Magnesium in PDB 6d8l: Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)

The structure of Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking), PDB code: 6d8l 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)	67.20 / 3.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.480, 132.950, 147.540, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 27

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Magnesium atom in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking) (pdb code 6d8l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 22 binding sites of Magnesium where determined in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking), PDB code: 6d8l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:89.6 occ:1.00 O6 A:G188 2.2 0.9 1.0 C6 A:G188 3.5 0.2 1.0 OP1 A:U168 3.7 0.5 1.0 OP1 A:C165 4.1 87.5 1.0 OP1 A:C166 4.1 98.3 1.0 N7 A:A183 4.3 92.5 1.0 OP2 A:U168 4.3 89.2 1.0 OP2 A:C166 4.3 0.7 1.0 N1 A:G188 4.4 0.2 1.0 C5 A:G188 4.4 0.5 1.0 P A:U168 4.5 93.2 1.0 C8 A:A183 4.5 90.8 1.0 C5 A:U168 4.5 0.8 1.0 OP1 A:U182 4.6 90.8 1.0 N7 A:G188 4.6 0.3 1.0 P A:C166 4.7 98.8 1.0 OP2 A:A183 4.7 0.7 1.0 C5' A:C165 4.9 95.3 1.0

Magnesium binding site 2 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:74.5 occ:1.00 OP1 A:A183 2.4 98.6 1.0 OP2 A:A184 2.4 0.4 1.0 OP2 A:A186 2.5 0.3 1.0 P A:A183 3.6 98.5 1.0 P A:A184 3.8 98.9 1.0 OP2 A:A183 3.9 0.7 1.0 P A:A186 4.0 0.5 1.0 N7 A:A184 4.2 91.9 1.0 N7 A:A186 4.2 0.8 1.0 OP1 A:A184 4.4 0.2 1.0 O5' A:A183 4.4 94.7 1.0 C8 A:A186 4.5 96.8 1.0 C8 A:A184 4.5 92.2 1.0 C3' A:U185 4.6 0.7 1.0 O5' A:A184 4.6 91.5 1.0 O3' A:U185 4.6 97.2 1.0 N3 A:A139 4.7 96.4 1.0 C2 A:A139 4.7 95.0 1.0 O5' A:A186 4.8 97.2 1.0 C3' A:A183 4.8 93.3 1.0 O3' A:U182 4.8 90.8 1.0 O3' A:A183 4.8 97.3 1.0 OP1 A:A186 4.9 0.9 1.0

Magnesium binding site 3 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:0.8 occ:1.00 OP1 A:A184 2.0 0.2 1.0 OP2 A:A187 2.2 0.6 1.0 OP1 A:A186 2.4 0.9 1.0 P A:A187 3.1 0.3 1.0 OP1 A:A187 3.2 0.6 1.0 OP2 A:G188 3.4 0.5 1.0 P A:A184 3.4 98.9 1.0 P A:A186 3.6 0.5 1.0 O3' A:A183 4.0 97.3 1.0 OP2 A:A186 4.0 0.3 1.0 O3' A:A186 4.1 0.3 1.0 OP2 A:A184 4.3 0.4 1.0 O5' A:A187 4.4 1.0 1.0 C3' A:A186 4.4 0.1 1.0 O5' A:A184 4.4 91.5 1.0 C5' A:A187 4.6 0.7 1.0 O5' A:A186 4.6 97.2 1.0 OP1 A:A183 4.6 98.6 1.0 P A:G188 4.7 0.9 1.0 O3' A:U185 4.7 97.2 1.0 O5' A:G188 4.8 0.4 1.0 C5' A:A183 4.9 96.8 1.0 C5' A:A184 5.0 92.2 1.0 C4' A:U185 5.0 0.3 1.0

Magnesium binding site 4 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:91.4 occ:1.00 O6 A:G164 2.4 0.7 1.0 N7 A:G163 2.6 0.7 1.0 C8 A:G163 3.3 0.4 1.0 C6 A:G164 3.4 0.9 1.0 C5 A:G163 3.8 0.3 1.0 N7 A:G164 3.8 0.3 1.0 OP2 A:G163 3.8 0.5 1.0 C5 A:G164 3.9 0.1 1.0 O6 A:G163 4.3 0.8 1.0 O2' A:U177 4.3 0.1 1.0 C6 A:G163 4.4 0.0 1.0 N7 A:A178 4.4 0.5 1.0 OP2 A:U162 4.5 0.5 1.0 N9 A:G163 4.5 0.1 1.0 O2 A:U177 4.6 0.4 1.0 N1 A:G164 4.6 0.1 1.0 C4 A:G163 4.8 0.8 1.0 C2' A:U177 4.8 0.5 1.0 N6 A:A178 4.9 0.9 1.0 O5' A:G163 4.9 96.1 1.0 P A:G163 5.0 0.9 1.0

Magnesium binding site 5 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:88.6 occ:1.00 OP2 A:A171 2.6 0.0 1.0 OP2 A:U168 3.9 89.2 1.0 P A:A171 4.0 0.9 1.0 O3' A:U167 4.0 86.3 1.0 N7 A:A171 4.0 0.4 1.0 C8 A:A171 4.1 0.4 1.0 O2 A:U167 4.3 96.6 1.0 O2' A:U167 4.3 0.1 1.0 OP2 A:C170 4.4 97.2 1.0 OP1 A:A171 4.5 98.6 1.0 OP1 A:C170 4.5 99.2 1.0 OP2 A:C165 4.6 84.0 1.0 P A:U168 4.7 93.2 1.0 O5' A:C170 4.7 99.3 1.0 C1' A:U167 4.7 92.8 1.0 P A:C170 4.7 97.1 1.0 O3' A:C170 4.8 92.9 1.0 C2' A:U167 4.9 95.1 1.0 C3' A:C170 5.0 90.6 1.0

Magnesium binding site 6 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:90.0 occ:1.00 OP2 A:A173 2.5 0.4 1.0 P A:A173 3.9 0.9 1.0 N7 A:A173 3.9 0.5 1.0 O6 A:G174 4.0 0.0 1.0 OP2 A:A172 4.1 93.7 1.0 C8 A:A173 4.1 0.4 1.0 N7 A:G174 4.1 0.3 1.0 O5' A:A173 4.2 0.0 1.0 O2' A:A171 4.4 0.9 1.0 C3' A:A172 4.7 0.9 1.0 O3' A:A172 4.8 0.2 1.0 O3' A:A171 4.8 0.7 1.0 C6 A:G174 4.8 0.1 1.0 C5 A:G174 4.9 0.1 1.0 OP1 A:A173 4.9 0.1 1.0 C5 A:A173 5.0 0.7 1.0

Magnesium binding site 7 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:0.6 occ:1.00 OP1 A:C255 3.2 0.8 1.0 OP1 A:C213 3.6 94.3 1.0 OP2 A:A214 4.0 0.1 1.0 C5' A:C255 4.5 0.1 1.0 P A:C255 4.6 0.7 1.0 P A:C213 4.8 95.5 1.0 OP1 A:A214 4.8 0.9 1.0 P A:A214 4.9 0.9 1.0 O5' A:C255 4.9 0.5 1.0

Magnesium binding site 8 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:0.8 occ:1.00 O3' A:C127 4.0 0.4 1.0 OP1 A:U202 4.2 0.2 1.0 OP1 A:C128 4.3 0.0 1.0 OP2 A:A113 4.4 91.6 1.0 OP1 A:C203 4.5 83.3 1.0 O2' A:C127 4.5 0.1 1.0 OP2 A:C203 4.7 88.3 1.0 OP1 A:A113 4.7 93.1 1.0 P A:C128 4.9 0.2 1.0

Magnesium binding site 9 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:0.5 occ:1.00 OP2 A:G250 2.3 0.3 1.0 O2' A:A248 3.2 0.5 1.0 OP2 A:U249 3.4 0.0 1.0 P A:G250 3.8 0.3 1.0 O5' A:U249 3.9 0.8 1.0 P A:U249 4.2 0.9 1.0 C2' A:A248 4.3 0.0 1.0 N7 A:G250 4.4 0.2 1.0 O3' A:A248 4.4 0.6 1.0 OP1 A:G250 4.6 0.0 1.0 O5' A:G250 4.6 0.2 1.0 C3' A:A248 4.6 0.8 1.0 O3' A:U249 4.6 0.9 1.0 C8 A:G250 4.8 0.9 1.0 N7 A:G251 4.9 0.4 1.0 C3' A:U249 4.9 0.2 1.0

Magnesium binding site 10 out of 22 in the Group I Self-Splicing Intron P4-P6 Domain Mutant U131A (Without Isopropanol Soaking)


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 U131A (Without Isopropanol Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:0.4 occ:1.00 OP1 A:U155 3.3 99.0 1.0 OP2 A:U155 4.1 0.7 1.0 O3' A:A252 4.1 99.6 1.0 P A:U155 4.2 0.7 1.0 OP1 A:U253 4.3 0.5 1.0 O2' A:A252 4.7 0.6 1.0 OP1 A:U142 4.8 0.8 1.0 O3' A:C154 4.9 96.5 1.0 P A:U253 5.0 0.8 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