Magnesium in PDB 2hyi: Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna

The structure of Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna, PDB code: 2hyi was solved by C.B.F.Andersen, H.Le Hir, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.830, 88.260, 145.770, 90.00, 110.77, 90.00
R / Rfree (%)	21.2 / 23.1

The binding sites of Magnesium atom in the Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna (pdb code 2hyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna, PDB code: 2hyi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:35.1 occ:1.00 O3G C:ANP801 2.2 34.0 1.0 O2B C:ANP801 2.2 32.9 1.0 O C:HOH802 2.3 31.0 1.0 O C:HOH804 2.3 31.4 1.0 O C:HOH803 2.3 32.8 1.0 OG1 C:THR89 2.5 39.0 1.0 PG C:ANP801 3.5 34.2 1.0 PB C:ANP801 3.5 31.1 1.0 OD2 C:ASP187 3.5 33.0 1.0 N3B C:ANP801 3.6 35.0 1.0 CB C:THR89 3.9 40.3 1.0 OE1 C:GLU188 3.9 33.5 1.0 OD1 C:ASP187 3.9 32.0 1.0 CG C:ASP187 4.1 34.0 1.0 CA C:GLY340 4.1 31.9 1.0 O2A C:ANP801 4.2 34.0 1.0 N C:THR89 4.2 34.8 1.0 O C:HOH830 4.4 39.0 1.0 O1B C:ANP801 4.4 33.6 1.0 O1G C:ANP801 4.4 37.8 1.0 O2G C:ANP801 4.5 34.6 1.0 CA C:THR89 4.5 38.1 1.0 CE C:LYS88 4.5 27.1 1.0 O C:GLY340 4.5 33.5 1.0 O3A C:ANP801 4.6 35.6 1.0 O1A C:ANP801 4.7 35.3 1.0 CB C:LYS88 4.7 29.5 1.0 PA C:ANP801 4.7 35.4 1.0 C C:GLY340 4.9 33.2 1.0 CD C:GLU188 4.9 35.7 1.0 CG2 C:THR89 4.9 41.5 1.0 O C:HOH805 5.0 24.8 1.0 CD1 C:LEU118 5.0 32.9 1.0

Magnesium binding site 2 out of 2 in the Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Human Exon Junction Complex with A Trapped Dead-Box Helicase Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg702 b:39.7 occ:1.00 O3G I:ANP802 2.2 36.5 1.0 O2B I:ANP802 2.2 36.3 1.0 O I:HOH803 2.3 32.4 1.0 O I:HOH805 2.3 39.0 1.0 O I:HOH804 2.3 32.6 1.0 OG1 I:THR89 2.5 44.9 1.0 PG I:ANP802 3.5 37.5 1.0 PB I:ANP802 3.5 36.6 1.0 OD2 I:ASP187 3.6 39.7 1.0 N3B I:ANP802 3.6 36.3 1.0 CB I:THR89 3.8 44.0 1.0 OD1 I:ASP187 3.8 37.2 1.0 OE1 I:GLU188 3.9 40.6 1.0 CG I:ASP187 4.1 40.0 1.0 CA I:GLY340 4.2 38.1 1.0 O2A I:ANP802 4.2 41.2 1.0 N I:THR89 4.2 38.8 1.0 O1B I:ANP802 4.3 33.9 1.0 O1G I:ANP802 4.4 35.1 1.0 O I:HOH816 4.4 38.3 1.0 CA I:THR89 4.5 42.2 1.0 O2G I:ANP802 4.5 35.4 1.0 CE I:LYS88 4.6 31.3 1.0 O3A I:ANP802 4.6 39.0 1.0 O I:GLY340 4.6 36.7 1.0 O1A I:ANP802 4.7 42.2 1.0 CB I:LYS88 4.7 34.4 1.0 PA I:ANP802 4.7 41.2 1.0 CD I:GLU188 4.9 39.9 1.0 CG2 I:THR89 4.9 45.3 1.0 C I:GLY340 4.9 37.3 1.0 O I:HOH912 5.0 63.0 1.0

C.B.F.Andersen, L.Ballut, J.S.Johansen, H.Chamieh, K.H.Nielsen, C.L.Oliveira, J.S.Pedersen, B.Seraphin, H.Le Hir, G.R.Andersen. Structure of the Exon Junction Core Complex with A Trapped Dead-Box Atpase Bound to Rna. Science V. 313 1968 2006.
ISSN: ISSN 0036-8075
PubMed: 16931718
DOI: 10.1126/SCIENCE.1131981