Magnesium in PDB 6d8m: Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U

The structure of Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U, PDB code: 6d8m 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)	64.20 / 3.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.600, 132.880, 146.780, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Magnesium atom in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U (pdb code 6d8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 23 binding sites of Magnesium where determined in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U, PDB code: 6d8m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:71.1 occ:1.00 O6 A:G188 1.9 0.2 1.0 C6 A:G188 3.2 0.9 1.0 OP2 A:C166 3.9 0.8 1.0 OP1 A:C165 4.1 91.3 1.0 OP1 A:U182 4.1 95.5 1.0 C5 A:G188 4.1 0.2 1.0 OP1 A:C166 4.1 0.2 1.0 N1 A:G188 4.1 0.9 1.0 OP1 A:U168 4.2 0.9 1.0 OP2 A:U168 4.3 93.5 1.0 N7 A:G188 4.3 0.6 1.0 P A:C166 4.5 0.8 1.0 N7 A:A183 4.6 98.7 1.0 OP2 A:A183 4.7 0.7 1.0 C5' A:C165 4.7 0.4 1.0 P A:U168 4.7 98.2 1.0 C5 A:U168 4.8 0.4 1.0 C8 A:A183 4.9 98.0 1.0

Magnesium binding site 2 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:89.9 occ:1.00 OP2 A:A184 2.1 0.6 1.0 OP1 A:A183 2.3 0.1 1.0 OP2 A:A186 2.9 0.8 1.0 P A:A183 3.4 0.8 1.0 P A:A184 3.6 0.7 1.0 OP2 A:A183 3.7 0.7 1.0 N7 A:A184 3.7 0.2 1.0 C8 A:A184 4.1 0.1 1.0 O5' A:A183 4.1 0.2 1.0 C3' A:A183 4.2 0.2 1.0 P A:A186 4.3 1.0 1.0 OP1 A:A184 4.4 0.3 1.0 O3' A:A183 4.4 0.0 1.0 O5' A:A184 4.5 0.3 1.0 C2 A:A139 4.6 0.4 1.0 N7 A:A186 4.7 0.3 1.0 O3' A:U182 4.7 97.0 1.0 N3 A:A139 4.8 0.9 1.0 C3' A:U185 4.8 0.5 1.0 O3' A:U185 4.9 0.3 1.0 C5' A:A183 5.0 0.8 1.0 C8 A:A186 5.0 0.2 1.0

Magnesium binding site 3 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:0.2 occ:1.00 OP1 A:A184 1.9 0.3 1.0 OP2 A:A187 2.3 0.2 1.0 OP1 A:A186 2.5 1.0 1.0 OP2 A:G188 2.9 0.2 1.0 P A:A184 3.2 0.7 1.0 O3' A:A183 3.5 0.0 1.0 P A:A186 3.6 1.0 1.0 P A:A187 3.6 0.9 1.0 OP2 A:A186 3.8 0.8 1.0 OP1 A:A187 4.1 0.1 1.0 OP2 A:A184 4.2 0.6 1.0 O5' A:A184 4.2 0.3 1.0 P A:G188 4.3 0.1 1.0 O5' A:A187 4.3 0.1 1.0 C5' A:A187 4.5 1.0 1.0 O5' A:A186 4.5 0.0 1.0 C5' A:A184 4.6 0.5 1.0 OP1 A:A183 4.7 0.1 1.0 C3' A:A183 4.7 0.2 1.0 O3' A:U185 4.7 0.3 1.0 O5' A:G188 4.7 0.5 1.0 O3' A:A186 4.8 0.5 1.0 C3' A:A186 4.9 0.7 1.0 C5' A:A186 4.9 0.1 1.0 C4' A:U185 4.9 0.6 1.0 C3' A:U185 5.0 0.5 1.0

Magnesium binding site 4 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:0.6 occ:1.00 O6 A:G164 1.9 0.7 1.0 N7 A:G163 2.6 0.1 1.0 C6 A:G164 3.0 0.6 1.0 C8 A:G163 3.4 0.4 1.0 C5 A:G163 3.7 0.5 1.0 C5 A:G164 3.7 0.5 1.0 N7 A:G164 3.7 0.2 1.0 OP2 A:G163 3.8 0.7 1.0 O6 A:G163 4.0 0.5 1.0 N1 A:G164 4.1 0.8 1.0 N7 A:A178 4.2 0.5 1.0 C6 A:G163 4.2 0.3 1.0 O2' A:U177 4.4 0.9 1.0 OP2 A:U162 4.4 0.9 1.0 N6 A:A178 4.5 0.6 1.0 N9 A:G163 4.6 0.4 1.0 O2 A:U177 4.7 0.8 1.0 C4 A:G163 4.7 0.5 1.0 C2' A:U177 4.9 0.8 1.0 C8 A:G164 5.0 0.4 1.0

Magnesium binding site 5 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:85.2 occ:1.00 OP2 A:A171 2.0 0.6 1.0 P A:A171 3.4 0.4 1.0 O5' A:A171 4.0 0.9 1.0 OP1 A:C170 4.3 0.5 1.0 OP2 A:C165 4.3 84.0 1.0 OP1 A:A171 4.3 0.0 1.0 N7 A:A171 4.4 0.9 1.0 O3' A:C170 4.4 96.0 1.0 C8 A:A171 4.4 0.2 1.0 OP2 A:U168 4.4 93.5 1.0 O2' A:U167 4.5 0.5 1.0 O5' A:C170 4.5 0.6 1.0 O3' A:U167 4.5 93.0 1.0 OP2 A:C170 4.6 0.6 1.0 P A:C170 4.7 0.1 1.0 O2 A:U167 4.7 98.2 1.0 C3' A:C170 4.7 91.8 1.0

Magnesium binding site 6 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:97.5 occ:1.00 OP2 A:A173 2.4 0.4 1.0 P A:A173 3.8 0.9 1.0 O6 A:G174 4.1 0.7 1.0 N7 A:G174 4.2 0.6 1.0 O5' A:A173 4.2 1.0 1.0 N7 A:A173 4.3 0.8 1.0 O5' A:A172 4.6 0.7 1.0 C8 A:A173 4.6 0.8 1.0 O2' A:A171 4.7 0.9 1.0 OP1 A:A173 4.8 0.0 1.0 O3' A:A172 4.8 0.3 1.0 C6 A:G174 4.9 0.2 1.0 C3' A:A172 4.9 0.2 1.0 C5 A:G174 4.9 0.6 1.0

Magnesium binding site 7 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:0.4 occ:1.00 OP2 A:A113 3.7 0.8 1.0 OP1 A:U202 4.1 0.5 1.0 OP2 A:C203 4.2 0.5 1.0 OP1 A:C203 4.3 1.0 1.0 OP1 A:A113 4.3 0.4 1.0 P A:A113 4.5 0.0 1.0 P A:C203 4.8 0.8 1.0 O3' A:C127 4.8 0.3 1.0 O2' A:C127 4.9 0.2 1.0

Magnesium binding site 8 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:0.4 occ:1.00 N7 A:G160 3.7 0.9 1.0 O6 A:G160 3.8 0.3 1.0 N7 A:A159 4.3 0.3 1.0 C5 A:G160 4.4 0.1 1.0 N6 A:A161 4.4 0.6 1.0 C6 A:G160 4.4 0.8 1.0 C8 A:G160 4.7 0.2 1.0 C5 A:A159 4.8 0.2 1.0 N6 A:A159 4.8 0.7 1.0 C8 A:A159 4.9 0.1 1.0

Magnesium binding site 9 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:88.9 occ:1.00 O6 A:G176 3.4 0.6 1.0 N7 A:G175 3.8 0.1 1.0 N7 A:G176 3.8 0.3 1.0 OP2 A:G174 4.2 0.1 1.0 OP2 A:G175 4.2 0.4 1.0 C6 A:G176 4.3 1.0 1.0 O4 A:U177 4.4 0.6 1.0 C5 A:G176 4.4 0.7 1.0 C8 A:G175 4.5 0.4 1.0 C5 A:G175 4.6 0.6 1.0 O6 A:G175 4.7 0.0 1.0 C8 A:G176 5.0 0.2 1.0 C6 A:G175 5.0 0.9 1.0

Magnesium binding site 10 out of 23 in the Group I Self-Splicing Intron P4-P6 Domain Mutant A125U/G126U


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 A125U/G126U within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:0.1 occ:1.00 O6 A:G148 3.2 0.2 1.0 O6 A:G149 3.7 0.4 1.0 N7 A:G148 4.0 0.9 1.0 C6 A:G148 4.1 0.4 1.0 O4 A:U155 4.2 1.0 1.0 O6 A:G147 4.4 0.5 1.0 C5 A:G148 4.4 0.6 1.0 C6 A:G149 4.7 0.5 1.0 O6 A:G150 4.8 0.6 1.0 N4 A:C154 4.9 0.8 1.0 C6 A:G147 5.0 0.3 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