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Magnesium in PDB 3n7x: Crystal Structure of Penaeus Stylirostris Densovirus Capsid

Protein crystallography data

The structure of Crystal Structure of Penaeus Stylirostris Densovirus Capsid, PDB code: 3n7x was solved by B.Kaufmann, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 21 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 235.890, 245.471, 268.467, 90.00, 90.00, 90.00
R / Rfree (%) 27.8 / 28.5

Other elements in 3n7x:

The structure of Crystal Structure of Penaeus Stylirostris Densovirus Capsid also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Penaeus Stylirostris Densovirus Capsid (pdb code 3n7x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Penaeus Stylirostris Densovirus Capsid, PDB code: 3n7x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3n7x

Go back to Magnesium Binding Sites List in 3n7x
Magnesium binding site 1 out of 2 in the Crystal Structure of Penaeus Stylirostris Densovirus Capsid


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 Penaeus Stylirostris Densovirus Capsid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg331

b:5.8
occ:1.00
O A:HOH479 2.9 25.8 1.0
O A:HOH477 3.1 20.7 1.0
N A:TYR324 3.1 23.3 1.0
CE1 A:HIS77 3.2 23.3 1.0
NE1 A:TRP78 3.4 20.1 1.0
CZ A:PHE232 3.5 23.4 1.0
NE2 A:HIS77 3.7 23.2 1.0
CE1 A:PHE232 3.9 22.9 1.0
CA A:CYS323 3.9 24.0 1.0
O A:TYR324 3.9 24.2 1.0
CD2 A:TYR324 4.0 23.8 1.0
CB A:TYR324 4.0 22.5 1.0
C A:CYS323 4.0 24.3 1.0
CA A:TYR324 4.0 22.9 1.0
CZ2 A:TRP78 4.0 20.1 1.0
CE2 A:TRP78 4.0 19.8 1.0
O A:LYS322 4.1 25.2 1.0
O A:HOH389 4.4 28.6 1.0
CE2 A:PHE232 4.4 22.7 1.0
NE2 A:GLN263 4.4 25.9 1.0
ND1 A:HIS77 4.4 23.4 1.0
C A:TYR324 4.4 22.4 1.0
CG A:TYR324 4.5 23.6 1.0
CD1 A:TRP78 4.5 19.6 1.0
N A:CYS323 4.7 24.4 1.0
C A:LYS322 4.7 25.5 1.0
CB A:CYS323 4.9 25.0 1.0
CD1 A:PHE232 5.0 22.7 1.0

Magnesium binding site 2 out of 2 in 3n7x

Go back to Magnesium Binding Sites List in 3n7x
Magnesium binding site 2 out of 2 in the Crystal Structure of Penaeus Stylirostris Densovirus Capsid


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 Penaeus Stylirostris Densovirus Capsid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg332

b:36.7
occ:1.00
OE1 A:GLU139 3.1 40.7 1.0
OE2 A:GLU139 3.4 41.0 1.0
CD A:GLU139 3.6 37.7 1.0
CB A:LYS128 4.1 28.1 1.0
O A:LYS280 4.3 23.0 1.0
C A:LEU281 4.5 22.1 1.0
O A:LEU281 4.5 22.4 1.0
C A:LYS280 4.6 23.5 1.0
CD A:LYS128 4.7 33.8 1.0
N A:GLY282 4.7 21.4 1.0
N A:LYS128 4.7 26.1 1.0
CB A:LYS280 4.9 25.3 1.0
C A:MET127 4.9 24.9 1.0
N A:LEU281 4.9 21.9 1.0
CA A:GLY282 5.0 20.5 1.0
CA A:LEU281 5.0 22.4 1.0

Reference:

B.Kaufmann, V.D.Bowman, Y.Li, J.Szelei, P.J.Waddell, P.Tijssen, M.G.Rossmann. Structure of Penaeus Stylirostris Densovirus, A Shrimp Pathogen. J.Virol. V. 84 11289 2010.
ISSN: ISSN 0022-538X
PubMed: 20702621
DOI: 10.1128/JVI.01240-10
Page generated: Mon Dec 14 08:27:48 2020

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