Magnesium in PDB 8hd6: The Relaxed Pre-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 - 24;

Binding sites:

The binding sites of Magnesium atom in the The Relaxed Pre-Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside (pdb code 8hd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the The Relaxed Pre-Tet-S1 State of G264A Mutated Tetrahymena Group I Intron with 6NT 3'/5'-Exon and 2-Aminopurine Nucleoside, PDB code: 8hd6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:53.8 occ:0.77 N7 N:G111 4.1 94.6 1.0 C8 N:G111 4.8 94.6 1.0 O6 N:G111 4.9 94.6 1.0 OP2 N:G111 4.9 94.6 1.0 C5 N:G111 5.0 94.6 1.0 N7 N:G112 5.0 104.2 1.0

Magnesium binding site 2 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:151.4 occ:1.00 OP1 N:A207 2.1 120.0 1.0 OP2 N:C262 2.8 195.7 1.0 OP1 N:C262 3.1 195.7 1.0 C5' N:A207 3.3 120.0 1.0 P N:A207 3.4 120.0 1.0 P N:C262 3.4 195.7 1.0 O5' N:A207 3.7 120.0 1.0 O3' N:A206 4.3 108.9 1.0 C5' N:C262 4.4 195.7 1.0 O5' N:C262 4.4 195.7 1.0 OP2 N:A207 4.5 120.0 1.0 O2' N:U305 4.6 147.7 1.0 C4' N:A207 4.6 120.0 1.0 O3' N:A261 4.7 178.6 1.0 OP2 N:C208 4.7 120.9 1.0

Magnesium binding site 3 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:82.2 occ:0.87 O6 N:G116 4.0 120.3 1.0 OP2 N:A114 4.2 117.4 1.0 N7 N:G116 4.4 120.3 1.0 O6 N:G117 4.4 118.8 1.0 OP1 N:A114 4.6 117.4 1.0 O4 N:U205 4.7 109.1 1.0 OP2 N:A115 4.8 121.2 1.0 N7 N:A115 4.8 121.2 1.0 C6 N:G116 4.8 120.3 1.0 P N:A114 4.9 117.4 1.0

Magnesium binding site 4 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:73.2 occ:1.00 OP2 N:A187 2.2 98.9 1.0 OP1 N:A184 2.4 84.4 1.0 OP1 N:A186 3.0 90.6 1.0 OP2 N:G188 3.4 88.7 1.0 P N:A187 3.4 98.9 1.0 OP1 N:G188 3.5 88.7 1.0 P N:A184 3.8 84.4 1.0 P N:G188 3.8 88.7 1.0 C5' N:A187 3.8 98.9 1.0 OP1 N:A187 3.9 98.9 1.0 O5' N:A187 4.0 98.9 1.0 P N:A186 4.1 90.6 1.0 O3' N:A183 4.1 81.6 1.0 O3' N:A187 4.2 98.9 1.0 OP2 N:A186 4.3 90.6 1.0 C4' N:A187 4.6 98.9 1.0 O5' N:A184 4.6 84.4 1.0 OP1 N:A183 4.7 81.6 1.0 O3' N:A186 4.7 90.6 1.0 OP2 N:A184 4.8 84.4 1.0 O5' N:A186 4.8 90.6 1.0 C3' N:A187 4.9 98.9 1.0 O2' N:U182 4.9 89.1 1.0 C5' N:A183 4.9 81.6 1.0 C3' N:A186 5.0 90.6 1.0 C5' N:A184 5.0 84.4 1.0

Magnesium binding site 5 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:80.2 occ:0.81 OP1 N:A183 2.1 81.6 1.0 OP2 N:A186 2.1 90.6 1.0 OP2 N:A184 2.1 84.4 1.0 P N:A184 3.2 84.4 1.0 P N:A183 3.4 81.6 1.0 OP1 N:A184 3.5 84.4 1.0 P N:A186 3.6 90.6 1.0 OP2 N:A183 3.9 81.6 1.0 O3' N:A183 4.2 81.6 1.0 C3' N:A183 4.2 81.6 1.0 O5' N:A186 4.3 90.6 1.0 O3' N:U182 4.3 89.1 1.0 O3' N:U185 4.4 97.6 1.0 O5' N:A184 4.4 84.4 1.0 O5' N:A183 4.5 81.6 1.0 N7 N:A186 4.5 90.6 1.0 C8 N:A186 4.5 90.6 1.0 OP1 N:A186 4.5 90.6 1.0 C3' N:U185 4.6 97.6 1.0 N7 N:A184 4.9 84.4 1.0 C5' N:A183 4.9 81.6 1.0

Magnesium binding site 6 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:58.9 occ:0.81 N7 N:G188 3.1 88.7 1.0 O6 N:G188 4.0 88.7 1.0 C8 N:G188 4.0 88.7 1.0 C5 N:G188 4.1 88.7 1.0 OP1 N:U168 4.2 83.4 1.0 C6 N:G188 4.4 88.7 1.0 OP1 N:C165 4.5 89.7 1.0 OP2 N:U168 4.6 83.4 1.0 OP2 N:C166 4.6 90.3 1.0 OP1 N:C166 4.7 90.3 1.0 N7 N:A183 4.8 81.6 1.0 OP2 N:A183 4.8 81.6 1.0 OP1 N:U182 4.8 89.1 1.0 P N:U168 4.9 83.4 1.0 P N:C166 5.0 90.3 1.0

Magnesium binding site 7 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:82.8 occ:0.78 O6 N:G164 2.0 93.8 1.0 C6 N:G164 3.1 93.8 1.0 N7 N:G163 3.9 104.3 1.0 C5 N:G164 4.0 93.8 1.0 N7 N:A178 4.0 120.9 1.0 N1 N:G164 4.1 93.8 1.0 N7 N:G164 4.1 93.8 1.0 OP2 N:G163 4.5 104.3 1.0 C8 N:G163 4.5 104.3 1.0 N6 N:A178 4.6 120.9 1.0 C5 N:G163 4.7 104.3 1.0 O6 N:G163 4.9 104.3 1.0 C8 N:A178 4.9 120.9 1.0 C5 N:A178 4.9 120.9 1.0

Magnesium binding site 8 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:88.3 occ:0.78 O4 N:U142 3.4 117.5 1.0 OP2 N:A140 3.8 100.8 1.0 N7 N:G141 3.8 105.5 1.0 C4 N:U142 4.2 117.5 1.0 C5 N:U142 4.3 117.5 1.0 OP2 N:G141 4.4 105.5 1.0 C8 N:G141 4.5 105.5 1.0 C5 N:G141 4.6 105.5 1.0 P N:A140 4.6 100.8 1.0 O6 N:G141 4.7 105.5 1.0 OP1 N:A140 4.8 100.8 1.0 O5' N:A140 4.9 100.8 1.0 C6 N:G141 5.0 105.5 1.0

Magnesium binding site 9 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:101.6 occ:0.80 O6 N:G148 4.1 159.0 1.0 O4 N:U155 4.4 146.1 1.0 O6 N:G149 4.6 158.8 1.0

Magnesium binding site 10 out of 24 in the The Relaxed Pre-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 Relaxed Pre-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:162.9 occ:0.87 OP2 N:G150 2.2 156.5 1.0 OP1 N:G149 3.3 158.8 1.0 OP2 N:G149 3.4 158.8 1.0 P N:G149 3.6 158.8 1.0 P N:G150 3.6 156.5 1.0 O5' N:G149 3.7 158.8 1.0 OP1 N:G150 4.3 156.5 1.0 O5' N:G150 4.4 156.5 1.0 C5' N:G149 4.6 158.8 1.0 O3' N:G149 4.6 158.8 1.0 C3' N:G149 4.8 158.8 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