Magnesium in PDB 5bpj: All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin

The structure of All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin, PDB code: 5bpj was solved by L.P.Burakova, P.V.Natashin, N.P.Malikova, F.Niu, E.S.Vysotski, Z.-J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.59 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.816, 33.165, 72.074, 90.00, 126.70, 90.00
R / Rfree (%)	22.2 / 24.3

The binding sites of Magnesium atom in the All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin (pdb code 5bpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin, PDB code: 5bpj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:42.6 occ:1.00 OD1 A:ASP46 1.7 57.4 1.0 OD1 A:ASP50 2.2 57.1 1.0 O A:LYS52 2.2 51.7 1.0 OE2 A:GLU57 2.4 48.2 1.0 OD1 A:ASP48 2.6 72.4 1.0 OE1 A:GLU57 2.7 52.7 1.0 CD A:GLU57 2.8 53.6 1.0 CG A:ASP46 2.9 51.6 1.0 CG A:ASP50 3.0 65.5 1.0 OD2 A:ASP50 3.4 73.4 1.0 CG A:ASP48 3.4 84.3 1.0 C A:LYS52 3.5 53.4 1.0 OD2 A:ASP46 3.6 54.7 1.0 OD2 A:ASP48 3.8 0.5 1.0 CB A:ASP46 4.1 55.8 1.0 CA A:ASP46 4.1 51.1 1.0 CB A:ASP50 4.1 69.5 1.0 N A:LYS52 4.2 54.1 1.0 N A:ASP50 4.2 64.2 1.0 N A:ASP48 4.2 56.4 1.0 CG A:GLU57 4.2 50.0 1.0 CA A:LYS52 4.3 48.7 1.0 N A:MET53 4.4 43.0 1.0 N A:LEU47 4.4 51.7 1.0 CA A:MET53 4.5 43.6 1.0 N A:SER49 4.5 61.2 1.0 CB A:ASP48 4.6 71.3 1.0 C A:ASP46 4.6 52.3 1.0 CA A:ASP50 4.6 72.0 1.0 OE1 A:GLU54 4.6 61.5 1.0 O A:HOH465 4.7 42.8 1.0 CA A:ASP48 4.7 72.1 1.0 CB A:LYS52 4.8 57.1 1.0 N A:GLY51 4.8 61.0 1.0 C A:ASP48 4.8 71.2 1.0 C A:ASP50 4.8 65.2 1.0 N A:GLU54 4.9 40.8 1.0 CG A:GLU54 4.9 52.9 1.0

Magnesium binding site 2 out of 3 in the All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:40.5 occ:1.00 OD1 A:ASP138 1.8 44.8 1.0 OD1 A:ASP142 2.3 74.6 1.0 OE2 A:GLU149 2.3 47.6 1.0 O A:THR144 2.5 56.6 1.0 OD1 A:ASP140 2.6 55.7 1.0 CG A:ASP138 2.9 55.0 1.0 OE1 A:GLU149 3.0 46.8 1.0 CD A:GLU149 3.0 50.2 1.0 CG A:ASP140 3.2 65.4 1.0 OD2 A:ASP140 3.2 76.1 1.0 CG A:ASP142 3.4 90.8 1.0 CB A:ASP138 3.6 52.5 1.0 C A:THR144 3.7 56.1 1.0 OD2 A:ASP138 3.8 54.5 1.0 CA A:ASP138 3.9 48.2 1.0 CB A:ASP142 4.2 84.0 1.0 OD2 A:ASP142 4.3 84.0 1.0 C A:ASP138 4.3 58.5 1.0 N A:ASP140 4.4 69.2 1.0 N A:THR144 4.4 59.7 1.0 N A:ASP139 4.4 58.9 1.0 N A:ASP142 4.4 65.1 1.0 CG A:GLU149 4.5 47.3 1.0 CB A:ASP140 4.6 71.6 1.0 CA A:VAL145 4.6 41.5 1.0 N A:VAL145 4.6 45.5 1.0 N A:GLY141 4.6 64.9 1.0 CA A:THR144 4.6 57.1 1.0 N A:GLY143 4.7 55.9 1.0 N A:ASP146 4.8 38.5 1.0 CA A:ASP142 4.9 71.6 1.0 CA A:ASP140 4.9 71.6 1.0 OG1 A:THR144 5.0 62.2 1.0

Magnesium binding site 3 out of 3 in the All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of All Three Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:39.6 occ:1.00 OD1 A:ASP172 1.8 46.0 1.0 OE1 A:GLU180 2.0 75.2 1.0 OG A:SER176 2.3 46.4 1.0 O A:LYS178 2.4 44.2 1.0 OE2 A:GLU183 2.5 41.3 1.0 OE1 A:GLU183 2.5 50.0 1.0 OD1 A:ASP174 2.7 52.6 1.0 CD A:GLU183 2.8 42.6 1.0 CD A:GLU180 3.0 80.2 1.0 CG A:ASP172 3.1 47.6 1.0 OE2 A:GLU180 3.2 80.0 1.0 OD2 A:ASP174 3.3 46.4 1.0 CG A:ASP174 3.3 54.3 1.0 CB A:SER176 3.3 52.3 1.0 C A:LYS178 3.7 51.7 1.0 OD2 A:ASP172 3.8 47.0 1.0 N A:GLU180 4.2 38.7 1.0 N A:SER176 4.3 52.0 1.0 CB A:ASP172 4.3 48.4 1.0 CG A:GLU183 4.3 54.5 1.0 CG A:GLU180 4.3 65.8 1.0 CA A:SER176 4.3 56.9 1.0 CA A:LEU179 4.4 46.0 1.0 N A:LEU179 4.5 40.7 1.0 N A:LYS178 4.6 52.9 1.0 CA A:ASP172 4.6 48.4 1.0 CB A:GLU180 4.7 56.8 1.0 CA A:LYS178 4.7 48.7 1.0 C A:LEU179 4.7 44.8 1.0 CB A:ASP174 4.7 72.5 1.0 O A:HOH429 4.8 55.9 1.0 N A:GLY177 4.9 57.6 1.0

L.P.Burakova, P.V.Natashin, N.P.Malikova, F.Niu, M.Pu, E.S.Vysotski, Z.J.Liu. All Ca(2+)-Binding Loops of Light-Sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: the Spatial Structure of Mg(2+)-Loaded Apo-Berovin. J. Photochem. Photobiol. B, V. 154 57 2016BIOL..
ISSN: ISSN 1873-2682
PubMed: 26690016
DOI: 10.1016/J.JPHOTOBIOL.2015.11.012