Manganese in PDB 4u3o: Octameric Rna Duplex Soaked in Manganese(II)Chloride

The structure of Octameric Rna Duplex Soaked in Manganese(II)Chloride, PDB code: 4u3o was solved by M.F.Schaffer, B.Spingler, J.Schnabl, G.Peng, V.Olieric, R.K.O.Sigel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.16 / 1.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	46.328, 46.328, 58.075, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 17.5

The binding sites of Manganese atom in the Octameric Rna Duplex Soaked in Manganese(II)Chloride (pdb code 4u3o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Octameric Rna Duplex Soaked in Manganese(II)Chloride, PDB code: 4u3o:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Octameric Rna Duplex Soaked in Manganese(II)Chloride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Octameric Rna Duplex Soaked in Manganese(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:14.0 occ:0.63 O A:HOH213 2.0 22.2 1.0 O A:HOH227 2.0 22.4 1.0 O A:HOH226 2.1 25.5 1.0 O A:HOH225 2.2 18.9 1.0 O A:HOH228 2.2 18.9 1.0 O B:HOH213 2.2 23.2 1.0 O A:HOH218 4.2 30.8 1.0 O A:HOH211 4.2 25.2 1.0 O A:HOH224 4.3 22.6 1.0 O6 A:G7 4.3 18.4 1.0 N4 A:C6 4.3 16.3 1.0 O B:HOH204 4.4 22.4 1.0 O A:HOH232 4.4 23.3 1.0 N7 A:G7 4.4 18.0 1.0 O A:HOH203 4.4 23.8 1.0 O A:HOH223 4.5 19.1 1.0 C5 A:C6 4.7 17.7 1.0 N6 A:A8 4.8 19.9 1.0 C4 A:C6 4.9 20.1 1.0

Manganese binding site 2 out of 4 in the Octameric Rna Duplex Soaked in Manganese(II)Chloride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Octameric Rna Duplex Soaked in Manganese(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:22.2 occ:0.22 OP1 A:G7 2.6 28.4 1.0 O5' A:G7 3.3 28.5 1.0 P A:G7 3.6 25.7 1.0 C5' A:G7 3.8 26.2 1.0 O A:HOH210 4.1 29.1 1.0 O3' A:C6 4.3 23.4 1.0 C4' A:G7 4.5 19.6 1.0 OP2 A:G7 4.8 25.6 1.0

Manganese binding site 3 out of 4 in the Octameric Rna Duplex Soaked in Manganese(II)Chloride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Octameric Rna Duplex Soaked in Manganese(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:14.7 occ:0.67 O B:HOH217 2.1 16.5 1.0 O B:HOH216 2.1 20.4 1.0 O A:HOH221 2.2 19.5 1.0 O B:HOH219 2.2 21.4 1.0 O B:HOH221 2.2 22.9 1.0 O B:HOH220 2.3 18.4 1.0 O B:HOH227 3.9 22.7 1.0 O A:HOH222 3.9 23.6 1.0 N4 B:C2 4.0 18.6 1.0 O4 B:U4 4.0 20.1 1.0 O B:HOH226 4.0 27.0 1.0 O A:HOH230 4.2 26.5 1.0 O4 A:U4 4.2 17.7 1.0 O A:HOH224 4.2 22.6 1.0 O B:HOH223 4.3 26.9 1.0 O A:HOH229 4.3 24.4 1.0 O6 B:G3 4.4 17.8 1.0 C4 B:C2 4.5 19.5 1.0 C5 B:C2 4.5 21.1 1.0 N7 B:G3 4.7 19.9 1.0 N6 A:A5 4.8 17.2 1.0

Manganese binding site 4 out of 4 in the Octameric Rna Duplex Soaked in Manganese(II)Chloride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Octameric Rna Duplex Soaked in Manganese(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:15.3 occ:0.42 O B:HOH229 2.1 30.6 1.0 O B:HOH201 2.1 23.1 1.0 O B:HOH218 2.1 25.9 1.0 O B:HOH228 2.1 26.2 1.0 O A:HOH216 2.2 26.2 1.0 O B:HOH210 2.3 26.5 1.0 O B:HOH215 3.9 31.4 1.0 O A:HOH207 4.1 23.5 1.0 O B:HOH230 4.2 28.5 1.0 O6 B:G7 4.2 20.8 1.0 N4 B:C6 4.4 18.0 1.0 O B:HOH203 4.5 28.3 1.0 N7 B:G7 4.5 20.9 1.0 N6 B:A8 4.6 19.9 1.0 C5 B:C6 4.7 19.1 1.0 C4 B:C6 4.9 18.9 1.0 O4 A:U1 4.9 20.9 1.0

M.F.Schaffer, G.Peng, B.Spingler, J.Schnabl, M.Wang, V.Olieric, R.K.Sigel. The X-Ray Structures of Six Octameric Rna Duplexes in the Presence of Different Di- and Trivalent Cations. Int J Mol Sci V. 17 2016.
ISSN: ESSN 1422-0067
PubMed: 27355942
DOI: 10.3390/IJMS17070988