Strontium in PDB 4tzw: Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization

The structure of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization, PDB code: 4tzw was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.79 / 4.67
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.316, 75.316, 268.942, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 33.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Strontium atom in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization (pdb code 4tzw). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 36 binding sites of Strontium where determined in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization, PDB code: 4tzw:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr101 b:0.3 occ:0.50 OP1 B:G45 4.7 0.7 1.0 OP1 B:G10 5.0 0.1 1.0

Strontium binding site 2 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr102 b:0.1 occ:1.00 OP1 B:G7 3.9 0.1 1.0 OP2 B:G15 4.2 0.1 1.0 N7 B:G15 4.5 0.5 1.0 OP2 B:G7 4.9 0.8 1.0 P B:G7 4.9 0.8 1.0

Strontium binding site 3 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr103 b:0.1 occ:1.00 N7 B:G70 4.0 0.8 1.0 N7 B:G69 4.2 0.7 1.0 O6 B:G70 4.2 1.0 1.0 C5 B:G69 4.6 0.4 1.0 O6 B:G69 4.8 0.2 1.0 C8 B:G69 4.8 0.7 1.0 C6 B:G69 4.8 0.1 1.0 OP2 B:G69 4.8 0.6 1.0 C5 B:G70 4.8 0.8 1.0 C6 B:G70 4.9 0.0 1.0

Strontium binding site 4 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr104 b:0.3 occ:1.00 SR B:SR112 2.3 0.0 1.0 N7 B:G43 3.6 0.2 1.0 O6 B:G43 4.0 0.6 1.0 N7 B:G42 4.1 0.2 1.0 O6 B:G44 4.1 0.1 1.0 C5 B:G42 4.4 0.5 1.0 C5 B:G43 4.5 0.9 1.0 C8 B:G42 4.6 0.3 1.0 SR B:SR108 4.6 0.0 1.0 C6 B:G43 4.6 0.5 1.0 C8 B:G43 4.6 0.8 1.0 C6 B:G42 4.7 0.9 1.0 O6 B:G42 4.7 0.3 1.0

Strontium binding site 5 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr105 b:0.0 occ:1.00 OP2 B:G50 3.6 0.7 1.0 OP2 B:G51 3.6 0.9 1.0 SR B:SR111 4.2 0.8 1.0 P B:G50 4.8 0.9 1.0

Strontium binding site 6 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr106 b:0.6 occ:1.00 O4 B:U54 3.0 0.8 1.0 C4 B:U54 3.8 0.2 1.0 OP1 B:G56 4.0 0.8 1.0 C5 B:U54 4.0 0.2 1.0 OP2 B:U53 4.5 0.4 1.0 N3 B:U54 5.0 0.7 1.0

Strontium binding site 7 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr107 b:0.1 occ:1.00 OP2 B:A73 4.6 0.1 1.0 N7 B:G72 4.7 0.7 1.0

Strontium binding site 8 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr108 b:0.0 occ:1.00 O6 B:G41 2.9 0.5 1.0 N7 B:G41 3.3 0.4 1.0 C6 B:G41 3.4 0.9 1.0 O6 B:G42 3.5 0.3 1.0 C5 B:G41 3.6 0.0 1.0 N7 B:G42 3.6 0.2 1.0 C6 B:G42 4.2 0.9 1.0 C5 B:G42 4.3 0.5 1.0 C8 B:G41 4.4 0.4 1.0 SR B:SR104 4.6 0.3 1.0 N1 B:G41 4.6 0.6 1.0 C8 B:G42 4.8 0.3 1.0 C4 B:G41 4.8 0.4 1.0 O4 B:U40 4.9 0.7 1.0

Strontium binding site 9 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr109 b:1.0 occ:1.00 OP2 B:C29 4.3 0.1 1.0 O2' B:U31 4.7 0.4 1.0

Strontium binding site 10 out of 36 in the Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Co-Crystals of the Ternary Complex Containing A T-Box Stem I Rna, Its Cognate Trnagly, and B. Subtilis Ybxf Protein, Treated By Removing Lithium Sulfate and Replacing MG2+ with SR2+ Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr110 b:0.7 occ:1.00 OP1 B:U8 3.3 0.5 1.0 OP2 B:U8 3.6 0.9 1.0 OP2 B:A9 3.6 0.5 1.0 P B:U8 4.0 0.3 1.0 OP2 B:U11 4.4 0.3 1.0 OP2 B:U12 4.5 0.8 1.0 P B:A9 4.8 0.2 1.0 OP1 B:A9 4.9 0.0 1.0 O5' B:U8 5.0 0.8 1.0

J.Zhang, A.R.Ferre-D'amare. Dramatic Improvement of Crystals of Large Rnas By Cation Replacement and Dehydration. Structure V. 22 1363 2014.
ISSN: ISSN 0969-2126
PubMed: 25185828
DOI: 10.1016/J.STR.2014.07.011