Magnesium in PDB 5a98: Crystal Structure of Trichoplusia Ni CPV15 Polyhedra

The structure of Crystal Structure of Trichoplusia Ni CPV15 Polyhedra, PDB code: 5a98 was solved by X.Ji, D.Axford, R.Owen, G.Evans, H.M.Ginn, G.Sutton, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.005 / 1.82
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	102.890, 102.890, 102.890, 90.00, 90.00, 90.00
R / Rfree (%)	16.17 / 21.99

The binding sites of Magnesium atom in the Crystal Structure of Trichoplusia Ni CPV15 Polyhedra (pdb code 5a98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Trichoplusia Ni CPV15 Polyhedra, PDB code: 5a98:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Trichoplusia Ni CPV15 Polyhedra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trichoplusia Ni CPV15 Polyhedra within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg250 b:20.3 occ:1.00 O2B A:ATP249 2.1 16.8 1.0 O A:HOH2166 2.2 15.6 1.0 O1A A:ATP249 2.2 18.6 1.0 O A:HOH2165 2.2 18.0 1.0 O A:HOH2006 2.2 13.4 1.0 O2G A:ATP249 2.3 18.9 1.0 PB A:ATP249 3.2 19.9 1.0 PA A:ATP249 3.3 18.6 1.0 PG A:ATP249 3.5 18.5 1.0 H8 A:ATP249 3.6 24.3 1.0 O3A A:ATP249 3.6 21.3 1.0 O3B A:ATP249 3.6 19.5 1.0 O5' A:ATP249 4.0 17.3 1.0 O A:HOH2167 4.0 30.2 1.0 OH A:TYR14 4.1 14.5 1.0 O1G A:ATP249 4.2 18.0 1.0 H2' A:ATP249 4.5 23.5 1.0 C8 A:ATP249 4.5 20.4 1.0 O1B A:ATP249 4.6 17.8 1.0 O2A A:ATP249 4.6 21.4 1.0 O3G A:ATP249 4.7 17.2 1.0 O A:HOH2164 5.0 27.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Trichoplusia Ni CPV15 Polyhedra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trichoplusia Ni CPV15 Polyhedra within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg251 b:36.9 occ:1.00 O3G A:ATP252 2.2 38.4 1.0 O A:HOH2116 2.3 29.0 1.0 O A:HOH2013 2.3 34.7 1.0 O1A A:ATP252 2.5 41.8 1.0 O A:HOH2014 2.5 27.6 1.0 O A:HOH2173 2.6 42.0 1.0 O A:HOH2174 3.3 30.9 0.5 O2B A:ATP252 3.4 43.0 1.0 PG A:ATP252 3.6 39.3 1.0 OE2 A:GLU165 3.6 21.6 1.0 O A:LYS164 3.8 18.4 1.0 H5'2 A:ATP252 3.9 45.4 1.0 PA A:ATP252 3.9 47.7 1.0 O2G A:ATP252 4.1 36.5 1.0 NZ A:LYS20 4.1 33.5 1.0 OE1 A:GLU165 4.2 20.8 1.0 CD A:GLU165 4.3 21.8 1.0 PB A:ATP252 4.3 47.4 1.0 O3B A:ATP252 4.4 38.8 1.0 O3A A:ATP252 4.5 43.5 1.0 O5' A:ATP252 4.6 37.6 1.0 O1G A:ATP252 4.6 34.5 1.0 C5' A:ATP252 4.7 38.0 1.0 H3' A:ATP252 4.9 39.6 1.0 C A:LYS164 4.9 19.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Trichoplusia Ni CPV15 Polyhedra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trichoplusia Ni CPV15 Polyhedra within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg253 b:25.3 occ:1.00 O A:HOH2170 2.3 18.4 1.0 O A:HOH2012 2.3 24.4 1.0 HN62 A:ATP249 4.1 24.6 1.0 O1B A:ATP249 4.1 17.8 1.0 CE1 A:TYR14 4.2 13.1 1.0 O A:HOH2011 4.3 17.9 1.0 CD1 A:TYR14 4.5 15.5 1.0 OE1 A:GLN17 4.6 18.5 1.0 O1G A:ATP249 4.7 18.0 1.0 N7 A:ATP249 4.8 17.7 1.0 N6 A:ATP249 4.8 20.6 1.0 PB A:ATP249 5.0 19.9 1.0

X.Ji, D.Axford, R.Owen, G.Evans, H.M.Ginn, G.Sutton, D.I.Stuart. Polyhedra Structures and the Evolution of the Insect Viruses. J.Struct.Biol. V. 192 88 2015.
ISSN: ISSN 1047-8477
PubMed: 26291392
DOI: 10.1016/J.JSB.2015.08.009