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

The structure of Lna Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kum 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 / 1.71
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	47.769, 47.769, 84.122, 90, 90, 120
R / Rfree (%)	20.5 / 22

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

Magnesium binding site 1 out of 4 in the Lna 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 Lna 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:4.9 occ:0.33 O2D B:GP3101 2.1 5.2 1.0 O3D B:GP3101 2.1 5.4 1.0 C3D B:GP3101 3.0 5.9 1.0 C2D B:GP3101 3.0 5.1 1.0 C4D B:GP3101 3.5 6.3 1.0 C1D B:GP3101 4.2 5.1 1.0 O B:HOH211 4.2 16.6 1.0 O4D B:GP3101 4.4 5.4 1.0 C5D B:GP3101 4.6 8.0 1.0 O B:HOH241 4.7 16.2 1.0

Magnesium binding site 2 out of 4 in the Lna 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 Lna 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:34.9 occ:1.00 O2A B:GP3101 1.9 15.0 1.0 O B:HOH204 2.1 33.4 1.0 O B:HOH201 2.4 34.9 1.0 O3B B:GP3101 2.7 21.5 1.0 PA B:GP3101 3.2 11.7 1.0 O2B B:GP3101 3.2 21.8 1.0 O2G B:GP3101 3.5 25.2 1.0 PB B:GP3101 3.5 18.7 1.0 O3A B:GP3101 3.6 14.2 1.0 PG B:GP3101 3.7 22.3 1.0 O1A B:GP3101 4.1 12.1 1.0 O5D B:GP3101 4.2 9.6 1.0 O B:HOH211 4.4 16.6 1.0 C5E B:GP3101 4.4 17.2 1.0 O5E B:GP3101 4.4 21.0 1.0 O B:HOH219 4.7 20.0 1.0 O1B B:GP3101 4.9 16.5 1.0 O1G B:GP3101 4.9 24.8 1.0

Magnesium binding site 3 out of 4 in the Lna 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 Lna 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:5.1 occ:0.33 O2D A:GP3101 2.1 5.6 1.0 O3D A:GP3101 2.1 5.7 1.0 C3D A:GP3101 3.0 6.2 1.0 C2D A:GP3101 3.0 5.5 1.0 C4D A:GP3101 3.5 6.5 1.0 C1D A:GP3101 4.2 5.4 1.0 O A:HOH208 4.3 20.4 1.0 O4D A:GP3101 4.3 5.8 1.0 C5D A:GP3101 4.6 8.1 1.0 O A:HOH231 4.6 14.5 1.0

Magnesium binding site 4 out of 4 in the Lna 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 Lna 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:40.2 occ:1.00 O2A A:GP3101 1.9 16.0 1.0 O3B A:GP3101 2.0 24.6 1.0 O2G A:GP3101 2.7 25.5 1.0 PG A:GP3101 2.8 23.1 1.0 PA A:GP3101 3.0 12.4 1.0 C5E A:GP3101 3.0 16.5 1.0 O3A A:GP3101 3.1 14.6 1.0 PB A:GP3101 3.1 19.6 1.0 O5E A:GP3101 3.2 20.6 1.0 O2B A:GP3101 3.5 22.7 1.0 O A:HOH208 3.5 20.4 1.0 O5D A:GP3101 3.7 10.2 1.0 O1G A:GP3101 4.2 25.7 1.0 O1A A:GP3101 4.3 12.3 1.0 O1B A:GP3101 4.4 16.2 1.0 C5D A:GP3101 4.5 8.1 1.0 C4E A:GP3101 4.5 15.2 1.0 O4E A:GP3101 5.0 12.9 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