Potassium in PDB 5v3f: Co-Crystal Structure of the Fluorogenic Rna Mango

The structure of Co-Crystal Structure of the Fluorogenic Rna Mango, PDB code: 5v3f was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.199, 63.199, 138.413, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 20.3

The binding sites of Potassium atom in the Co-Crystal Structure of the Fluorogenic Rna Mango (pdb code 5v3f). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Co-Crystal Structure of the Fluorogenic Rna Mango, PDB code: 5v3f:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:34.8 occ:1.00 O6 B:G8 2.7 35.1 1.0 O6 A:G8 2.7 31.8 1.0 O6 B:G18 2.7 34.2 1.0 O6 A:G18 2.7 32.8 1.0 O6 B:G13 2.8 32.0 1.0 O6 A:G13 2.9 33.4 1.0 O6 B:G23 2.9 35.9 1.0 O6 A:G23 2.9 32.1 1.0 K B:K101 3.3 33.1 1.0 K A:K102 3.4 31.9 1.0 C6 B:G8 3.6 33.3 1.0 C6 B:G13 3.7 30.4 1.0 C6 A:G8 3.7 31.2 1.0 C6 B:G18 3.7 34.3 1.0 C6 A:G13 3.7 32.5 1.0 C6 A:G18 3.7 34.6 1.0 C6 A:G23 3.7 35.8 1.0 C6 B:G23 3.7 33.8 1.0 N1 B:G8 3.9 30.5 1.0 N1 B:G18 4.0 31.1 1.0 N1 A:G8 4.0 30.4 1.0 N1 A:G13 4.0 30.4 1.0 N1 A:G23 4.0 34.3 1.0 N1 B:G13 4.0 31.5 1.0 N1 A:G18 4.0 35.3 1.0 N1 B:G23 4.1 33.0 1.0 C5 B:G13 4.8 30.4 1.0 C5 A:G13 4.9 30.9 1.0 C5 B:G23 4.9 32.8 1.0 C5 B:G8 4.9 33.0 1.0 C5 A:G23 4.9 32.1 1.0 C5 A:G8 4.9 33.5 1.0 C5 B:G18 5.0 31.3 1.0

Potassium binding site 2 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:31.9 occ:1.00 O6 A:G24 2.6 32.6 1.0 O6 A:G14 2.7 33.8 1.0 O6 A:G13 2.8 33.4 1.0 O6 A:G19 2.8 34.4 1.0 O6 A:G23 2.8 32.1 1.0 O6 A:G9 2.9 29.1 1.0 O6 A:G8 2.9 31.8 1.0 O6 A:G18 3.0 32.8 1.0 K A:K101 3.4 34.8 1.0 K A:K103 3.5 32.2 1.0 C6 A:G24 3.6 31.4 1.0 C6 A:G14 3.6 31.5 1.0 C6 A:G18 3.7 34.6 1.0 C6 A:G8 3.7 31.2 1.0 C6 A:G13 3.7 32.5 1.0 C6 A:G19 3.7 34.1 1.0 C6 A:G23 3.7 35.8 1.0 C6 A:G9 3.8 29.9 1.0 N1 A:G18 3.9 35.3 1.0 N1 A:G24 3.9 29.8 1.0 N1 A:G14 3.9 31.7 1.0 N1 A:G8 4.0 30.4 1.0 N1 A:G13 4.0 30.4 1.0 N1 A:G19 4.0 33.9 1.0 N1 A:G23 4.0 34.3 1.0 N1 A:G9 4.1 28.2 1.0 C5 A:G24 4.8 30.8 1.0 C5 A:G14 4.8 33.1 1.0 C5 A:G18 4.8 34.1 1.0 C5 A:G8 4.8 33.5 1.0 C5 A:G13 4.9 30.9 1.0 C5 A:G19 5.0 31.1 1.0 C5 A:G23 5.0 32.1 1.0 C5 A:G9 5.0 31.1 1.0

Potassium binding site 3 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:32.2 occ:1.00 O6 A:G21 2.6 35.5 1.0 O6 A:G10 2.7 31.0 1.0 O6 A:G16 2.7 32.3 1.0 O6 A:G26 2.8 31.3 1.0 O6 A:G14 2.8 33.8 1.0 O6 A:G9 2.8 29.1 1.0 O6 A:G24 2.9 32.6 1.0 O6 A:G19 3.0 34.4 1.0 K A:K102 3.5 31.9 1.0 C6 A:G21 3.5 32.0 1.0 C6 A:G16 3.6 33.2 1.0 C6 A:G26 3.6 35.1 1.0 C6 A:G9 3.6 29.9 1.0 C6 A:G14 3.7 31.5 1.0 C6 A:G24 3.7 31.4 1.0 C6 A:G10 3.7 29.5 1.0 N1 A:G21 3.9 30.1 1.0 N1 A:G26 3.9 30.9 1.0 C6 A:G19 3.9 34.1 1.0 N1 A:G16 3.9 31.4 1.0 N1 A:G24 3.9 29.8 1.0 N1 A:G14 4.0 31.7 1.0 N1 A:G9 4.0 28.2 1.0 N1 A:G10 4.1 31.1 1.0 N1 A:G19 4.2 33.9 1.0 C17 A:74G104 4.3 33.2 1.0 C5 A:G21 4.8 34.9 1.0 C5 A:G9 4.8 31.1 1.0 C5 A:G16 4.8 30.2 1.0 C5 A:G14 4.9 33.1 1.0 C5 A:G26 4.9 28.7 1.0 C5 A:G24 4.9 30.8 1.0 N1 A:74G104 5.0 31.9 1.0

Potassium binding site 4 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:33.1 occ:1.00 O6 B:G14 2.7 33.2 1.0 O6 B:G24 2.7 33.9 1.0 O6 B:G19 2.8 32.0 1.0 O6 B:G23 2.8 35.9 1.0 O6 B:G9 2.8 34.4 1.0 O6 B:G13 2.8 32.0 1.0 O6 B:G18 2.9 34.2 1.0 O6 B:G8 3.0 35.1 1.0 K A:K101 3.3 34.8 1.0 K B:K102 3.5 32.9 1.0 C6 B:G14 3.5 33.4 1.0 C6 B:G18 3.6 34.3 1.0 C6 B:G24 3.6 32.3 1.0 C6 B:G9 3.7 32.4 1.0 C6 B:G19 3.7 34.7 1.0 C6 B:G8 3.7 33.3 1.0 C6 B:G23 3.7 33.8 1.0 C6 B:G13 3.8 30.4 1.0 N1 B:G18 3.9 31.1 1.0 N1 B:G14 4.0 32.5 1.0 N1 B:G19 4.0 34.3 1.0 N1 B:G8 4.0 30.5 1.0 N1 B:G9 4.0 29.6 1.0 N1 B:G24 4.0 33.7 1.0 N1 B:G13 4.1 31.5 1.0 N1 B:G23 4.1 33.0 1.0 C5 B:G14 4.7 30.4 1.0 C5 B:G18 4.7 31.3 1.0 C5 B:G24 4.8 32.7 1.0 C5 B:G8 4.8 33.0 1.0 C5 B:G9 4.9 33.5 1.0 C5 B:G19 5.0 34.9 1.0 C5 B:G23 5.0 32.8 1.0 C5 B:G13 5.0 30.4 1.0

Potassium binding site 5 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:32.9 occ:1.00 O6 B:G21 2.6 31.2 1.0 O6 B:G10 2.7 32.7 1.0 O6 B:G9 2.7 34.4 1.0 O6 B:G14 2.8 33.2 1.0 O6 B:G16 2.8 31.9 1.0 O6 B:G26 2.8 33.7 1.0 O6 B:G24 2.9 33.9 1.0 O6 B:G19 3.0 32.0 1.0 K B:K101 3.5 33.1 1.0 C6 B:G21 3.6 31.0 1.0 C6 B:G9 3.6 32.4 1.0 C6 B:G26 3.6 35.1 1.0 C6 B:G16 3.6 32.0 1.0 C6 B:G14 3.7 33.4 1.0 C6 B:G10 3.7 31.6 1.0 C6 B:G24 3.7 32.3 1.0 C6 B:G19 3.9 34.7 1.0 N1 B:G26 3.9 33.1 1.0 N1 B:G16 3.9 28.1 1.0 N1 B:G9 3.9 29.6 1.0 N1 B:G21 4.0 31.5 1.0 N1 B:G24 4.0 33.7 1.0 N1 B:G14 4.0 32.5 1.0 N1 B:G10 4.0 28.7 1.0 N1 B:G19 4.2 34.3 1.0 C17 B:74G104 4.4 35.8 1.0 C5 B:G9 4.7 33.5 1.0 C5 B:G21 4.8 32.9 1.0 C5 B:G14 4.9 30.4 1.0 C5 B:G16 4.9 29.2 1.0 C5 B:G26 4.9 34.2 1.0 C5 B:G24 4.9 32.7 1.0

Potassium binding site 6 out of 6 in the Co-Crystal Structure of the Fluorogenic Rna Mango


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Co-Crystal Structure of the Fluorogenic Rna Mango within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:98.5 occ:1.00 O B:HOH245 2.7 44.2 1.0 O4' A:G13 3.7 34.3 1.0 O4' B:G9 3.8 35.7 1.0 N3 B:G8 4.0 33.4 1.0 O4' B:G8 4.1 37.5 1.0 C1' B:G8 4.2 35.0 1.0 O5' A:G13 4.2 47.1 1.0 O3' B:G8 4.2 45.2 1.0 C8 A:G13 4.3 33.9 1.0 O B:HOH247 4.4 57.3 1.0 C5' A:G13 4.6 38.6 1.0 N2 B:G8 4.6 33.6 1.0 C1' B:G9 4.6 35.2 1.0 O5' B:G9 4.6 53.0 1.0 C1' A:G13 4.7 32.7 1.0 C4' B:G8 4.7 42.2 1.0 C4' A:G13 4.7 33.2 1.0 OP1 B:G9 4.7 54.9 1.0 C2 B:G8 4.7 30.6 1.0 C4' B:G9 4.8 33.8 1.0 N9 A:G13 4.8 31.6 1.0 C4 B:G8 4.8 31.6 1.0 P B:G9 4.9 55.3 1.0 N9 B:G8 5.0 32.5 1.0 O A:HOH287 5.0 47.1 1.0 O B:HOH251 5.0 48.2 1.0

R.J.Trachman, N.A.Demeshkina, M.W.L.Lau, S.S.S.Panchapakesan, S.C.Y.Jeng, P.J.Unrau, A.R.Ferre-D'amare. Structural Basis For High-Affinity Fluorophore Binding and Activation By Rna Mango. Nat. Chem. Biol. V. 13 807 2017.
ISSN: ESSN 1552-4469
PubMed: 28553947
DOI: 10.1038/NCHEMBIO.2392