Magnesium in PDB 6dvk: Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)

The structure of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6), PDB code: 6dvk was solved by D.R.Eiler, J.D.Yesselman, D.A.Costantino, R.Das, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.00 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	233.372, 25.358, 42.861, 90.00, 99.74, 90.00
R / Rfree (%)	23.2 / 26.9

The structure of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) also contains other interesting chemical elements:

Cobalt

(Co)

4 atoms

The binding sites of Magnesium atom in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) (pdb code 6dvk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6), PDB code: 6dvk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:13.5 occ:1.00 OP2 H:C94 4.1 31.1 1.0

Magnesium binding site 2 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg102 b:24.2 occ:1.00 OP2 H:U8 3.3 59.9 1.0 O2' H:A7 3.7 43.9 1.0 O6 H:G10 3.8 16.9 1.0 O6 H:G9 4.4 14.4 1.0 C2' H:A7 4.7 44.2 1.0 P H:U8 4.7 61.3 1.0 N7 H:G10 4.8 19.0 1.0 C6 H:G10 4.8 17.6 1.0 O4 H:U83 4.9 31.6 1.0 N4 H:C84 5.0 21.4 1.0

Magnesium binding site 3 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg103 b:23.0 occ:1.00 OP1 H:G61 3.7 65.1 1.0 N7 H:A24 4.4 28.1 1.0 O6 H:G25 4.4 30.4 1.0 N7 H:G25 4.8 34.9 1.0 N6 H:A24 5.0 28.9 1.0

Magnesium binding site 4 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg104 b:13.6 occ:1.00 O2' H:A87 2.3 25.0 1.0 N7 H:G89 2.7 18.3 1.0 O3' H:A87 2.8 26.0 1.0 O6 H:G89 2.8 16.6 1.0 O4 H:U90 2.9 22.1 1.0 C2' H:A87 3.3 26.1 1.0 C5 H:G89 3.4 18.0 1.0 OP2 H:A88 3.4 29.0 1.0 C6 H:G89 3.4 17.7 1.0 C3' H:A87 3.6 26.3 1.0 P H:A88 3.6 27.1 1.0 C4 H:U90 3.7 22.5 1.0 C1' H:A87 3.9 26.1 1.0 C8 H:G89 3.9 19.7 1.0 N6 H:A5 4.0 17.6 1.0 O5' H:A88 4.0 25.2 1.0 C5 H:U90 4.2 21.4 1.0 N7 H:A88 4.4 21.4 1.0 C8 H:A88 4.6 21.8 1.0 N3 H:U90 4.6 23.8 1.0 O4 H:U6 4.7 28.4 1.0 C4 H:G89 4.7 18.7 1.0 C4' H:A87 4.8 26.5 1.0 O4' H:A87 4.8 26.6 1.0 N1 H:G89 4.8 18.2 1.0 N9 H:A87 4.9 26.0 1.0 N9 H:G89 5.0 20.0 1.0 N3 H:U6 5.0 26.1 1.0 OP1 H:A88 5.0 24.8 1.0

Magnesium binding site 5 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg109 b:35.0 occ:1.00 O H:HOH205 2.2 39.0 1.0 O H:HOH206 2.2 38.1 1.0 O H:HOH202 2.2 42.2 1.0 O H:HOH208 2.2 40.5 1.0 O H:HOH207 2.2 40.0 1.0 OP2 H:C19 4.0 20.8 1.0 O6 H:G20 4.3 17.1 1.0 O6 H:G73 4.4 21.0 1.0 N7 H:G20 4.5 18.9 1.0 C6 H:G73 5.0 20.2 1.0

J.D.Yesselman, D.Eiler, E.D.Carlson, M.R.Gotrik, A.E.D'aquino, A.N.Ooms, W.Kladwang, P.D.Carlson, X.Shi, D.A.Costantino, D.Herschlag, J.B.Lucks, M.C.Jewett, J.S.Kieft, R.Das. Computational Design of Three-Dimensional Rna Structure and Function. Nat Nanotechnol V. 14 866 2019.
ISSN: ESSN 1748-3395
PubMed: 31427748
DOI: 10.1038/S41565-019-0517-8