Magnesium in PDB 7kul: Dna Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

The structure of Dna Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kul 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 / 1.64
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	47.443, 47.443, 82.803, 90, 90, 120
R / Rfree (%)	20.8 / 24.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Dna Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G (pdb code 7kul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Dna Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kul:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Dna 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 Dna 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:12.8 occ:0.33 O2D B:GP3101 2.1 14.3 1.0 O3D B:GP3101 2.1 14.8 1.0 C3D B:GP3101 3.0 14.1 1.0 C2D B:GP3101 3.0 14.1 1.0 C4D B:GP3101 3.5 15.6 1.0 C1D B:GP3101 4.2 12.5 1.0 O4D B:GP3101 4.4 13.0 1.0 O B:HOH226 4.4 34.1 1.0 O B:HOH228 4.5 20.3 1.0 C5D B:GP3101 4.7 17.5 1.0

Magnesium binding site 2 out of 12 in the Dna 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 Dna 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:19.4 occ:1.00 O A:HOH223 2.1 15.3 1.0 O B:HOH252 2.1 19.2 1.0 O A:HOH253 2.1 20.7 1.0 O B:HOH222 2.1 14.4 1.0 O A:HOH214 2.1 18.7 1.0 O B:HOH216 2.2 18.1 1.0 O4 A:U7 4.2 15.4 1.0 O4 B:U7 4.2 14.9 1.0 O4 A:U8 4.4 21.3 1.0 O A:HOH238 4.4 18.9 1.0 O4 B:U8 4.4 20.5 1.0 O B:HOH238 4.5 20.9 1.0 O A:HOH241 4.5 20.6 1.0 O B:HOH242 4.5 20.1 1.0 N6 B:A9 4.9 26.8 1.0 N6 A:A9 4.9 25.9 1.0 C4 A:U7 4.9 17.0 1.0

Magnesium binding site 3 out of 12 in the Dna 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 Dna 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:11.8 occ:1.00 O B:HOH247 2.0 9.1 1.0 O A:HOH236 2.0 13.3 1.0 O B:HOH232 2.1 20.1 1.0 O B:HOH240 2.2 19.3 1.0 O A:HOH203 2.2 18.5 1.0 MG B:MG104 4.1 17.1 1.0 OP2 A:A5 4.1 7.5 1.0 O B:HOH220 4.2 11.5 1.0 OP1 A:A5 4.3 7.3 1.0 OP1 A:LCG4 4.4 9.9 1.0 OP2 B:U7 4.4 12.2 1.0 OP1 B:C6 4.6 6.8 1.0 O A:HOH250 4.6 32.2 1.0 P A:A5 4.6 8.0 1.0 OP2 A:LCG4 4.8 8.9 1.0 OP1 B:U7 4.8 17.0 1.0 P A:LCG4 5.0 9.5 1.0 P B:U7 5.0 16.0 1.0

Magnesium binding site 4 out of 12 in the Dna 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 Dna 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:36.3 occ:1.00 O A:HOH257 1.9 33.9 1.0 O A:HOH202 2.0 25.7 1.0 O A:HOH242 2.0 28.0 1.0 O A:HOH222 2.0 28.7 1.0 O A:HOH255 2.1 37.2 1.0 O A:HOH248 2.1 41.0 1.0 O A:HOH205 3.9 38.7 1.0 O6 A:G11 4.1 17.3 1.0 N7 A:A10 4.1 28.8 1.0 N6 A:A10 4.2 24.4 1.0 O A:HOH210 4.2 29.1 1.0 O B:HOH243 4.4 23.0 1.0 N7 A:G11 4.4 26.3 1.0 O A:HOH231 4.4 26.9 1.0 O A:HOH252 4.4 29.8 1.0 C5 A:A10 4.8 28.5 1.0 C6 A:A10 4.9 26.2 1.0 C6 A:G11 4.9 21.8 1.0

Magnesium binding site 5 out of 12 in the Dna 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 Dna 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:Mg106 b:36.4 occ:1.00 O B:HOH205 1.9 21.3 1.0 O A:HOH256 2.1 32.5 1.0 O A:HOH215 2.1 27.6 1.0 O A:HOH229 2.2 29.1 1.0 O1B B:GP3101 4.1 32.6 1.0 N7A B:GP3101 4.2 9.8 1.0 N7 A:DG14 4.4 12.2 1.0 O6 A:DG14 4.5 13.1 1.0 O A:HOH245 4.5 28.3 1.0 O6A B:GP3101 4.5 10.8 1.0

Magnesium binding site 6 out of 12 in the Dna 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 Dna 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:Mg107 b:43.1 occ:1.00 O2B B:GP3101 1.9 38.0 1.0 O2G B:GP3101 1.9 41.8 1.0 O2A B:GP3101 1.9 27.6 1.0 O B:HOH201 2.2 31.7 1.0 PB B:GP3101 2.9 32.8 1.0 PG B:GP3101 3.0 37.0 1.0 O3B B:GP3101 3.0 38.2 1.0 PA B:GP3101 3.1 23.7 1.0 O3A B:GP3101 3.4 28.1 1.0 O1G B:GP3101 4.0 34.5 1.0 O5E B:GP3101 4.1 30.9 1.0 O5D B:GP3101 4.2 21.2 1.0 O1A B:GP3101 4.2 24.6 1.0 O1B B:GP3101 4.3 32.6 1.0 C5E B:GP3101 4.3 24.6 1.0 O B:HOH226 4.6 34.1 1.0

Magnesium binding site 7 out of 12 in the Dna 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 Dna 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:12.3 occ:0.33 O2D A:GP3101 2.1 14.3 1.0 O3D A:GP3101 2.1 14.2 1.0 C3D A:GP3101 3.0 13.7 1.0 C2D A:GP3101 3.0 13.8 1.0 C4D A:GP3101 3.5 15.1 1.0 C1D A:GP3101 4.2 12.5 1.0 O A:HOH218 4.3 27.3 1.0 O4D A:GP3101 4.4 12.8 1.0 O A:HOH230 4.5 20.7 1.0 C5D A:GP3101 4.6 17.1 1.0

Magnesium binding site 8 out of 12 in the Dna 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 Dna 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:11.1 occ:1.00 O A:HOH247 1.9 9.4 1.0 O B:HOH233 2.0 12.3 1.0 O A:HOH232 2.1 19.3 1.0 O A:HOH244 2.1 18.9 1.0 O B:HOH203 2.2 19.0 1.0 OP2 B:A5 4.1 7.5 1.0 O A:HOH228 4.2 11.5 1.0 OP1 B:A5 4.3 7.6 1.0 OP1 B:LCG4 4.4 10.2 1.0 OP2 A:U7 4.4 12.6 1.0 OP1 A:C6 4.6 6.7 1.0 P B:A5 4.6 8.3 1.0 OP2 B:LCG4 4.8 8.6 1.0 OP1 A:U7 4.8 18.3 1.0 P B:LCG4 5.0 9.9 1.0 P A:U7 5.0 15.9 1.0

Magnesium binding site 9 out of 12 in the Dna 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 9 of Dna 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:17.1 occ:1.00 OP1 B:C6 2.6 6.8 1.0 O B:HOH247 2.7 9.1 1.0 C5' B:C6 3.5 8.9 1.0 P B:C6 3.8 8.3 1.0 O B:HOH230 3.8 9.8 1.0 O B:HOH240 3.8 19.3 1.0 O5' B:C6 4.0 9.5 1.0 MG A:MG104 4.1 11.8 1.0 O B:HOH234 4.1 31.4 1.0 O3' B:A5 4.2 8.1 1.0 O B:HOH220 4.5 11.5 1.0 C4' B:C6 4.8 10.3 1.0

Magnesium binding site 10 out of 12 in the Dna 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 10 of Dna 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:35.0 occ:1.00 O B:HOH255 1.8 33.2 1.0 O B:HOH225 2.0 29.9 1.0 O B:HOH202 2.1 25.8 1.0 O B:HOH254 2.1 36.5 1.0 O B:HOH246 2.1 39.2 1.0 O B:HOH239 2.1 27.2 1.0 O B:HOH206 3.8 36.7 1.0 O6 B:G11 4.1 19.8 1.0 N7 B:A10 4.2 29.8 1.0 N6 B:A10 4.3 25.2 1.0 O B:HOH210 4.3 27.9 1.0 O A:HOH240 4.3 23.4 1.0 N7 B:G11 4.4 26.4 1.0 O B:HOH219 4.4 26.5 1.0 O B:HOH250 4.5 35.8 1.0 C5 B:A10 4.9 29.4 1.0 C6 B:G11 4.9 22.3 1.0 C6 B:A10 4.9 27.6 1.0 O A:HOH217 5.0 30.6 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