Strontium in PDB 6cab: Rna-Dgmp Complex with Sr Ion

The structure of Rna-Dgmp Complex with Sr Ion, PDB code: 6cab was solved by W.Zhang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.707, 48.707, 80.580, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 28

The binding sites of Strontium atom in the Rna-Dgmp Complex with Sr Ion (pdb code 6cab). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 4 binding sites of Strontium where determined in the Rna-Dgmp Complex with Sr Ion, PDB code: 6cab:
Jump to Strontium binding site number: 1; 2; 3; 4;

Strontium binding site 1 out of 4 in the Rna-Dgmp Complex with Sr Ion


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Rna-Dgmp Complex with Sr Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr103 b:77.0 occ:1.00 O B:HOH201 2.8 63.5 1.0 O6 A:G14 2.9 62.7 1.0 N7 A:G101 2.9 71.6 1.0 O6 A:G101 3.0 64.0 1.0 C5 A:G101 3.6 69.4 1.0 C6 A:G101 3.6 64.5 1.0 C6 A:G14 3.7 70.2 1.0 C8 A:G101 4.1 77.0 1.0 N7 A:G14 4.3 69.7 1.0 C5 A:G14 4.3 69.7 1.0 N7 B:G101 4.4 71.6 1.0 N4 B:LCC3 4.7 65.1 1.0 N1 A:G14 4.8 65.0 1.0 C4 A:G101 4.9 72.6 1.0 N1 A:G101 5.0 63.1 1.0

Strontium binding site 2 out of 4 in the Rna-Dgmp Complex with Sr Ion


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Rna-Dgmp Complex with Sr Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr104 b:83.5 occ:0.18 O3' A:G101 2.6 68.1 1.0 O2' A:G101 3.3 63.3 1.0 C3' A:G101 3.8 71.9 1.0 C2' A:G101 4.0 66.2 1.0 C4' A:G101 4.5 74.8 1.0

Strontium binding site 3 out of 4 in the Rna-Dgmp Complex with Sr Ion


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Rna-Dgmp Complex with Sr Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr103 b:77.0 occ:1.00 O A:HOH202 2.8 54.9 1.0 O6 B:G102 2.9 64.0 1.0 O6 B:G14 3.0 64.0 1.0 N7 B:G102 3.1 71.6 1.0 C6 B:G102 3.6 64.5 1.0 C5 B:G102 3.7 69.4 1.0 C6 B:G14 3.8 64.5 1.0 N7 B:G14 4.3 71.6 1.0 C8 B:G102 4.3 77.0 1.0 C5 B:G14 4.4 69.4 1.0 N7 A:G102 4.6 71.6 1.0 N4 A:LCC3 4.8 68.5 1.0 N1 B:G14 4.9 63.1 1.0 N1 B:G102 5.0 63.1 1.0

Strontium binding site 4 out of 4 in the Rna-Dgmp Complex with Sr Ion


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Rna-Dgmp Complex with Sr Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr104 b:0.5 occ:0.16 O3' B:G102 2.4 70.8 1.0 C3' B:G102 3.6 75.6 1.0 O2' B:G102 4.4 82.1 1.0 C2' B:G102 4.6 74.1 1.0 C4' B:G102 4.6 79.2 1.0 C5' A:G102 4.9 0.3 1.0 C4' A:G102 5.0 0.0 1.0

W.Zhang, T.Walton, L.Li, J.W.Szostak. Crystallographic Observation of Nonenzymatic Rna Primer Extension. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29851379
DOI: 10.7554/ELIFE.36422