5 1.0 OP2 N:A263 4.1 51.9 1.0 O3' N:A261 4.2 43.0 1.0 C3' N:A261 4.2 43.0 1.0 O2 N:U305 4.3 39.5 1.0 MG N:MG526 4.3 56.7 1.0 P N:A207 4.6 71.3 1.0 C5' N:C262 4.7 53.5 1.0 O3' N:A206 5.0 71.5 1.0

Magnesium binding site 3 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:81.1 occ:0.87 O6 N:G116 4.2 87.6 1.0 OP2 N:A115 4.4 83.2 1.0 O4 N:U205 4.5 75.9 1.0 N7 N:A115 4.5 83.2 1.0 N7 N:G116 4.6 87.6 1.0 OP2 N:A114 4.7 77.0 1.0 O6 N:G117 4.7 87.9 1.0 N6 N:A115 4.9 83.2 1.0 N4 N:C204 4.9 78.8 1.0

Magnesium binding site 4 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:55.9 occ:0.78 OP2 N:A187 1.8 65.1 1.0 OP1 N:A184 1.9 43.4 1.0 OP2 N:G188 2.1 56.5 1.0 OP1 N:A186 2.1 57.7 1.0 P N:A187 3.3 65.1 1.0 P N:A184 3.3 43.4 1.0 P N:G188 3.5 56.5 1.0 P N:A186 3.5 57.7 1.0 O5' N:A187 4.0 65.1 1.0 OP2 N:A184 4.0 43.4 1.0 OP1 N:A187 4.0 65.1 1.0 OP1 N:G188 4.1 56.5 1.0 O3' N:A183 4.1 46.7 1.0 C5' N:A187 4.1 65.1 1.0 O5' N:A186 4.2 57.7 1.0 OP2 N:A186 4.2 57.7 1.0 O5' N:A184 4.3 43.4 1.0 O3' N:A186 4.3 57.7 1.0 C5' N:A186 4.4 57.7 1.0 C3' N:A186 4.4 57.7 1.0 O5' N:G188 4.4 56.5 1.0 O3' N:A187 4.5 65.1 1.0 O3' N:U185 4.5 51.6 1.0 C5' N:A184 4.7 43.4 1.0 OP1 N:A183 4.9 46.7 1.0 C4' N:A187 4.9 65.1 1.0 C4' N:U185 5.0 51.6 1.0 C4' N:A186 5.0 57.7 1.0

Magnesium binding site 5 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:43.4 occ:0.85 OP1 N:A183 2.0 46.7 1.0 OP2 N:A184 2.1 43.4 1.0 OP2 N:A186 2.6 57.7 1.0 P N:A183 3.4 46.7 1.0 P N:A184 3.6 43.4 1.0 P N:A186 4.0 57.7 1.0 O5' N:A183 4.0 46.7 1.0 OP2 N:A183 4.0 46.7 1.0 C3' N:A183 4.2 46.7 1.0 N7 N:A184 4.4 43.4 1.0 O3' N:A183 4.4 46.7 1.0 N7 N:A186 4.4 57.7 1.0 OP1 N:A184 4.4 43.4 1.0 O3' N:U182 4.5 59.5 1.0 O5' N:A184 4.5 43.4 1.0 OP1 N:A186 4.5 57.7 1.0 C8 N:A186 4.6 57.7 1.0 C8 N:A184 4.7 43.4 1.0 C5' N:A183 4.7 46.7 1.0 O5' N:A186 4.8 57.7 1.0

Magnesium binding site 6 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:37.0 occ:0.81 N7 N:G188 3.7 56.5 1.0 OP1 N:U168 4.1 51.8 1.0 OP2 N:U168 4.1 51.8 1.0 O6 N:G188 4.2 56.5 1.0 N7 N:A183 4.5 46.7 1.0 C5 N:G188 4.6 56.5 1.0 OP1 N:C165 4.6 59.3 1.0 OP2 N:A183 4.6 46.7 1.0 C8 N:G188 4.6 56.5 1.0 C8 N:A183 4.6 46.7 1.0 P N:U168 4.6 51.8 1.0 C6 N:G188 4.7 56.5 1.0 OP1 N:C166 4.8 58.9 1.0 OP2 N:C166 4.9 58.9 1.0 OP1 N:U182 4.9 59.5 1.0 C5 N:U168 5.0 51.8 1.0

Magnesium binding site 7 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:59.5 occ:0.84 O6 N:G164 2.4 63.2 1.0 N7 N:G163 3.0 67.1 1.0 C6 N:G164 3.4 63.2 1.0 C8 N:G163 3.7 67.1 1.0 C5 N:G163 3.9 67.1 1.0 N7 N:G164 4.0 63.2 1.0 OP2 N:G163 4.0 67.1 1.0 C5 N:G164 4.0 63.2 1.0 O6 N:G163 4.1 67.1 1.0 C6 N:G163 4.3 67.1 1.0 OP2 N:U162 4.5 74.2 1.0 N1 N:G164 4.5 63.2 1.0 N6 N:A178 4.7 77.0 1.0 N7 N:A178 4.8 77.0 1.0 N9 N:G163 4.8 67.1 1.0 C4 N:G163 4.9 67.1 1.0 O5' N:U162 5.0 74.2 1.0

Magnesium binding site 8 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:55.3 occ:0.78 OP2 N:A140 3.1 63.4 1.0 N7 N:G141 3.4 69.3 1.0 O4 N:U142 3.8 76.8 1.0 P N:A140 4.1 63.4 1.0 O6 N:G141 4.2 69.3 1.0 C8 N:G141 4.2 69.3 1.0 C5 N:G141 4.3 69.3 1.0 O5' N:A140 4.3 63.4 1.0 OP1 N:A140 4.5 63.4 1.0 OP2 N:G141 4.5 69.3 1.0 C6 N:G141 4.6 69.3 1.0 C4 N:U142 4.7 76.8 1.0 C5 N:U142 4.8 76.8 1.0

Magnesium binding site 9 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:79.2 occ:0.80 O6 N:G148 3.6 91.5 1.0 O6 N:G149 3.8 88.7 1.0 N7 N:G148 4.1 91.5 1.0 O6 N:G150 4.2 87.7 1.0 C6 N:G148 4.4 91.5 1.0 O4 N:U155 4.5 84.0 1.0 C5 N:G148 4.6 91.5 1.0 C6 N:G149 4.8 88.7 1.0 N7 N:G149 4.9 88.7 1.0 C6 N:G150 5.0 87.7 1.0

Magnesium binding site 10 out of 29 in the The Pre-Tet-C 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 Pre-Tet-C 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:87.8 occ:0.87 OP2 N:G150 3.1 87.7 1.0 OP2 N:G149 4.5 88.7 1.0 P N:G150 4.5 87.7 1.0 O5' N:G150 4.7 87.7 1.0 N7 N:G150 4.8 87.7 1.0 OP1 N:G149 4.9 88.7 1.0 OP2 N:A151 5.0 90.6 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