Cobalt in PDB 7lnf: 3'-Deoxy Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

The structure of 3'-Deoxy Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7lnf 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)	27.75 / 1.65
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.822, 46.822, 83.199, 90, 90, 120
R / Rfree (%)	20.8 / 23.9

The structure of 3'-Deoxy Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

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

Cobalt binding site 1 out of 2 in the 3'-Deoxy 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 Cobalt with other atoms in the Co binding site number 1 of 3'-Deoxy 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:Co111 b:28.3 occ:1.00 N7B A:GP3106 2.1 13.1 1.0 O1B A:GP3106 2.1 31.9 1.0 O A:HOH206 2.2 28.2 1.0 O A:HOH246 2.3 27.5 1.0 O A:HOH234 2.4 26.2 1.0 O A:HOH254 2.6 28.9 1.0 C8B A:GP3106 2.8 11.9 1.0 O A:HOH201 3.0 26.6 1.0 C5B A:GP3106 3.3 11.6 1.0 PB A:GP3106 3.8 36.5 1.0 O6B A:GP3106 3.8 11.8 1.0 C6B A:GP3106 4.0 11.0 1.0 N9B A:GP3106 4.1 12.1 1.0 O1G A:GP3106 4.1 30.8 1.0 O6A A:GP3106 4.2 8.9 1.0 C4B A:GP3106 4.3 11.3 1.0 N7A A:GP3106 4.3 9.6 1.0 O2B A:GP3106 4.7 35.6 1.0 C6A A:GP3106 4.7 9.3 1.0 O3A A:GP3106 4.7 30.8 1.0 O3B A:GP3106 4.7 36.6 1.0 C5A A:GP3106 4.8 9.1 1.0 O5E A:GP3106 4.8 24.3 1.0 PG A:GP3106 4.8 28.3 1.0

Cobalt binding site 2 out of 2 in the 3'-Deoxy 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 Cobalt with other atoms in the Co binding site number 2 of 3'-Deoxy 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:Co111 b:28.1 occ:1.00 N7B B:GP3103 2.1 12.1 1.0 O1B B:GP3103 2.1 31.7 1.0 O B:HOH204 2.2 28.8 1.0 O B:HOH249 2.2 31.1 1.0 O B:HOH227 2.5 22.1 1.0 O B:HOH254 2.5 28.6 1.0 C8B B:GP3103 2.8 11.6 1.0 O B:HOH201 3.1 26.1 1.0 C5B B:GP3103 3.3 11.2 1.0 PB B:GP3103 3.8 36.9 1.0 O6B B:GP3103 3.8 11.7 1.0 C6B B:GP3103 3.9 10.6 1.0 O1G B:GP3103 4.1 30.1 1.0 N9B B:GP3103 4.1 11.8 1.0 O6A B:GP3103 4.1 8.9 1.0 C4B B:GP3103 4.3 11.0 1.0 N7A B:GP3103 4.3 10.0 1.0 O B:HOH255 4.3 31.0 1.0 C6A B:GP3103 4.7 9.8 1.0 O2B B:GP3103 4.7 34.6 1.0 O3B B:GP3103 4.8 36.1 1.0 C5A B:GP3103 4.8 9.4 1.0 O3A B:GP3103 4.8 30.7 1.0 O5E B:GP3103 4.8 24.7 1.0 PG B:GP3103 4.9 29.2 1.0

C.Giurgiu, Z.Fang, J.W.Szostak. Sugar Conformation Impacts on Nonezymatic Rna Primer Extension To Be Published.