Magnesium in PDB 6d8o: Group I Self-Splicing Intron P4-P6 Domain Mutant A230U

The structure of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U, PDB code: 6d8o was solved by G.M.Shoffner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.20 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.250, 129.490, 146.130, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 22.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U (pdb code 6d8o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U, PDB code: 6d8o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:87.2 occ:1.00 O6 A:G188 2.2 90.7 1.0 C6 A:G188 3.5 82.7 1.0 OP1 A:U168 3.6 75.5 1.0 OP2 A:U168 3.6 85.3 1.0 N7 A:A183 4.0 86.3 1.0 OP1 A:C165 4.0 0.4 1.0 P A:U168 4.1 77.2 1.0 C5 A:U168 4.2 87.2 1.0 C8 A:A183 4.3 76.3 1.0 N1 A:G188 4.3 76.0 1.0 OP2 A:C166 4.3 82.9 1.0 OP1 A:C166 4.3 89.5 1.0 C5 A:G188 4.5 78.6 1.0 OP2 A:A183 4.7 93.2 1.0 C6 A:U168 4.8 80.0 1.0 P A:C166 4.8 80.0 1.0 N7 A:G188 4.8 88.5 1.0 OP1 A:U182 5.0 83.0 1.0

Magnesium binding site 2 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:65.4 occ:1.00 OP1 A:A183 2.2 86.1 1.0 OP2 A:A184 2.3 94.9 1.0 OP2 A:A186 2.6 91.2 1.0 P A:A183 3.4 84.5 1.0 P A:A184 3.6 88.1 1.0 OP2 A:A183 3.7 93.2 1.0 P A:A186 4.1 91.5 1.0 OP1 A:A184 4.1 0.3 1.0 N7 A:A184 4.2 78.2 1.0 N7 A:A186 4.2 89.2 1.0 O5' A:A183 4.3 66.9 1.0 C8 A:A184 4.5 96.8 1.0 C8 A:A186 4.5 94.7 1.0 C3' A:A183 4.5 76.5 1.0 O3' A:U182 4.6 63.4 1.0 O3' A:A183 4.6 82.0 1.0 O5' A:A184 4.6 80.1 1.0 O3' A:U185 4.7 84.5 1.0 C3' A:U185 4.7 87.6 1.0 C2 A:A139 4.8 92.1 1.0 N3 A:A139 4.8 88.6 1.0 O5' A:A186 4.8 91.0 1.0 C5' A:A183 4.9 77.8 1.0

Magnesium binding site 3 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:77.4 occ:1.00 OP1 A:A184 2.0 0.3 1.0 OP2 A:A187 2.0 0.8 1.0 OP1 A:A186 2.5 93.8 1.0 OP2 A:G188 3.3 0.9 1.0 P A:A187 3.3 92.6 1.0 P A:A184 3.4 88.1 1.0 P A:A186 3.7 91.5 1.0 OP1 A:A187 3.9 0.7 1.0 OP2 A:A186 3.9 91.2 1.0 O3' A:A183 3.9 82.0 1.0 O5' A:A184 4.3 80.1 1.0 O5' A:A187 4.3 94.2 1.0 C5' A:A187 4.3 0.4 1.0 O3' A:A186 4.4 0.5 1.0 OP2 A:A184 4.4 94.9 1.0 C3' A:A186 4.6 97.6 1.0 O5' A:A186 4.6 91.0 1.0 P A:G188 4.7 0.4 1.0 OP1 A:A183 4.7 86.1 1.0 C5' A:A184 4.8 82.4 1.0 O3' A:U185 4.8 84.5 1.0 C4' A:U185 4.9 87.2 1.0 O5' A:G188 4.9 97.3 1.0 C5' A:A186 5.0 96.8 1.0

Magnesium binding site 4 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:97.4 occ:1.00 O6 A:G164 2.3 96.3 1.0 N7 A:G163 2.6 98.0 1.0 C8 A:G163 3.3 97.3 1.0 C6 A:G164 3.3 89.5 1.0 N7 A:G164 3.7 89.9 1.0 C5 A:G163 3.7 99.6 1.0 C5 A:G164 3.9 89.9 1.0 OP2 A:G163 3.9 0.7 1.0 O2' A:U177 4.2 0.9 1.0 O6 A:G163 4.2 92.4 1.0 C6 A:G163 4.4 94.0 1.0 N7 A:A178 4.4 0.3 1.0 N1 A:G164 4.5 0.1 1.0 N9 A:G163 4.5 88.9 1.0 N6 A:A178 4.6 97.9 1.0 OP2 A:U162 4.7 0.6 1.0 C4 A:G163 4.8 96.3 1.0 C2' A:U177 4.9 0.2 1.0 C5 A:U162 4.9 94.7 1.0 O2 A:U177 4.9 0.4 1.0 O5' A:G163 4.9 88.2 1.0 C8 A:G164 5.0 90.1 1.0

Magnesium binding site 5 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:76.0 occ:1.00 OP2 A:A171 2.1 94.7 1.0 P A:A171 3.4 88.4 1.0 O5' A:A171 3.8 76.7 1.0 C8 A:A171 3.9 86.4 1.0 N7 A:A171 4.0 97.1 1.0 OP2 A:C165 4.2 82.1 1.0 OP1 A:A171 4.3 80.8 1.0 OP2 A:U168 4.3 85.3 1.0 O3' A:U167 4.4 64.4 1.0 O2 A:U167 4.4 80.2 1.0 O2' A:U167 4.4 82.4 1.0 O3' A:C170 4.5 74.0 1.0 OP2 A:C170 4.6 89.9 1.0 OP1 A:C170 4.7 0.1 1.0 C3' A:C170 4.8 63.9 1.0 O5' A:C170 4.8 82.7 1.0 P A:C170 4.9 81.7 1.0

Magnesium binding site 6 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:66.9 occ:1.00 OP2 A:A173 2.4 91.3 1.0 P A:A173 3.7 97.0 1.0 N7 A:A173 3.7 97.3 1.0 C8 A:A173 3.9 94.9 1.0 O5' A:A173 3.9 98.3 1.0 N7 A:G174 3.9 94.7 1.0 O6 A:G174 4.2 98.6 1.0 O2' A:A171 4.4 95.2 1.0 OP2 A:A172 4.5 75.9 1.0 OP1 A:A173 4.7 88.9 1.0 O3' A:A172 4.7 90.5 1.0 C3' A:A172 4.7 90.7 1.0 C5 A:G174 4.8 83.6 1.0 C5 A:A173 4.8 86.5 1.0 C6 A:G174 4.9 93.0 1.0 C8 A:G174 4.9 0.7 1.0 O3' A:A171 5.0 83.9 1.0

Magnesium binding site 7 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:96.2 occ:1.00 O3' A:C127 4.1 0.6 1.0 OP1 A:U202 4.2 92.5 1.0 OP1 A:C203 4.2 93.6 1.0 OP2 A:A113 4.3 93.7 1.0 OP2 A:C203 4.4 90.7 1.0 OP1 A:C128 4.4 0.8 1.0 O2' A:C127 4.6 0.5 1.0 OP1 A:A113 4.6 95.5 1.0 P A:C203 4.8 97.4 1.0 P A:C128 5.0 0.4 1.0 P A:A113 5.0 89.7 1.0

Magnesium binding site 8 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:97.2 occ:1.00 OP2 A:G250 2.0 0.4 1.0 O2' A:A248 2.5 97.2 1.0 OP2 A:U249 3.1 1.0 1.0 O5' A:U249 3.5 0.2 1.0 P A:G250 3.5 92.2 1.0 O3' A:A248 3.6 0.3 1.0 P A:U249 3.6 0.4 1.0 C2' A:A248 3.8 84.5 1.0 N7 A:G250 3.8 85.9 1.0 C3' A:A248 4.0 93.2 1.0 C8 A:G250 4.1 89.1 1.0 O5' A:G250 4.2 86.8 1.0 O3' A:U249 4.3 0.1 1.0 C3' A:U249 4.4 0.7 1.0 OP1 A:G250 4.5 0.2 1.0 C1' A:A248 4.8 88.2 1.0 C5' A:U249 4.8 0.5 1.0 C5 A:G250 4.9 93.8 1.0 N7 A:G251 5.0 81.3 1.0

Magnesium binding site 9 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:96.7 occ:1.00 OP2 A:G112 2.3 0.8 1.0 P A:G112 3.5 94.8 1.0 O5' A:G112 3.7 95.6 1.0 N7 A:A113 3.9 85.8 1.0 C8 A:G112 4.0 85.2 1.0 N7 A:G112 4.0 82.7 1.0 N6 A:A113 4.1 89.4 1.0 OP1 A:G112 4.4 88.7 1.0 O3' A:G111 4.6 86.5 1.0 C5 A:A113 4.7 82.5 1.0 C3' A:G111 4.7 95.9 1.0 C6 A:A113 4.8 88.6 1.0 C8 A:A113 4.9 88.2 1.0 OP2 A:A113 4.9 93.7 1.0

Magnesium binding site 10 out of 19 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A230U


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Group I Self-Splicing Intron P4-P6 Domain Mutant A230U within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:79.9 occ:1.00 O6 B:G188 2.1 89.7 1.0 C6 B:G188 3.3 88.0 1.0 OP1 B:U168 3.7 87.2 1.0 OP1 B:C165 3.8 98.3 1.0 OP2 B:U168 3.9 79.7 1.0 N7 B:A183 4.0 85.1 1.0 OP2 B:C166 4.2 89.1 1.0 C5 B:G188 4.3 82.7 1.0 N1 B:G188 4.3 80.9 1.0 P B:U168 4.3 76.1 1.0 C8 B:A183 4.3 78.3 1.0 OP1 B:C166 4.4 86.0 1.0 N7 B:G188 4.4 83.9 1.0 OP2 B:A183 4.5 91.9 1.0 C5 B:U168 4.7 80.3 1.0 OP1 B:U182 4.7 87.8 1.0 P B:C166 4.7 84.1 1.0 P B:C165 5.0 70.1 1.0 C5' B:C165 5.0 86.4 1.0

G.M.Shoffner, R.Wang, E.Podell, T.R.Cech, F.Guo. In Crystallo Selection to Establish New Rna Crystal Contacts. Structure V. 26 1275 2018.
ISSN: ISSN 1878-4186
PubMed: 29910185
DOI: 10.1016/J.STR.2018.05.005