Magnesium in PDB 5uee: Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G

The structure of Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G, PDB code: 5uee was solved by W.Zhang, C.P.Tam, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.964, 46.964, 83.103, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.5

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

Magnesium binding site 1 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:24.6 occ:0.33 O2D B:GP3101 2.4 24.4 1.0 O3D B:GP3101 2.4 27.9 1.0 C3D B:GP3101 3.4 27.7 1.0 C2D B:GP3101 3.4 27.8 1.0 C4D B:GP3101 3.8 26.7 1.0 C1D B:GP3101 4.5 30.1 1.0 O B:HOH206 4.7 27.1 1.0 O4D B:GP3101 4.7 26.8 1.0 C5D B:GP3101 4.9 31.7 1.0

Magnesium binding site 2 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:51.9 occ:1.00 O2B B:GP3101 2.4 51.6 1.0 O2A B:GP3101 2.4 36.1 1.0 O2G B:GP3101 3.1 55.1 1.0 MG A:MG104 3.2 49.2 1.0 PB B:GP3101 3.5 42.8 1.0 PA B:GP3101 3.5 32.1 1.0 O3B B:GP3101 3.7 54.5 1.0 PG B:GP3101 3.8 45.5 1.0 O3A B:GP3101 3.8 39.1 1.0 O1G B:GP3101 4.2 38.3 1.0 O1A B:GP3101 4.2 31.4 1.0 O5D B:GP3101 4.8 31.9 1.0 O1B B:GP3101 4.9 45.2 1.0

Magnesium binding site 3 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:49.2 occ:1.00 O2A B:GP3101 2.2 36.1 1.0 MG A:MG103 3.2 51.9 1.0 PA B:GP3101 3.5 32.1 1.0 C5D B:GP3101 4.0 31.7 1.0 O1A B:GP3101 4.0 31.4 1.0 O5D B:GP3101 4.2 31.9 1.0 O2G B:GP3101 4.3 55.1 1.0 O3A B:GP3101 4.8 39.1 1.0 O2B B:GP3101 5.0 51.6 1.0

Magnesium binding site 4 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:24.6 occ:0.33 O3D A:GP3101 2.4 26.8 1.0 O2D A:GP3101 2.4 23.3 1.0 C3D A:GP3101 3.3 25.7 1.0 C2D A:GP3101 3.4 25.9 1.0 C4D A:GP3101 3.8 24.7 1.0 C1D A:GP3101 4.6 28.8 1.0 O A:HOH208 4.7 33.3 1.0 O4D A:GP3101 4.7 26.2 1.0 C5D A:GP3101 4.9 30.4 1.0

Magnesium binding site 5 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:52.9 occ:1.00 O2A A:GP3101 2.3 35.8 1.0 O2B A:GP3101 2.5 47.3 1.0 O2G A:GP3101 3.0 53.7 1.0 MG B:MG104 3.0 48.6 1.0 PA A:GP3101 3.5 31.6 1.0 PB A:GP3101 3.6 42.0 1.0 O3B A:GP3101 3.6 52.8 1.0 PG A:GP3101 3.8 43.5 1.0 O3A A:GP3101 3.9 40.1 1.0 O1G A:GP3101 4.2 36.2 1.0 O1A A:GP3101 4.3 32.2 1.0 O A:HOH208 4.5 33.3 1.0 O5D A:GP3101 4.8 30.7 1.0 O1B A:GP3101 5.0 41.5 1.0

Magnesium binding site 6 out of 6 in the Rna Primer-Template 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 Rna Primer-Template Complex with Guanosine Dinucleotide Ligand G(5') Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:48.6 occ:1.00 O2A A:GP3101 2.3 35.8 1.0 O A:HOH208 2.9 33.3 1.0 MG B:MG103 3.0 52.9 1.0 PA A:GP3101 3.5 31.6 1.0 O1A A:GP3101 4.1 32.2 1.0 C5D A:GP3101 4.1 30.4 1.0 O5D A:GP3101 4.2 30.7 1.0 O2G A:GP3101 4.3 53.7 1.0 O3A A:GP3101 4.9 40.1 1.0

W.Zhang, C.P.Tam, T.Walton, A.C.Fahrenbach, G.Birrane, J.W.Szostak. Insight Into the Mechanism of Nonenzymatic Rna Primer Extension From the Structure of An Rna-Gpppg Complex. Proc. Natl. Acad. Sci. V. 114 7659 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28673998
DOI: 10.1073/PNAS.1704006114