Mercury in PDB 5tip: The Structure of the Major Capsid Protein of Pbcv-1

The structure of The Structure of the Major Capsid Protein of Pbcv-1, PDB code: 5tip was solved by T.Klose, C.De Castro, I.Speciale, A.Molinaro, J.L.Van Etten, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.43 / 2.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	188.792, 188.792, 188.792, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.6

The binding sites of Mercury atom in the The Structure of the Major Capsid Protein of Pbcv-1 (pdb code 5tip). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the The Structure of the Major Capsid Protein of Pbcv-1, PDB code: 5tip:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in the The Structure of the Major Capsid Protein of Pbcv-1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of The Structure of the Major Capsid Protein of Pbcv-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg501 b:42.9 occ:0.51 SG A:CYS369 2.5 32.5 1.0 CD1 A:ILE374 3.6 36.8 1.0 CB A:CYS369 3.6 26.1 1.0 CE1 A:PHE356 3.7 29.8 1.0 CD1 A:LEU320 3.8 38.5 1.0 CZ A:PHE371 3.8 30.8 1.0 CZ A:PHE356 3.9 28.8 1.0 CE1 A:PHE371 4.0 30.8 1.0 CE2 A:PHE371 4.4 28.6 1.0 CD1 A:PHE356 4.5 27.4 1.0 CG A:LEU320 4.7 39.1 1.0 CD1 A:PHE371 4.7 27.1 1.0 NE A:ARG325 4.8 31.9 1.0 CE2 A:PHE356 4.8 23.2 1.0 CD A:ARG325 4.9 33.0 1.0 CG A:ARG325 5.0 32.0 1.0

Mercury binding site 2 out of 4 in the The Structure of the Major Capsid Protein of Pbcv-1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of The Structure of the Major Capsid Protein of Pbcv-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg501 b:46.9 occ:0.51 SG B:CYS369 2.6 38.3 1.0 CD1 B:LEU320 3.4 51.0 1.0 CD1 B:ILE374 3.5 45.4 1.0 CB B:CYS369 3.6 32.0 1.0 CE1 B:PHE356 3.8 28.6 1.0 CZ B:PHE356 3.8 28.1 1.0 CZ B:PHE371 4.1 31.9 1.0 CG B:LEU320 4.2 49.6 1.0 CE1 B:PHE371 4.3 33.9 1.0 CD1 B:PHE356 4.6 29.4 1.0 CE2 B:PHE371 4.7 30.0 1.0 CE2 B:PHE356 4.7 27.4 1.0 NE B:ARG325 4.7 28.1 1.0 CD B:ARG325 4.7 28.1 1.0 CB B:LEU320 4.9 44.6 1.0 CD1 B:PHE371 4.9 32.6 1.0 CG B:ARG325 4.9 25.7 1.0 CG1 B:ILE374 5.0 45.5 1.0

Mercury binding site 3 out of 4 in the The Structure of the Major Capsid Protein of Pbcv-1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of The Structure of the Major Capsid Protein of Pbcv-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg501 b:45.3 occ:0.56 SG C:CYS369 2.5 37.9 1.0 CB C:CYS369 3.5 33.1 1.0 CD1 C:ILE374 3.6 41.5 1.0 CE1 C:PHE356 3.7 40.8 1.0 CD1 C:LEU320 3.8 47.3 1.0 CZ C:PHE356 3.9 41.9 1.0 CZ C:PHE371 3.9 31.9 1.0 CE1 C:PHE371 4.0 33.5 1.0 CE2 C:PHE371 4.5 30.4 1.0 CD1 C:PHE356 4.6 39.8 1.0 CG C:LEU320 4.6 47.1 1.0 CD1 C:PHE371 4.7 35.2 1.0 CE2 C:PHE356 4.8 41.2 1.0 NE C:ARG325 4.8 36.0 1.0 CD C:ARG325 4.8 32.9 1.0 CA C:CYS369 4.9 31.8 1.0 CG C:ARG325 5.0 31.4 1.0

Mercury binding site 4 out of 4 in the The Structure of the Major Capsid Protein of Pbcv-1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of The Structure of the Major Capsid Protein of Pbcv-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg501 b:49.3 occ:0.57 SG D:CYS369 2.6 39.8 1.0 CD1 D:ILE374 3.5 38.6 1.0 CE1 D:PHE356 3.6 30.5 1.0 CB D:CYS369 3.7 36.1 1.0 CZ D:PHE356 3.7 28.6 1.0 CD1 D:LEU320 3.9 48.2 1.0 CZ D:PHE371 4.0 32.7 1.0 CE1 D:PHE371 4.1 33.6 1.0 CD1 D:PHE356 4.6 29.6 1.0 CE2 D:PHE371 4.6 32.7 1.0 CE2 D:PHE356 4.7 28.4 1.0 CG D:LEU320 4.8 48.2 1.0 CD1 D:PHE371 4.8 29.8 1.0 NE D:ARG325 4.9 38.5 1.0 CG1 D:ILE374 5.0 38.9 1.0

C.De Castro, T.Klose, I.Speciale, R.Lanzetta, A.Molinaro, J.L.Van Etten, M.G.Rossmann. Structure of the Chlorovirus Pbcv-1 Major Capsid Glycoprotein Determined By Combining Crystallographic and Carbohydrate Molecular Modeling Approaches. Proc. Natl. Acad. Sci. V. 115 E44 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29255015
DOI: 10.1073/PNAS.1613432115