Potassium in PDB 4pjo: Minimal U1 Snrnp

The structure of Minimal U1 Snrnp, PDB code: 4pjo was solved by Y.Kondo, C.Oubridge, A.M.Van Roon, K.Nagai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.359, 172.627, 256.322, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.5

The structure of Minimal U1 Snrnp also contains other interesting chemical elements:

Magnesium	(Mg)	20 atoms
Chlorine	(Cl)	1 atom
Zinc	(Zn)	4 atoms

The binding sites of Potassium atom in the Minimal U1 Snrnp (pdb code 4pjo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Minimal U1 Snrnp, PDB code: 4pjo:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:K210 b:91.2 occ:1.00 O2' 1:U124 2.4 73.7 1.0 O3' 1:U124 3.6 50.8 1.0 O2 1:U124 3.7 73.0 1.0 C2' 1:U124 3.7 58.8 1.0 OP2 1:A125 3.9 58.5 1.0 C3' 1:U124 4.1 56.0 1.0 C1' 1:U124 4.4 57.4 1.0 P 1:A125 4.5 51.6 1.0 OP2 1:A123 4.6 60.2 1.0 C2 1:U124 4.7 66.4 1.0

Potassium binding site 2 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ b:K101 b:0.8 occ:1.00 OE2 b:GLU62 3.6 0.8 1.0 NH2 b:ARG18 4.0 66.9 1.0 CE2 b:PHE48 4.2 65.3 1.0 CD1 b:ILE28 4.3 49.1 1.0 CD2 b:PHE48 4.4 61.5 1.0 CZ b:PHE48 4.4 67.5 1.0 OE2 b:GLU83 4.4 75.1 1.0 CD b:GLU62 4.8 0.2 1.0 CG b:PHE48 4.9 60.9 1.0 CE1 b:PHE48 4.9 67.9 1.0

Potassium binding site 3 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ b:K102 b:0.8 occ:1.00 OE1 b:GLN22 2.9 94.8 1.0 CD b:GLN22 3.9 76.3 1.0 ND2 b:ASN76 4.0 89.5 1.0 O4' 2:U134 4.0 89.1 1.0 O b:GLU75 4.3 65.1 1.0 C6 2:U134 4.3 0.7 1.0 C5' 2:U134 4.6 85.9 1.0 NE2 b:GLN22 4.7 82.8 1.0 N1 2:U134 4.7 1.0 1.0 C5 2:U134 4.7 0.5 1.0 CG b:GLN22 4.7 64.4 1.0 C b:GLU75 4.8 59.6 1.0 CG b:ASN76 4.8 87.0 1.0 CB b:GLU75 4.9 72.9 1.0 C1' 2:U134 4.9 97.0 1.0 C4' 2:U134 4.9 90.1 1.0 CB b:GLN22 5.0 58.3 1.0

Potassium binding site 4 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ Q:K101 b:97.0 occ:1.00 OG Q:SER73 2.8 88.0 1.0 O Q:SER73 3.8 74.6 1.0 CB Q:SER73 3.9 80.9 1.0 C Q:SER73 4.1 71.5 1.0 CD Q:PRO75 4.2 72.2 1.0 OE1 Q:GLU13 4.2 89.1 1.0 CA Q:LEU74 4.2 76.5 1.0 N Q:LEU74 4.3 75.0 1.0 CA Q:SER73 4.7 73.5 1.0 N Q:PRO75 4.9 72.2 1.0 OE2 Q:GLU13 5.0 93.1 1.0

Potassium binding site 5 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 3:K205 b:0.8 occ:1.00 OP2 3:G15 4.2 0.8 1.0 OP1 3:A14 4.9 0.7 1.0 OP2 3:A24 4.9 0.1 1.0 OP1 3:G15 5.0 0.2 1.0

Potassium binding site 6 out of 6 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 3:K206 b:0.3 occ:1.00 N2 3:G15 3.8 0.6 1.0 O2' 3:U30 4.4 0.9 1.0 C1' 3:U30 4.5 0.6 1.0 N3 3:G15 4.6 0.7 1.0 C2 3:G15 4.6 0.2 1.0 O4' 3:U30 4.8 0.8 1.0 C1' 3:U16 4.9 0.8 1.0 O4' 3:U16 5.0 0.1 1.0

Y.Kondo, C.Oubridge, A.M.Van Roon, K.Nagai. Crystal Structure of Human U1 Snrnp, A Small Nuclear Ribonucleoprotein Particle, Reveals the Mechanism of 5' Splice Site Recognition. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 25555158
DOI: 10.7554/ELIFE.04986