Potassium in PDB 5de5: Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna.

The structure of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna., PDB code: 5de5 was solved by N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.22 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.060, 130.010, 36.750, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.1

The binding sites of Potassium atom in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. (pdb code 5de5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna., PDB code: 5de5:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:39.2 occ:1.00 O6 A:G29 2.8 25.8 1.0 O6 A:G18 3.0 23.1 1.0 O6 A:G26 3.0 25.1 1.0 O6 A:G9 3.0 20.4 1.0 O4 A:U8 3.4 34.0 1.0 N1 A:A17 3.4 18.2 1.0 K A:K102 3.5 15.9 1.0 O6 A:G6 3.5 40.9 1.0 C6 A:G26 3.7 22.1 1.0 C6 A:G29 3.8 25.8 1.0 C6 A:G9 3.8 20.4 1.0 C6 A:G18 3.9 18.1 1.0 C6 A:G6 3.9 32.6 1.0 C2 A:A17 4.0 18.4 1.0 N1 A:G9 4.0 20.0 1.0 N1 A:G26 4.0 27.9 1.0 N1 A:G18 4.1 18.3 1.0 N7 A:G29 4.1 27.0 1.0 N1 A:G6 4.1 24.7 1.0 N3 A:U8 4.2 32.7 1.0 C4 A:U8 4.2 28.8 1.0 C5 A:G29 4.3 25.3 1.0 C6 A:A17 4.4 21.2 1.0 N6 A:A17 4.6 28.5 1.0 N4 A:C30 4.8 42.4 1.0 C5 A:G26 4.8 18.8 1.0 C5 A:G6 4.8 35.6 1.0 O2 A:U28 4.9 25.8 1.0

Potassium binding site 2 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:15.9 occ:1.00 O6 A:G6 2.7 40.9 1.0 O6 A:G26 2.8 25.1 1.0 O6 A:G18 2.8 23.1 1.0 O6 A:G9 2.8 20.4 1.0 O6 A:G21 3.0 19.1 1.0 O6 A:G12 3.0 19.2 1.0 O6 A:G16 3.0 19.4 1.0 O6 A:G25 3.2 35.0 1.0 K A:K103 3.3 17.7 1.0 K A:K101 3.5 39.2 1.0 C6 A:G6 3.6 32.6 1.0 C6 A:G26 3.6 22.1 1.0 C6 A:G18 3.6 18.1 1.0 C6 A:G9 3.7 20.4 1.0 C6 A:G21 3.7 19.4 1.0 C6 A:G16 3.8 24.2 1.0 C6 A:G12 3.8 33.1 1.0 N1 A:G6 3.8 24.7 1.0 N1 A:G26 3.8 27.9 1.0 N1 A:G21 3.8 19.4 1.0 N1 A:G12 3.9 41.2 1.0 C6 A:G25 3.9 21.9 1.0 N1 A:G9 3.9 20.0 1.0 N1 A:G18 4.0 18.3 1.0 N1 A:G16 4.0 19.7 1.0 N1 A:G25 4.1 19.5 1.0 C5 A:G18 4.8 18.7 1.0 C5 A:G16 4.9 20.4 1.0 C5 A:G9 4.9 28.5 1.0 C5 A:G21 4.9 20.0 1.0 C5 A:G26 5.0 18.8 1.0 C5 A:G6 5.0 35.6 1.0

Potassium binding site 3 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:17.7 occ:1.00 O6 A:G12 2.6 19.2 1.0 O6 A:G15 2.7 21.6 1.0 O6 A:G20 2.7 24.9 1.0 O6 A:G11 2.7 30.4 1.0 O6 A:G24 2.7 21.1 1.0 O6 A:G16 2.8 19.4 1.0 O6 A:G21 2.8 19.1 1.0 O6 A:G25 3.1 35.0 1.0 K A:K102 3.3 15.9 1.0 C6 A:G12 3.4 33.1 1.0 C6 A:G15 3.6 22.2 1.0 C6 A:G20 3.6 22.0 1.0 C6 A:G21 3.7 19.4 1.0 N1 A:G12 3.7 41.2 1.0 C6 A:G11 3.7 22.3 1.0 C6 A:G24 3.7 21.6 1.0 N1 A:G25 3.7 19.5 1.0 C6 A:G16 3.8 24.2 1.0 C6 A:G25 3.8 21.9 1.0 N1 A:G20 3.9 24.9 1.0 N1 A:G15 3.9 24.6 1.0 N1 A:G21 3.9 19.4 1.0 N1 A:G11 3.9 29.2 1.0 N1 A:G24 4.0 21.9 1.0 N1 A:G16 4.0 19.7 1.0 C5 A:G12 4.6 22.5 1.0 C2 A:G12 4.9 20.7 1.0 O6 A:G6 4.9 40.9 1.0 C5 A:G20 4.9 22.8 1.0 C5 A:G15 4.9 26.0 1.0 C5 A:G21 4.9 20.0 1.0 C2 A:G25 5.0 20.2 1.0

Potassium binding site 4 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:43.2 occ:1.00 O6 C:G20 2.6 47.5 1.0 O6 C:G24 2.7 43.4 1.0 O6 C:G21 2.8 55.5 1.0 O6 C:G16 2.8 27.1 1.0 O6 C:G11 2.8 30.1 1.0 O6 C:G15 2.8 29.1 1.0 O6 C:G12 2.8 34.0 1.0 O6 C:G25 2.9 38.3 1.0 K C:K102 3.2 31.9 1.0 C6 C:G20 3.5 39.6 1.0 C6 C:G21 3.6 42.8 1.0 C6 C:G24 3.6 45.8 1.0 C6 C:G12 3.7 28.3 1.0 C6 C:G25 3.7 38.1 1.0 C6 C:G16 3.7 26.7 1.0 N1 C:G20 3.7 41.6 1.0 C6 C:G15 3.8 28.8 1.0 C6 C:G11 3.8 38.6 1.0 N1 C:G24 3.8 55.4 1.0 N1 C:G12 3.9 33.5 1.0 N1 C:G16 3.9 26.6 1.0 N1 C:G21 3.9 29.9 1.0 N1 C:G25 4.0 40.4 1.0 N1 C:G11 4.0 32.5 1.0 N1 C:G15 4.1 28.5 1.0 C5 C:G20 4.8 29.1 1.0 C5 C:G21 4.8 26.9 1.0 O6 C:G6 4.9 25.9 1.0 C5 C:G25 4.9 39.1 1.0 C5 C:G12 4.9 31.8 1.0 C5 C:G24 5.0 45.8 1.0

Potassium binding site 5 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:31.9 occ:1.00 O6 C:G6 2.7 25.9 1.0 O6 C:G25 2.7 38.3 1.0 O6 C:G18 2.8 25.0 1.0 O6 C:G9 2.9 30.4 1.0 O6 C:G12 2.9 34.0 1.0 O6 C:G21 3.0 55.5 1.0 O6 C:G26 3.0 38.7 1.0 O6 C:G16 3.1 27.1 1.0 K C:K101 3.2 43.2 1.0 C6 C:G18 3.6 26.6 1.0 C6 C:G6 3.7 25.4 1.0 C6 C:G12 3.7 28.3 1.0 C6 C:G25 3.7 38.1 1.0 K C:K103 3.7 46.5 1.0 N1 C:G12 3.7 33.5 1.0 C6 C:G26 3.8 38.3 1.0 C6 C:G16 3.8 26.7 1.0 N1 C:G26 3.8 38.1 1.0 C6 C:G21 3.9 42.8 1.0 N1 C:G6 3.9 28.9 1.0 C6 C:G9 3.9 30.5 1.0 N1 C:G18 4.0 24.5 1.0 N1 C:G16 4.1 26.6 1.0 N1 C:G21 4.1 29.9 1.0 N1 C:G25 4.1 40.4 1.0 N1 C:G9 4.2 27.2 1.0 C5 C:G18 4.6 31.3 1.0 C5 C:G25 4.9 39.1 1.0 C5 C:G16 4.9 26.4 1.0 C5 C:G12 4.9 31.8 1.0 C2 C:G12 5.0 27.8 1.0

Potassium binding site 6 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex 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 the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:46.5 occ:1.00 O4 C:U8 2.9 30.8 1.0 O6 C:G29 2.9 35.5 1.0 O6 C:G18 3.0 25.0 1.0 N1 C:A17 3.1 23.1 1.0 O6 C:G9 3.1 30.4 1.0 O6 C:G6 3.4 25.9 1.0 O6 C:G26 3.5 38.7 1.0 C6 C:G6 3.6 25.4 1.0 K C:K102 3.7 31.9 1.0 N1 C:G6 3.8 28.9 1.0 C6 C:G18 3.8 26.6 1.0 C2 C:A17 3.8 22.9 1.0 C4 C:U8 3.9 28.1 1.0 N1 C:G18 4.0 24.5 1.0 C6 C:A17 4.0 30.5 1.0 C6 C:G29 4.0 35.7 1.0 C6 C:G9 4.0 30.5 1.0 N6 C:A17 4.1 23.2 1.0 N3 C:U8 4.1 29.3 1.0 C6 C:G26 4.3 38.3 1.0 N1 C:G9 4.4 27.2 1.0 N7 C:G29 4.5 35.6 1.0 C5 C:G6 4.5 28.1 1.0 N1 C:G26 4.5 38.1 1.0 C5 C:G29 4.6 37.6 1.0 C2 C:G6 4.6 25.9 1.0 N4 C:C30 4.9 40.4 1.0

Potassium binding site 7 out of 7 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna. within 5.0Å range: probe atom residue distance (Å) B Occ C:K104 b:89.1 occ:1.00 O C:HOH201 3.3 13.5 1.0 O3' C:G6 3.4 62.3 1.0 O2' C:G6 3.4 57.3 1.0 OP2 C:G7 3.6 52.5 1.0 P C:G7 4.2 50.1 1.0 C2' C:G6 4.2 42.5 1.0 C1' C:G6 4.4 31.4 1.0 C3' C:G6 4.4 51.4 1.0 OP2 C:G16 4.6 36.3 1.0 OP2 C:U8 4.6 59.6 1.0 C5' C:G7 4.6 40.0 1.0 O5' C:G7 4.9 23.7 1.0 OP2 C:A13 5.0 45.4 1.0

N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov. Crystal Structure Reveals Specific Recognition of A G-Quadruplex Rna By A Beta-Turn in the Rgg Motif of Fmrp. Proc.Natl.Acad.Sci.Usa V. 112 E5391 2015.
ISSN: ESSN 1091-6490
PubMed: 26374839
DOI: 10.1073/PNAS.1515737112