Magnesium in PDB 4tzz: 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 Increasing PEG3350 Concentration From 20% to 45% 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization, PDB code: 4tzz 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)	70.61 / 3.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.641, 260.733, 70.698, 90.00, 92.80, 90.00
R / Rfree (%)	21.7 / 26.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Magnesium 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization (pdb code 4tzz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 29 binding sites of Magnesium 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization, PDB code: 4tzz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:77.6 occ:1.00 OP1 B:A74 3.9 88.4 1.0 OP2 B:A74 4.2 89.4 1.0 N7 B:G72 4.4 87.6 1.0 P B:A74 4.5 87.5 1.0 OP2 B:A73 4.7 0.0 1.0 C5 B:G72 4.7 85.0 1.0 C8 B:G72 4.9 87.9 1.0 C5' B:A73 4.9 71.7 1.0

Magnesium binding site 2 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:60.0 occ:1.00 N7 B:G76 4.1 85.5 1.0 OP2 B:A75 4.4 71.2 1.0 O6 B:G76 4.9 90.1 1.0 N4 B:C77 4.9 88.4 1.0 C8 B:G76 5.0 84.0 1.0

Magnesium binding site 3 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:49.9 occ:1.00 O6 C:G15 3.4 74.1 1.0 N7 C:A14 4.0 80.0 1.0 N6 C:A14 4.1 80.7 1.0 N7 C:G15 4.2 72.0 1.0 C6 C:G15 4.3 73.3 1.0 OP2 C:C89 4.6 97.3 1.0 C5 C:G15 4.6 72.3 1.0 C5 C:A14 4.6 79.7 1.0 C6 C:A14 4.7 80.1 1.0 N6 C:A16 4.7 96.8 1.0 C8 C:A14 5.0 80.2 1.0

Magnesium binding site 4 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:50.4 occ:1.00 O2' C:C102 2.2 0.5 1.0 O3' C:C102 2.8 0.3 1.0 C2' C:C102 3.3 0.5 1.0 C3' C:C102 3.6 0.7 1.0 C1' C:C102 4.0 0.2 1.0 C4' C:C102 4.8 0.1 1.0 O2 C:C102 5.0 98.4 1.0 O4' C:C102 5.0 99.2 1.0 N1 C:C102 5.0 98.1 1.0

Magnesium binding site 5 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:48.3 occ:1.00 OP2 C:A11 2.4 97.4 1.0 N7 C:G12 3.1 83.9 1.0 P C:A11 3.8 97.7 1.0 C8 C:G12 3.9 83.1 1.0 C5 C:G12 4.0 84.4 1.0 O6 C:G12 4.0 86.0 1.0 O5' C:A11 4.2 93.0 1.0 O3' C:G10 4.3 83.0 1.0 OP2 C:G12 4.3 99.0 1.0 C6 C:G12 4.4 85.8 1.0 N6 C:A13 4.4 76.0 1.0 O2' C:G10 4.6 83.7 1.0 OP1 C:C89 4.7 99.8 1.0 N7 C:A13 4.8 75.0 1.0 OP1 C:A11 4.9 97.8 1.0

Magnesium binding site 6 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:58.9 occ:1.00 OP2 C:G20 3.8 97.8 1.0 OP1 C:A17 3.9 0.5 1.0 O2' C:A19 4.1 97.1 1.0 OP2 C:G18 4.3 91.1 1.0 O3' C:A19 4.5 97.1 1.0 C5' C:A17 4.8 0.4 1.0 P C:G20 4.8 97.7 1.0

Magnesium binding site 7 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:33.9 occ:1.00 OP2 E:U12 2.5 76.4 1.0 OP2 E:A9 3.0 88.9 1.0 OP2 E:U11 3.7 82.3 1.0 OP1 E:U8 3.9 76.3 1.0 O5' E:U11 4.0 59.3 1.0 P E:U12 4.0 77.5 1.0 P E:A9 4.0 87.2 1.0 P E:U11 4.1 82.5 1.0 OP2 E:U8 4.1 77.6 1.0 OP1 E:A9 4.1 85.6 1.0 OP1 E:U11 4.2 82.3 1.0 P E:U8 4.5 76.8 1.0 C3' E:U11 4.6 70.2 1.0 C5 E:U12 4.7 84.2 1.0 O3' E:U11 4.7 72.2 1.0 O5' E:U12 4.7 81.4 1.0 OP1 E:U12 4.9 76.3 1.0 C5' E:U11 4.9 62.1 1.0 O5' E:A9 4.9 78.0 1.0

Magnesium binding site 8 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:93.7 occ:1.00 OP1 E:A74 2.4 71.0 1.0 OP2 E:A74 3.0 72.6 1.0 P E:A74 3.1 71.6 1.0 C5 E:G72 3.5 74.1 1.0 N7 E:G72 3.5 74.8 1.0 C6 E:G72 3.6 74.5 1.0 O6 E:G72 3.7 74.3 1.0 MG E:MG105 3.8 59.5 1.0 C4 E:G72 4.1 73.5 1.0 C8 E:G72 4.2 75.2 1.0 O3' E:A73 4.2 72.5 1.0 N1 E:G72 4.3 74.8 1.0 O5' E:A74 4.3 70.5 1.0 N9 E:G72 4.5 74.1 1.0 C5' E:A73 4.7 75.3 1.0 N3 E:G72 4.8 73.7 1.0 C2 E:G72 4.8 74.1 1.0

Magnesium binding site 9 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg103 b:86.1 occ:1.00 O6 E:G44 2.8 76.2 1.0 N7 E:G43 3.3 78.6 1.0 N7 E:G44 3.6 77.0 1.0 C6 E:G44 3.7 76.9 1.0 C5 E:G44 4.0 77.0 1.0 C8 E:G43 4.1 80.6 1.0 C5 E:G43 4.2 78.2 1.0 O6 E:G43 4.3 77.1 1.0 C6 E:G43 4.6 77.4 1.0 C8 E:G44 4.9 78.0 1.0 N1 E:G44 5.0 78.2 1.0

Magnesium binding site 10 out of 29 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Increasing PEG3350 Concentration From 20% to 45% Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg104 b:48.1 occ:1.00 C2' E:U46 2.4 0.5 1.0 OP1 E:C47 2.6 96.2 1.0 O2' E:U46 2.8 0.7 1.0 OP2 E:G50 3.4 66.0 1.0 C3' E:U46 3.5 0.6 1.0 C1' E:U46 3.5 0.8 1.0 OP1 E:C49 3.7 73.5 1.0 P E:C47 3.7 97.9 1.0 O3' E:U46 3.8 0.7 1.0 O5' E:C49 4.1 64.3 1.0 P E:C49 4.2 73.1 1.0 C5' E:C47 4.2 75.5 1.0 O5' E:C47 4.3 76.7 1.0 OP2 E:C49 4.3 72.0 1.0 P E:G50 4.5 67.3 1.0 OP1 E:G50 4.6 68.9 1.0 O4' E:U46 4.7 0.8 1.0 C4' E:U46 4.8 0.9 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