Magnesium in PDB 4oq9: Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints

The structure of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints, PDB code: 4oq9 was solved by S.B.Larson, J.S.Day, A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 1.45
Space group	I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.690, 190.300, 201.690, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25

The structure of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints also contains other interesting chemical elements:

Sodium

(Na)

17 atoms

The binding sites of Magnesium atom in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints (pdb code 4oq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints, PDB code: 4oq9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:74.0 occ:1.00 O4 A:PO4201 2.1 34.2 0.2 O4 A:PO4201 2.3 29.1 0.2 O4 A:PO4201 2.3 19.8 0.2 O4 A:PO4201 2.4 26.3 0.2 O4 A:PO4201 2.4 28.6 0.2 O3 A:PO4201 3.4 26.5 0.2 P A:PO4201 3.5 26.3 1.0 O3 A:PO4201 3.6 30.2 0.2 O A:HOH571 3.6 55.7 1.0 O3 A:PO4201 3.6 28.8 0.2 O3 A:PO4201 3.6 25.4 0.2 ND2 E:ASN115 3.7 27.9 1.0 O3 A:PO4201 3.8 31.4 0.2 ND2 D:ASN115 3.9 27.5 1.0 O E:HOH386 3.9 39.5 0.6 ND2 A:ASN115 4.0 27.1 1.0 O2 A:PO4201 4.0 32.0 0.2 O D:HOH379 4.1 55.8 1.0 O B:HOH379 4.1 39.3 0.6 O2 A:PO4201 4.2 31.8 0.2 O2 A:PO4201 4.2 25.5 0.2 O2 A:PO4201 4.2 26.6 0.2 O2 A:PO4201 4.2 21.4 0.2 ND2 C:ASN115 4.2 27.9 1.0 ND2 B:ASN115 4.3 27.6 1.0 O1 A:PO4201 4.5 32.1 0.2 O D:HOH499 4.6 38.1 0.4 O1 A:PO4201 4.6 24.8 0.2 O1 A:PO4201 4.6 32.6 0.2 O1 A:PO4201 4.7 35.5 0.2 O B:HOH565 4.7 49.9 1.0 O1 A:PO4201 4.7 22.8 0.2 O A:HOH706 4.8 42.6 0.5 CG E:ASN115 4.9 23.3 1.0

Magnesium binding site 2 out of 3 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:56.5 occ:1.00 O4 H:PO4201 2.0 38.8 0.2 O4 H:PO4201 2.0 33.8 0.2 O4 H:PO4201 2.1 33.6 0.2 O4 H:PO4201 2.3 30.3 0.2 O4 H:PO4201 2.6 27.6 0.2 P H:PO4201 3.4 26.5 1.0 O3 H:PO4201 3.5 19.3 0.2 O3 H:PO4201 3.6 20.4 0.2 O3 H:PO4201 3.6 20.1 0.2 O2 H:PO4201 3.7 21.3 0.2 O3 H:PO4201 3.8 17.1 0.2 O3 H:PO4201 3.9 16.7 0.2 ND2 F:ASN115 3.9 27.6 1.0 ND2 I:ASN115 4.0 27.7 1.0 ND2 J:ASN115 4.0 27.4 1.0 ND2 G:ASN115 4.0 27.6 1.0 O F:HOH377 4.1 40.0 0.7 ND2 H:ASN115 4.1 27.4 1.0 O2 H:PO4201 4.1 19.0 0.2 O2 H:PO4201 4.2 30.9 0.2 O2 H:PO4201 4.2 30.5 0.2 O I:HOH512 4.2 51.5 0.7 O I:HOH544 4.3 53.8 1.0 O2 H:PO4201 4.3 23.3 0.2 O F:HOH544 4.3 49.3 1.0 O H:HOH379 4.4 34.5 0.5 O1 H:PO4201 4.4 25.7 0.2 O1 H:PO4201 4.4 26.4 0.2 O1 H:PO4201 4.4 32.9 0.2 O G:HOH525 4.5 34.6 0.5 O F:HOH552 4.6 49.3 0.5 O1 H:PO4201 4.6 30.8 0.2 O J:HOH308 4.8 30.7 0.3 O1 H:PO4201 4.8 29.3 0.2 O H:HOH524 4.9 29.6 0.3

Magnesium binding site 3 out of 3 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg202 b:70.4 occ:1.00 O4 N:PO4201 2.1 29.4 0.2 O4 N:PO4201 2.1 35.2 0.2 O4 N:PO4201 2.3 32.4 0.2 O4 N:PO4201 2.4 17.6 0.2 O3 N:PO4201 3.2 35.7 0.2 O4 N:PO4201 3.3 27.5 0.2 O3 N:PO4201 3.4 22.4 0.2 P N:PO4201 3.5 25.8 1.0 O2 N:PO4201 3.5 30.1 0.2 O N:HOH379 3.8 35.1 0.5 O O:HOH387 3.8 29.5 0.5 O L:HOH5081 3.8 37.5 0.5 O3 N:PO4201 3.8 22.6 0.2 O3 N:PO4201 3.9 21.8 0.2 O2 N:PO4201 3.9 34.8 0.2 O3 N:PO4201 4.0 28.4 0.2 O M:HOH380 4.0 53.9 1.0 ND2 L:ASN115 4.0 27.7 1.0 ND2 K:ASN115 4.1 27.7 1.0 ND2 O:ASN115 4.1 27.6 1.0 ND2 N:ASN115 4.1 27.4 1.0 ND2 M:ASN115 4.1 27.6 1.0 O K:HOH531 4.2 39.2 0.4 O K:HOH532 4.2 36.8 0.5 O2 N:PO4201 4.4 31.8 0.2 O1 N:PO4201 4.4 30.8 0.2 O1 N:PO4201 4.4 29.9 0.2 O2 N:PO4201 4.4 30.8 0.2 O1 N:PO4201 4.5 35.5 0.2 O2 N:PO4201 4.5 32.2 0.2 O N:HOH522 4.5 39.2 0.5 O M:HOH518 4.5 38.7 0.6 O O:HOH603 4.6 46.4 0.6 O1 N:PO4201 4.7 19.5 0.2

S.B.Larson, J.S.Day, A.Mcpherson. Satellite Tobacco Mosaic Virus Refined to 1.4 Angstrom Resolution. Acta Crystallogr.,Sect.D V. 70 2316 2014.
ISSN: ISSN 0907-4449
PubMed: 25195746
DOI: 10.1107/S1399004714013789