Magnesium in PDB 5ns4: Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna

The structure of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna, PDB code: 5ns4 was solved by Y.J.Liu, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.88 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.757, 122.432, 51.013, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 28.3

The binding sites of Magnesium atom in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna (pdb code 5ns4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna, PDB code: 5ns4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:30.8 occ:1.00 O A:THR161 2.6 30.0 1.0 O A:ARG128 2.6 33.0 1.0 O A:ALA163 2.7 34.5 1.0 OD1 A:ASN130 2.8 29.5 1.0 O A:HOH308 2.9 44.2 1.0 CG A:ASN130 3.6 28.5 1.0 C A:THR161 3.6 30.7 1.0 ND2 A:ASN130 3.7 28.8 1.0 C A:ARG128 3.7 30.1 1.0 O A:GLY129 3.8 31.1 1.0 C A:GLY129 3.8 30.6 1.0 C A:ALA163 3.9 31.6 1.0 CA A:GLY129 4.0 31.1 1.0 OG1 A:THR161 4.0 32.5 1.0 N A:ALA163 4.2 30.8 1.0 N A:THR161 4.3 31.8 1.0 N A:GLY129 4.3 31.6 1.0 N A:ASN130 4.4 30.1 1.0 C A:THR162 4.4 32.6 1.0 CA A:THR161 4.5 31.6 1.0 N A:THR162 4.5 30.9 1.0 CA A:THR162 4.5 33.1 1.0 CA A:ALA163 4.6 30.4 1.0 N A:GLU164 4.8 30.2 1.0 CB A:ASN130 4.9 28.9 1.0 CB A:THR161 4.9 31.2 1.0 CA A:ARG128 4.9 31.3 1.0 CA A:GLU164 5.0 34.7 1.0

Magnesium binding site 2 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:30.0 occ:1.00 O B:ARG128 2.5 30.2 1.0 O B:THR161 2.6 32.5 1.0 O B:ALA163 2.6 29.3 1.0 O B:HOH315 2.8 30.0 1.0 OD1 B:ASN130 2.9 30.3 1.0 O B:HOH311 3.1 30.0 1.0 CG B:ASN130 3.6 29.9 1.0 C B:THR161 3.6 33.5 1.0 ND2 B:ASN130 3.7 26.6 1.0 C B:ARG128 3.7 28.9 1.0 O B:GLY129 3.7 29.3 1.0 C B:GLY129 3.7 30.6 1.0 C B:ALA163 3.8 34.3 1.0 O B:HOH307 3.9 30.0 1.0 CA B:GLY129 3.9 29.9 1.0 OG1 B:THR161 4.0 33.2 1.0 N B:ALA163 4.2 31.8 1.0 N B:GLY129 4.2 28.9 1.0 N B:ASN130 4.3 30.4 1.0 N B:THR161 4.3 34.0 1.0 C B:THR162 4.4 31.3 1.0 N B:THR162 4.5 31.6 1.0 CA B:THR162 4.5 33.9 1.0 CA B:THR161 4.5 33.5 1.0 CA B:ALA163 4.6 31.7 1.0 N B:GLU164 4.8 35.4 1.0 CB B:ASN130 4.9 28.3 1.0 CA B:ARG128 4.9 30.6 1.0 CB B:THR161 4.9 35.8 1.0 CA B:GLU164 4.9 36.0 1.0 CA B:ASN130 5.0 30.5 1.0 CB B:ARG128 5.0 33.0 1.0 O B:THR162 5.0 30.6 1.0

Magnesium binding site 3 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:30.0 occ:1.00 O C:HOH230 2.1 30.0 1.0 O C:HOH203 2.2 30.0 1.0 O C:HOH201 2.2 30.0 1.0 O C:HOH220 2.3 30.0 1.0 OP2 C:A46 4.0 37.0 1.0 O C:HOH209 4.0 37.4 1.0 O4 C:U32 4.1 31.1 1.0 O6 C:G33 4.4 27.2 1.0 N7 C:G33 4.5 29.8 1.0 OP2 C:A45 4.5 31.1 1.0 C4 C:U32 4.6 33.0 1.0 O C:HOH229 4.6 34.9 1.0 C5 C:U32 4.6 31.5 1.0 OP1 C:A46 4.8 38.0 1.0 P C:A46 4.9 35.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:30.0 occ:1.00 O2' C:A46 3.4 30.1 1.0 O D:HOH203 3.5 41.0 1.0 N3 D:A46 3.8 29.3 1.0 O2' D:A46 3.8 29.4 1.0 N3 C:A46 4.0 29.0 1.0 O4' C:C47 4.3 28.9 1.0 O C:HOH202 4.3 30.0 1.0 C2' C:A46 4.3 29.8 1.0 C2 D:A46 4.4 30.6 1.0 O C:HOH219 4.5 48.7 1.0 C2 C:A46 4.6 33.3 1.0 C2' D:A46 4.6 29.6 1.0 C1' D:A46 4.7 30.6 1.0 C1' C:A46 4.8 29.7 1.0 C4 D:A46 4.9 29.5 1.0 O4' D:C47 5.0 35.0 1.0

Magnesium binding site 5 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg104 b:30.0 occ:1.00 OP2 C:C35 2.0 35.9 1.0 OP2 C:C36 2.0 30.1 1.0 O C:HOH231 2.1 30.0 1.0 O C:HOH227 2.2 30.0 1.0 O C:HOH225 2.2 30.0 1.0 P C:C36 3.4 32.2 1.0 P C:C35 3.4 34.4 1.0 O3' C:A34 3.9 33.8 1.0 O3' C:C35 4.1 29.3 1.0 OP1 C:C36 4.1 32.1 1.0 O2' C:A34 4.2 34.1 1.0 O5' C:C35 4.3 31.5 1.0 OP1 C:C35 4.4 31.3 1.0 O5' C:C36 4.4 29.1 1.0 C3' C:C35 4.4 28.8 1.0 O6 C:G44 4.5 28.4 1.0 C5' C:C35 4.8 31.5 1.0 N4 C:C38 4.9 26.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg105 b:30.0 occ:1.00 O C:HOH222 2.5 30.0 1.0 N7 C:A50 4.2 30.7 1.0 O6 C:G51 4.4 36.6 1.0 N7 C:G51 4.7 36.9 1.0 N6 C:A50 4.8 28.7 1.0 C5 C:A50 4.9 30.0 1.0 C8 C:A50 4.9 31.5 1.0

Magnesium binding site 7 out of 7 in the Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of CY3 Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:30.0 occ:1.00 O D:HOH211 2.2 30.0 1.0 O D:HOH201 2.2 30.0 1.0 OP2 D:A46 4.0 31.6 1.0 O4 D:U32 4.2 30.8 1.0 O6 D:G33 4.2 39.2 1.0 N7 D:G33 4.2 47.9 1.0 OP2 D:A45 4.3 28.2 1.0 O D:HOH210 4.5 41.5 1.0 C4 D:U32 4.7 33.9 1.0 C5 D:U32 4.7 33.4 1.0 OP1 D:A46 4.9 33.6 1.0 C6 D:G33 5.0 42.2 1.0 P D:A46 5.0 32.3 1.0 C5 D:G33 5.0 46.6 1.0

Y.Liu, D.M.J.Lilley. Crystal Structures of Cyanine Fluorophores Stacked Onto the End of Double-Stranded Rna. Biophys. J. V. 113 2336 2017.
ISSN: ESSN 1542-0086
PubMed: 29211987
DOI: 10.1016/J.BPJ.2017.10.002