Magnesium 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:

Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom
Zinc	(Zn)	4 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Minimal U1 Snrnp (pdb code 4pjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Minimal U1 Snrnp, PDB code: 4pjo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in the Minimal U1 Snrnp


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg202 b:0.9 occ:1.00 MG 1:MG207 3.1 82.5 1.0 MG 1:MG203 3.3 52.3 1.0 OP2 1:G130 3.6 52.3 1.0 MG 1:MG208 3.7 75.7 1.0 OP1 1:G132 3.8 46.3 1.0 MG 1:MG206 4.2 86.6 1.0 C4' 1:G132 4.8 45.5 1.0 O2' 1:G132 4.8 43.1 1.0 P 1:G130 5.0 46.5 1.0 C5' 1:U131 5.0 49.9 1.0

Magnesium binding site 2 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg203 b:52.3 occ:1.00 OP1 1:G132 2.4 46.3 1.0 MG 1:MG202 3.3 0.9 1.0 MG 1:MG206 3.5 86.6 1.0 MG 1:MG207 3.5 82.5 1.0 P 1:G132 3.7 42.6 1.0 O2' 1:A125 3.8 46.7 1.0 OP2 1:G132 4.2 47.7 1.0 C5' 1:U131 4.3 49.9 1.0 C3' 1:U131 4.5 45.8 1.0 C4' 1:U131 4.6 47.3 1.0 O3' 1:U131 4.6 45.8 1.0 O5' 1:A126 4.8 52.2 1.0 O5' 1:G132 4.8 44.8 1.0 C5' 1:A126 4.8 53.9 1.0 C4' 1:A126 4.9 51.7 1.0

Magnesium binding site 3 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg204 b:64.2 occ:1.00 OP1 1:A126 3.0 51.0 1.0 O5' 1:A126 3.3 52.2 1.0 MG 1:MG206 3.3 86.6 1.0 P 1:A126 3.7 49.0 1.0 O3' 1:A125 3.7 51.0 1.0 OP1 1:U127 3.8 50.8 1.0 O 1:HOH306 4.2 68.7 1.0 OP1 1:U131 4.4 48.8 1.0 OP1 1:U129 4.5 52.9 1.0 C3' 1:A126 4.6 49.1 1.0 C5' 1:A126 4.6 53.9 1.0 N2 1:G130 4.8 80.2 1.0 C4' 1:A126 4.9 51.7 1.0 P 1:U127 5.0 51.0 1.0

Magnesium binding site 4 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg205 b:71.5 occ:1.00 O2' 1:A126 3.7 61.3 1.0 C2' 1:A126 3.9 51.7 1.0 OP1 1:A126 4.2 51.0 1.0 OP2 1:U124 4.4 81.3 1.0 OP2 1:A126 4.6 44.0 1.0 OP1 1:U124 4.6 63.1 1.0 C3' 1:A126 4.7 49.1 1.0 P 1:A126 4.8 49.0 1.0 P 1:U124 4.8 69.2 1.0 O5' 1:U124 4.9 73.2 1.0 CE1 E:TYR53 4.9 60.2 1.0

Magnesium binding site 5 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg206 b:86.6 occ:1.00 OP1 1:U131 3.1 48.8 1.0 MG 1:MG204 3.3 64.2 1.0 MG 1:MG203 3.5 52.3 1.0 OP2 1:G130 4.0 52.3 1.0 MG 1:MG202 4.2 0.9 1.0 C5' 1:U131 4.2 49.9 1.0 N2 1:G130 4.3 80.2 1.0 C5' 1:U129 4.3 54.7 1.0 P 1:U131 4.4 51.6 1.0 OP1 1:U129 4.5 52.9 1.0 O 1:HOH306 4.7 68.7 1.0 O5' 1:G130 4.8 48.1 1.0 O5' 1:U131 4.8 46.4 1.0 O3' 1:G130 4.8 50.5 1.0 O5' 1:U129 4.8 58.0 1.0

Magnesium binding site 6 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg207 b:82.5 occ:1.00 OP2 1:U128 2.8 44.1 1.0 MG 1:MG202 3.1 0.9 1.0 MG 1:MG203 3.5 52.3 1.0 P 1:U128 4.2 48.8 1.0 C4' 1:U127 4.7 50.6 1.0 C5' 1:U127 4.7 50.7 1.0 OP1 1:U128 4.7 55.8 1.0 OP1 1:G132 5.0 46.3 1.0

Magnesium binding site 7 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg208 b:75.7 occ:1.00 OE1 B:GLU75 3.3 0.4 1.0 OP2 1:G130 3.3 52.3 1.0 OP1 1:G130 3.7 47.5 1.0 MG 1:MG202 3.7 0.9 1.0 CG B:GLU75 3.8 77.3 1.0 P 1:G130 3.9 46.5 1.0 CD B:GLU75 4.1 91.0 1.0 O3' 1:U129 4.5 44.7 1.0 CB B:GLU75 4.7 68.3 1.0 C4' 1:U129 4.8 48.8 1.0

Magnesium binding site 8 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg209 b:95.6 occ:1.00 OP1 1:G19 3.1 0.3 1.0 C5' 1:A18 3.3 0.1 1.0 OP1 1:G17 3.8 0.3 1.0 O4' 1:G19 3.9 0.4 1.0 C4' 1:A18 4.0 0.8 1.0 OP2 1:A18 4.0 0.3 1.0 C3' 1:A18 4.1 0.7 1.0 O5' 1:A18 4.3 0.6 1.0 P 1:G19 4.3 0.3 1.0 N9 1:G19 4.4 0.3 1.0 C8 1:G19 4.5 0.2 1.0 O5' 1:G19 4.5 0.4 1.0 C1' 1:G19 4.5 0.8 1.0 O3' 1:A18 4.7 0.2 1.0 P 1:A18 4.8 0.7 1.0 C4 1:G19 4.9 0.5 1.0 P 1:G17 5.0 0.4 1.0 N7 1:G19 5.0 0.7 1.0

Magnesium binding site 9 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ l:Mg202 b:0.1 occ:1.00 ND2 l:ASN33 3.1 0.3 1.0 OD2 l:ASP36 3.2 0.6 1.0 CD l:GLU32 3.4 0.5 1.0 CG l:GLU32 3.6 0.8 1.0 N l:ASN33 3.6 0.7 1.0 OE1 l:GLU32 3.7 0.3 1.0 OE2 l:GLU32 3.7 0.8 1.0 CA l:ASN33 3.7 1.0 1.0 C l:GLU32 3.8 0.8 1.0 CG l:ASN33 3.8 0.5 1.0 CB l:GLU32 3.8 0.9 1.0 CG l:ASP36 3.8 0.1 1.0 O l:GLU32 3.9 0.5 1.0 O1G 2:GTP1 4.0 0.3 1.0 O2G 2:GTP1 4.3 0.9 1.0 OD1 l:ASP36 4.3 0.6 1.0 OD1 l:ASN33 4.4 0.0 1.0 CB l:ASN33 4.4 0.3 1.0 CA l:GLU32 4.5 0.1 1.0 O3B 2:GTP1 4.6 0.9 1.0 PG 2:GTP1 4.6 0.1 1.0 CB l:ASP36 4.6 0.0 1.0 O l:LYS29 4.7 99.5 1.0

Magnesium binding site 10 out of 20 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg202 b:69.6 occ:1.00 OP1 2:G132 3.7 44.2 1.0 O 2:HOH303 4.5 41.5 1.0 O2' 2:A125 4.5 65.7 1.0 OP2 2:U128 4.6 51.0 1.0 O5' 2:A126 4.7 56.7 1.0 OP1 2:U127 4.7 62.8 1.0 C5' 2:U131 4.8 47.3 1.0 C4' 2:A126 4.9 56.2 1.0 OP1 2:U131 4.9 58.3 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