Magnesium in PDB 7kup: 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

The structure of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kup was solved by Z.Fang, C.Giurgiu, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.44
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.972, 48.972, 82.204, 90, 90, 120
R / Rfree (%)	19.9 / 21.8

The binding sites of Magnesium atom in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G (pdb code 7kup). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kup:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:9.7 occ:0.33 O3D B:GP3101 2.1 10.9 1.0 O2D B:GP3101 2.1 9.9 1.0 C3D B:GP3101 3.0 9.7 1.0 C2D B:GP3101 3.0 8.9 1.0 C4D B:GP3101 3.5 10.5 1.0 C1D B:GP3101 4.2 8.6 1.0 O4D B:GP3101 4.3 9.2 1.0 O B:HOH224 4.3 21.4 1.0 O B:HOH256 4.5 16.5 1.0 C5D B:GP3101 4.7 12.8 1.0

Magnesium binding site 2 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:11.3 occ:1.00 O B:HOH240 2.1 13.8 1.0 O A:HOH212 2.1 13.2 1.0 O A:HOH235 2.1 13.8 1.0 O B:HOH269 2.1 11.6 1.0 O A:HOH221 2.1 10.0 1.0 O B:HOH238 2.1 11.2 1.0 O B:HOH227 4.1 9.2 1.0 O B:HOH270 4.1 26.9 1.0 OP2 A:A9 4.1 8.6 1.0 OP1 A:A9 4.2 8.5 1.0 O A:HOH236 4.2 17.8 1.0 O B:HOH273 4.2 26.2 1.0 O B:HOH229 4.3 13.2 1.0 O B:HOH267 4.4 28.1 1.0 O A:HOH269 4.4 25.7 1.0 OP2 B:U11 4.5 12.3 1.0 OP1 A:LCG4 4.5 7.9 1.0 OP1 B:C10 4.5 6.9 1.0 P A:A9 4.7 7.5 1.0

Magnesium binding site 3 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:41.7 occ:1.00 O2G B:GP3101 1.9 35.5 1.0 O2A B:GP3101 2.0 23.2 1.0 O B:HOH201 2.4 36.4 1.0 O B:HOH202 2.5 30.6 1.0 O B:HOH224 3.1 21.4 1.0 PA B:GP3101 3.2 17.9 1.0 PG B:GP3101 3.2 33.7 1.0 O3B B:GP3101 3.5 33.7 1.0 O2B B:GP3101 3.5 35.1 1.0 O5D B:GP3101 3.6 15.3 1.0 O3A B:GP3101 3.9 21.9 1.0 PB B:GP3101 3.9 29.4 1.0 C5E B:GP3101 4.0 27.2 1.0 O5E B:GP3101 4.0 27.7 1.0 C5D B:GP3101 4.1 12.8 1.0 O1G B:GP3101 4.4 27.4 1.0 O1A B:GP3101 4.4 23.1 1.0 C3D B:GP3101 5.0 9.7 1.0

Magnesium binding site 4 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:33.7 occ:0.33 O A:HOH225 3.3 16.2 1.0 O B:HOH226 3.3 16.4 1.0 O A:HOH270 3.7 21.5 0.3 O A:HOH214 3.7 20.9 1.0 O B:HOH218 3.7 20.4 1.0 O B:HOH272 3.8 25.1 0.3 O A:HOH242 4.3 17.9 1.0 O B:HOH245 4.3 17.6 1.0

Magnesium binding site 5 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:9.6 occ:0.33 O3D A:GP3101 2.1 11.5 1.0 O2D A:GP3101 2.1 9.7 1.0 C3D A:GP3101 3.0 9.9 1.0 C2D A:GP3101 3.0 9.0 1.0 C4D A:GP3101 3.5 10.6 1.0 C1D A:GP3101 4.2 8.7 1.0 O4D A:GP3101 4.3 9.3 1.0 O A:HOH224 4.3 21.1 1.0 O A:HOH256 4.5 17.4 1.0 C5D A:GP3101 4.7 12.8 1.0

Magnesium binding site 6 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:11.2 occ:1.00 O A:HOH241 2.0 13.7 1.0 O B:HOH215 2.1 13.6 1.0 O B:HOH236 2.1 13.6 1.0 O A:HOH267 2.1 12.0 1.0 O A:HOH237 2.1 11.0 1.0 O B:HOH223 2.2 10.5 1.0 O A:HOH268 4.1 24.9 1.0 OP2 B:A9 4.2 8.9 1.0 OP1 B:A9 4.2 8.9 1.0 O A:HOH272 4.2 25.7 1.0 O B:HOH239 4.2 19.8 1.0 O A:HOH238 4.3 13.8 1.0 O A:HOH265 4.4 27.6 1.0 O B:HOH271 4.4 26.4 1.0 OP1 B:LCG4 4.5 7.8 1.0 OP1 A:C10 4.5 7.0 1.0 OP2 A:U11 4.5 12.4 1.0 P B:A9 4.7 7.6 1.0

Magnesium binding site 7 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:40.9 occ:1.00 O2G A:GP3101 1.9 36.9 1.0 O2A A:GP3101 2.0 22.9 1.0 O A:HOH201 2.4 35.1 1.0 O A:HOH224 3.1 21.1 1.0 PA A:GP3101 3.2 18.2 1.0 PG A:GP3101 3.2 34.5 1.0 O3B A:GP3101 3.4 34.4 1.0 O2B A:GP3101 3.5 35.2 1.0 O5D A:GP3101 3.6 14.8 1.0 O3A A:GP3101 3.8 21.2 1.0 PB A:GP3101 3.9 29.8 1.0 C5E A:GP3101 4.0 27.4 1.0 O5E A:GP3101 4.0 27.7 1.0 C5D A:GP3101 4.1 12.8 1.0 O1G A:GP3101 4.4 27.1 1.0 O1A A:GP3101 4.4 22.6 1.0 C3D A:GP3101 5.0 9.9 1.0

Magnesium binding site 8 out of 8 in the 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2'-Ome Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:29.0 occ:0.33 O A:HOH261 2.7 37.5 1.0 O2' B:LCG4 3.5 6.4 1.0 O B:HOH246 3.7 28.6 1.0 C6' B:LCG4 3.9 6.7 1.0 O B:HOH256 4.1 16.5 1.0 O B:HOH233 4.2 21.1 1.0 C1' B:LCG4 4.3 5.9 1.0 C2' B:LCG4 4.5 5.5 1.0 O4' B:LCG4 4.6 6.0 1.0 C4' B:LCG4 4.9 5.9 1.0

C.Giurgiu, Z.Fang, H.R.M.Aitken, S.C.Kim, L.Pazienza, S.Mittal, J.W.Szostak. Structure-Activity Relationships in Nonenzymatic Template-Directed Rna Synthesis. Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
PubMed: 34428345
DOI: 10.1002/ANIE.202109714