Magnesium in PDB 4pkd: U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2

The structure of U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2, PDB code: 4pkd was solved by C.Oubridge, Y.Kondo, 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)	87.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.220, 66.600, 93.730, 90.00, 110.95, 90.00
R / Rfree (%)	19.7 / 25.8

The binding sites of Magnesium atom in the U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2 (pdb code 4pkd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2, PDB code: 4pkd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2 within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg201 b:22.5 occ:1.00 O V:HOH329 2.6 36.2 1.0 O V:HOH314 2.6 23.9 1.0 O6 V:G103 2.8 33.4 1.0 O V:HOH318 2.8 29.5 1.0 O4 V:U92 2.9 34.2 1.0 O V:HOH319 2.9 29.3 1.0 N6 V:A91 3.6 29.9 1.0 C4 V:U92 3.7 33.6 1.0 N3 V:U92 3.8 32.3 1.0 C6 V:G103 3.9 34.5 1.0 N7 V:G102 4.0 41.1 1.0 MG V:MG202 4.4 33.0 1.0 O6 V:G102 4.4 39.9 1.0 C6 V:A91 4.5 32.9 1.0 N7 V:G103 4.5 30.0 1.0 O4 V:U104 4.6 39.4 1.0 C5 V:G103 4.6 31.3 1.0 NH1 B:ARG265 4.8 30.6 1.0 C5 V:G102 4.8 42.3 1.0 C6 V:G102 5.0 40.0 1.0 C8 V:G102 5.0 40.6 1.0 N1 V:G103 5.0 30.4 1.0

Magnesium binding site 2 out of 3 in the U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2 within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg202 b:33.0 occ:1.00 O V:HOH319 2.4 29.3 1.0 O V:HOH317 2.6 19.4 1.0 O4 V:U92 2.8 34.2 1.0 C4 V:U92 3.6 33.6 1.0 O V:HOH329 3.9 36.2 1.0 C5 V:U92 3.9 32.4 1.0 MG V:MG201 4.4 22.5 1.0 NH1 B:ARG265 4.4 30.6 1.0 O V:HOH323 4.5 22.4 1.0 OP2 V:A91 4.6 37.2 1.0 N7 V:A91 4.7 34.9 1.0 N3 V:U92 4.9 32.3 1.0 O V:HOH318 4.9 29.5 1.0

Magnesium binding site 3 out of 3 in the U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of U1-70K in Complex with U1 Snrna Stem-Loops 1 and U1-A Rrm in Complex with Stem-Loop 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:63.3 occ:1.00 O B:HOH420 2.1 61.5 1.0 O B:TRP154 2.6 40.3 1.0 O B:LEU151 3.1 64.7 1.0 C B:TRP154 3.7 39.3 1.0 C B:LEU151 4.2 59.6 1.0 CA B:LYS152 4.3 68.4 1.0 N B:TRP154 4.4 46.5 1.0 CA B:TRP154 4.5 40.8 1.0 CE3 B:TRP154 4.6 33.5 1.0 C B:LYS152 4.7 62.7 1.0 N B:LYS152 4.7 63.5 1.0 N B:ASP155 4.7 42.0 1.0 CB B:TRP154 4.7 39.4 1.0 O B:LYS152 4.8 68.5 1.0 CA B:ASP155 4.8 43.3 1.0 CB B:ASP155 4.8 43.4 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