Magnesium in PDB 4nia: Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs Restraints

The structure of Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs Restraints, PDB code: 4nia 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)	87.04 / 1.82
Space group	I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.268, 191.774, 202.503, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 15.6

The binding sites of Magnesium atom in the Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs Restraints (pdb code 4nia). 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 at Room Temperature to 1.8 A Resolution Using Ncs Restraints, PDB code: 4nia:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs 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 at Room Temperature to 1.8 A Resolution Using Ncs Restraints within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:63.3 occ:1.00 O4 C:PO4201 2.1 11.0 0.2 O4 C:PO4201 2.2 23.8 0.2 O4 C:PO4201 2.4 16.8 0.2 O4 C:PO4201 2.5 7.6 0.2 O4 C:PO4201 2.7 13.7 0.2 P C:PO4201 3.5 15.1 1.0 O2 C:PO4201 3.6 12.5 0.2 O D:HOH304 3.6 33.8 0.5 O1 C:PO4201 3.7 8.5 0.2 O2 C:PO4201 3.7 10.4 0.2 ND2 E:ASN115 3.8 20.6 1.0 O1 C:PO4201 3.8 12.5 0.2 O1 C:PO4201 3.9 10.7 0.2 ND2 D:ASN115 3.9 19.2 1.0 O A:HOH400 4.0 48.6 1.0 O2 C:PO4201 4.0 17.9 0.2 O E:HOH400 4.0 27.4 0.5 O2 C:PO4201 4.0 23.3 0.2 O2 C:PO4201 4.1 5.0 0.2 O1 C:PO4201 4.1 21.5 0.2 O1 C:PO4201 4.1 4.8 0.2 ND2 A:ASN115 4.1 20.3 1.0 ND2 C:ASN115 4.3 20.9 1.0 ND2 B:ASN115 4.4 20.8 1.0 O C:HOH473 4.5 36.5 0.5 O B:HOH401 4.5 49.9 1.0 O3 C:PO4201 4.5 21.9 0.2 O3 C:PO4201 4.6 9.2 0.2 O3 C:PO4201 4.7 30.7 0.2 O A:HOH504 4.8 46.0 1.0 O3 C:PO4201 4.8 24.0 0.2 O3 C:PO4201 4.9 13.9 0.2

Magnesium binding site 2 out of 3 in the Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs 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 at Room Temperature to 1.8 A Resolution Using Ncs Restraints within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:57.6 occ:1.00 O4 H:PO4201 2.2 19.1 0.2 O4 H:PO4201 2.2 13.5 0.2 O4 H:PO4201 2.5 16.1 0.2 O4 H:PO4201 2.5 6.2 0.2 O4 H:PO4201 2.6 10.9 0.2 O2 H:PO4201 3.2 5.0 0.2 P H:PO4201 3.5 14.8 1.0 O2 H:PO4201 3.6 11.4 0.2 O2 H:PO4201 3.6 8.5 0.2 O2 H:PO4201 3.8 12.3 0.2 O2 H:PO4201 3.9 6.7 0.2 O F:HOH474 3.9 36.4 0.5 ND2 J:ASN115 4.0 20.1 1.0 ND2 I:ASN115 4.1 19.3 1.0 ND2 F:ASN115 4.1 19.9 1.0 O1 H:PO4201 4.1 9.7 0.2 ND2 H:ASN115 4.2 22.1 1.0 O1 H:PO4201 4.2 11.4 0.2 O F:HOH504 4.2 50.8 1.0 ND2 G:ASN115 4.2 19.9 1.0 O I:HOH410 4.2 50.6 1.0 O1 H:PO4201 4.3 7.2 0.2 O H:HOH514 4.3 42.0 1.0 O1 H:PO4201 4.4 13.1 0.2 O J:HOH201 4.4 31.2 0.5 O G:HOH405 4.4 42.9 1.0 O1 H:PO4201 4.5 15.3 0.2 O3 H:PO4201 4.5 12.6 0.2 O3 H:PO4201 4.6 18.8 0.2 O3 H:PO4201 4.6 19.6 0.2 O3 H:PO4201 4.8 19.0 0.2 O3 H:PO4201 4.8 26.6 0.2

Magnesium binding site 3 out of 3 in the Satellite Tobacco Mosaic Virus Refined at Room Temperature to 1.8 A Resolution Using Ncs 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 at Room Temperature to 1.8 A Resolution Using Ncs Restraints within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg202 b:64.5 occ:1.00 O4 K:PO4201 2.3 9.6 0.2 O4 K:PO4201 2.3 9.5 0.2 O4 K:PO4201 2.3 10.2 0.2 O4 K:PO4201 2.4 15.7 0.2 O4 K:PO4201 2.5 6.3 0.2 P K:PO4201 3.5 13.8 1.0 O2 K:PO4201 3.6 14.3 0.2 O2 K:PO4201 3.6 11.3 0.2 O2 K:PO4201 3.7 18.6 0.2 O2 K:PO4201 3.7 6.1 0.2 O M:HOH303 3.8 28.1 0.5 O1 K:PO4201 3.8 13.7 0.2 O2 K:PO4201 3.9 4.6 0.2 O L:HOH309 3.9 32.7 0.5 O1 K:PO4201 3.9 17.0 0.2 ND2 O:ASN115 4.0 18.9 1.0 O N:HOH405 4.0 53.6 1.0 O1 K:PO4201 4.0 10.4 0.2 O O:HOH215 4.0 32.7 0.5 ND2 K:ASN115 4.0 21.7 1.0 O1 K:PO4201 4.1 7.8 0.2 ND2 N:ASN115 4.1 18.9 1.0 ND2 L:ASN115 4.1 19.3 1.0 O1 K:PO4201 4.1 4.3 0.2 ND2 M:ASN115 4.2 20.1 1.0 O N:HOH306 4.5 36.0 0.5 O O:HOH219 4.5 42.1 0.5 O K:HOH463 4.6 27.3 0.5 O3 K:PO4201 4.6 19.7 0.2 O3 K:PO4201 4.7 18.8 0.2 O3 K:PO4201 4.7 13.8 0.2 O L:HOH378 4.7 29.5 0.5 O3 K:PO4201 4.7 30.1 0.2 O3 K:PO4201 4.8 29.0 0.2 O M:HOH377 5.0 36.3 0.5

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