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

Protein crystallography data

The structure of The Structure of the Major Capsid Protein of Pbcv-1, PDB code: 5tiq 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) 43.31 / 2.54
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 188.763, 188.763, 188.763, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.3

Mercury Binding Sites:

The binding sites of Mercury atom in the The Structure of the Major Capsid Protein of Pbcv-1 (pdb code 5tiq). 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: 5tiq:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 5tiq

Go back to Mercury Binding Sites List in 5tiq
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:42.6
occ:0.67
SG A:CYS369 2.5 40.3 1.0
CB A:CYS369 3.4 26.1 1.0
CD1 A:ILE374 3.5 30.4 1.0
CE1 A:PHE356 3.6 32.2 1.0
CZ A:PHE356 3.7 31.2 1.0
CE1 A:PHE371 3.8 26.7 1.0
CZ A:PHE371 3.9 29.4 1.0
CD1 A:LEU320 4.0 43.9 1.0
CD1 A:PHE356 4.5 36.2 1.0
CD1 A:PHE371 4.5 27.1 1.0
CE2 A:PHE371 4.5 33.5 1.0
CE2 A:PHE356 4.7 33.3 1.0
CA A:CYS369 4.8 25.9 1.0
NE A:ARG325 4.9 32.6 1.0
CG1 A:ILE374 5.0 31.7 1.0

Mercury binding site 2 out of 4 in 5tiq

Go back to Mercury Binding Sites List in 5tiq
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
A:Hg502

b:61.8
occ:0.80
SG A:CYS386 2.7 61.5 1.0
O A:CYS386 2.8 50.5 1.0
CG2 A:THR409 3.4 40.0 1.0
CB A:CYS386 3.4 52.7 1.0
O A:HOH608 3.6 42.2 1.0
O A:ASN406 3.6 39.2 1.0
CB A:ALA243 3.7 49.3 1.0
C A:CYS386 3.8 46.2 1.0
N A:ALA243 3.9 53.9 1.0
CA A:ASN406 4.0 42.0 1.0
O A:PRO241 4.0 57.9 1.0
CB A:ASN406 4.1 44.3 1.0
CA A:ALA243 4.2 52.8 1.0
CA A:CYS386 4.2 45.6 1.0
C A:ASN406 4.3 43.3 1.0
C A:SER242 4.3 55.5 1.0
O A:SER242 4.7 57.5 1.0
N A:CYS386 4.8 41.0 1.0
CA A:SER242 4.8 54.9 1.0
C A:PRO241 4.8 55.3 1.0
CB A:THR409 4.9 41.5 1.0

Mercury binding site 3 out of 4 in 5tiq

Go back to Mercury Binding Sites List in 5tiq
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
B:Hg501

b:60.1
occ:0.74
SG B:CYS386 2.8 56.3 1.0
O B:CYS386 2.8 46.1 1.0
CG2 B:THR409 3.3 44.1 1.0
CB B:CYS386 3.5 46.2 1.0
CB B:ALA243 3.7 44.3 1.0
O B:ASN406 3.7 53.4 1.0
C B:CYS386 3.8 39.5 1.0
N B:ALA243 3.8 42.4 1.0
O B:HOH657 3.9 39.5 1.0
O B:PRO241 4.0 59.1 1.0
CA B:ASN406 4.1 46.5 1.0
CA B:ALA243 4.1 44.7 1.0
CA B:CYS386 4.2 39.8 1.0
C B:SER242 4.3 55.2 1.0
CB B:ASN406 4.3 46.8 1.0
C B:ASN406 4.4 49.5 1.0
O B:SER242 4.7 55.2 1.0
CB B:THR409 4.7 41.1 1.0
CA B:SER242 4.8 49.8 1.0
N B:CYS386 4.8 39.2 1.0
C B:PRO241 4.8 52.9 1.0

Mercury binding site 4 out of 4 in 5tiq

Go back to Mercury Binding Sites List in 5tiq
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
B:Hg502

b:72.9
occ:0.48
SG B:CYS369 2.6 43.9 1.0
CD1 B:LEU320 3.1 50.5 1.0
CD2 B:LEU320 3.1 45.2 1.0
CB B:CYS369 3.3 38.4 1.0
CE1 B:PHE356 3.5 33.9 1.0
CD1 B:ILE374 3.5 34.8 1.0
CZ B:PHE356 3.6 30.5 1.0
O B:HOH756 3.6 0.0 1.0
CG B:LEU320 3.7 46.2 1.0
CE1 B:PHE371 3.7 34.5 1.0
CZ B:PHE371 3.8 36.0 1.0
CD1 B:PHE356 4.4 40.0 1.0
CD1 B:PHE371 4.5 37.4 1.0
CE2 B:PHE356 4.5 33.9 1.0
CE2 B:PHE371 4.5 39.2 1.0
CA B:CYS369 4.8 31.8 1.0
NE B:ARG325 4.8 30.1 1.0
CD B:ARG325 4.9 29.0 1.0
CB B:LEU320 5.0 41.7 1.0
CG1 B:ILE374 5.0 34.7 1.0
CG B:ARG325 5.0 31.7 1.0

Reference:

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
Page generated: Sun Dec 13 19:13:17 2020

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