Potassium in PDB 3pdr: Crystal Structure of Manganese Bound M-Box Rna

The structure of Crystal Structure of Manganese Bound M-Box Rna, PDB code: 3pdr was solved by A.Ramesh, W.C.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.49 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.780, 102.487, 126.375, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.8

The structure of Crystal Structure of Manganese Bound M-Box Rna also contains other interesting chemical elements:

Manganese

(Mn)

25 atoms

The binding sites of Potassium atom in the Crystal Structure of Manganese Bound M-Box Rna (pdb code 3pdr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Manganese Bound M-Box Rna, PDB code: 3pdr:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:K1 b:26.0 occ:1.00 OP2 X:A155 2.9 17.2 1.0 O4 X:U28 3.0 17.3 1.0 O6 X:G157 3.0 18.5 1.0 O X:HOH212 3.0 16.4 1.0 O X:HOH342 3.1 27.1 1.0 N4 X:C158 3.3 18.1 1.0 O6 X:G27 3.4 22.2 1.0 O X:HOH266 3.6 27.8 1.0 C5' X:A155 3.7 17.3 1.0 N2 X:G29 3.8 17.7 1.0 C4 X:U28 3.9 20.4 1.0 N1 X:G29 3.9 16.9 1.0 N3 X:U28 3.9 20.4 1.0 P X:A155 4.0 18.2 1.0 C6 X:G157 4.0 17.9 1.0 C2 X:G29 4.1 17.0 1.0 O5' X:A155 4.2 20.3 1.0 C4 X:C158 4.3 21.6 1.0 N7 X:G157 4.4 17.6 1.0 O X:HOH236 4.4 26.9 1.0 C6 X:G27 4.4 22.6 1.0 C5 X:G157 4.6 18.3 1.0 OP1 X:A155 4.7 19.8 1.0 O X:HOH213 4.7 19.3 1.0 OP1 X:A156 4.7 16.7 1.0 C6 X:G29 4.7 17.6 1.0 N3 X:C158 4.9 18.8 1.0 N3 X:G29 5.0 14.2 1.0

Potassium binding site 2 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:K2 b:41.4 occ:1.00 O2 X:U67 2.9 27.1 1.0 O3' X:A106 3.2 22.1 1.0 O2 X:C75 3.2 27.3 1.0 O X:HOH186 3.3 32.1 1.0 O2' X:A106 3.3 20.8 1.0 OP1 X:G107 4.0 32.4 1.0 C3' X:A106 4.0 23.0 1.0 N2 X:G66 4.0 29.3 1.0 O2' X:U67 4.1 31.9 1.0 C4' X:A106 4.1 21.6 1.0 C2 X:U67 4.1 30.9 1.0 C2 X:C75 4.2 27.5 1.0 P X:G107 4.2 26.6 1.0 C2' X:A106 4.3 20.6 1.0 C2 X:A74 4.3 23.4 1.0 C1' X:U67 4.3 30.5 1.0 C2' X:U67 4.5 32.5 1.0 C1' X:C75 4.6 22.1 1.0 O4' X:C68 4.7 29.0 1.0 N1 X:U67 4.8 29.3 1.0 N1 X:C75 4.9 24.5 1.0 O5' X:G107 4.9 26.3 1.0 N3 X:A74 4.9 22.0 1.0 C2 X:G66 4.9 29.8 1.0

Potassium binding site 3 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:K3 b:78.4 occ:1.00 OP1 X:G73 3.5 28.2 1.0 O X:HOH538 3.6 29.1 1.0 C1' X:A25 4.1 27.6 1.0 O4' X:A25 4.1 26.7 1.0 O3' X:A72 4.3 22.1 1.0 P X:G73 4.6 27.8 1.0 O2' X:A162 4.8 44.8 1.0 N9 X:A25 4.8 26.4 1.0 C1' X:A162 4.9 37.8 1.0

Potassium binding site 4 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K1 b:23.5 occ:1.00 O6 A:G157 2.9 17.6 1.0 OP2 A:A155 2.9 17.2 1.0 O4 A:U28 2.9 17.4 1.0 O A:HOH181 3.0 17.2 1.0 O A:HOH225 3.1 23.3 1.0 N4 A:C158 3.2 16.1 1.0 O A:HOH260 3.5 22.3 1.0 O6 A:G27 3.5 16.9 1.0 N2 A:G29 3.6 15.8 1.0 N1 A:G29 3.7 16.1 1.0 C4 A:U28 3.8 19.0 1.0 N3 A:U28 3.8 15.9 1.0 C5' A:A155 3.9 15.8 1.0 C2 A:G29 3.9 17.2 1.0 C6 A:G157 3.9 16.9 1.0 P A:A155 3.9 16.9 1.0 C4 A:C158 4.2 17.4 1.0 N7 A:G157 4.3 16.6 1.0 O5' A:A155 4.3 17.6 1.0 O A:HOH276 4.4 22.6 1.0 C5 A:G157 4.4 16.7 1.0 C6 A:G27 4.5 18.8 1.0 OP1 A:A155 4.5 17.1 1.0 C6 A:G29 4.6 18.0 1.0 O A:HOH235 4.7 21.1 1.0 N3 A:G29 4.8 15.6 1.0 N3 A:C158 4.8 17.0 1.0 OP1 A:A156 4.9 16.6 1.0 O6 A:G29 5.0 16.6 1.0

Potassium binding site 5 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K2 b:34.2 occ:1.00 O2 A:U67 2.9 27.0 1.0 O2 A:C75 3.1 26.2 1.0 O2' A:A106 3.1 22.4 1.0 O3' A:A106 3.2 24.6 1.0 O A:HOH270 3.2 30.7 1.0 O A:HOH349 3.4 34.7 1.0 N2 A:G66 3.8 26.8 1.0 OP1 A:G107 3.9 28.0 1.0 C3' A:A106 4.0 20.0 1.0 C2 A:U67 4.0 27.0 1.0 C2 A:C75 4.1 25.4 1.0 C2 A:A74 4.1 23.6 1.0 C2' A:A106 4.2 22.5 1.0 C4' A:A106 4.2 23.0 1.0 P A:G107 4.2 25.8 1.0 O A:HOH228 4.4 37.5 1.0 C1' A:C75 4.4 24.2 1.0 O2' A:U67 4.4 23.0 1.0 C1' A:U67 4.5 25.6 1.0 N3 A:A74 4.6 21.6 1.0 N1 A:C75 4.7 22.5 1.0 O5' A:G107 4.7 27.2 1.0 C2' A:U67 4.7 26.7 1.0 O2' A:C75 4.8 24.3 1.0 O4' A:C68 4.8 20.7 1.0 N1 A:U67 4.8 25.5 1.0 C2 A:G66 4.8 29.9 1.0 N3 A:U67 4.9 23.2 1.0 N3 A:C75 4.9 24.7 1.0 N1 A:A74 5.0 22.7 1.0

Potassium binding site 6 out of 6 in the Crystal Structure of Manganese Bound M-Box Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3 b:78.1 occ:1.00 O A:HOH530 3.6 26.6 1.0 O A:HOH353 3.8 34.6 1.0 OP1 A:G73 4.0 26.2 1.0 O2' A:A162 4.6 33.3 1.0 C1' A:A25 4.6 27.2 1.0 O3' A:A72 4.7 23.1 1.0 C1' A:A162 4.8 31.1 1.0 O4' A:A25 4.9 24.6 1.0

A.Ramesh, C.A.Wakeman, W.C.Winkler. Insights Into Metalloregulation By M-Box Riboswitch Rnas Via Structural Analysis of Manganese-Bound Complexes. J.Mol.Biol. V. 407 556 2011.
ISSN: ISSN 0022-2836
PubMed: 21315082
DOI: 10.1016/J.JMB.2011.01.049