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Mercury in PDB 1wqs: Crystal Structure of Norovirus 3C-Like Protease

Protein crystallography data

The structure of Crystal Structure of Norovirus 3C-Like Protease, PDB code: 1wqs was solved by K.Nakamura, Y.Someya, T.Kumasaka, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 128.890, 128.890, 118.080, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 24

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Norovirus 3C-Like Protease (pdb code 1wqs). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the Crystal Structure of Norovirus 3C-Like Protease, PDB code: 1wqs:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Mercury binding site 1 out of 8 in 1wqs

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Mercury binding site 1 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1001

b:81.4
occ:0.47
SG A:CYS169 2.8 55.5 1.0
CB A:CYS154 2.9 41.2 1.0
CB A:CYS77 3.5 78.7 1.0
N A:CYS77 3.6 52.7 1.0
HG A:HG1002 3.6 65.2 0.3
SG A:CYS154 3.9 65.3 1.0
OE1 A:GLN117 3.9 35.7 1.0
CB A:CYS169 3.9 34.1 1.0
CB A:TYR143 4.0 32.5 1.0
CA A:CYS77 4.1 59.6 1.0
CE A:MET101 4.1 19.7 1.0
N A:GLY155 4.2 39.5 1.0
CA A:CYS154 4.2 38.0 1.0
C A:CYS154 4.2 44.7 1.0
CD1 A:TYR143 4.2 35.2 1.0
CG A:MET101 4.3 30.1 1.0
CG A:TYR143 4.3 36.5 1.0
CD A:GLN117 4.5 40.2 1.0
SD A:MET101 4.6 54.4 1.0
C A:GLY76 4.6 48.0 1.0
O A:CYS154 4.8 41.8 1.0
CA A:GLY155 4.8 42.4 1.0
CG1 A:VAL171 4.8 33.2 1.0
CA A:GLY76 4.8 40.9 1.0
SG A:CYS83 4.9 48.3 1.0
CB A:GLN117 4.9 41.0 1.0

Mercury binding site 2 out of 8 in 1wqs

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Mercury binding site 2 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1002

b:65.2
occ:0.35
SG A:CYS83 2.1 48.3 1.0
SG A:CYS154 2.2 65.3 1.0
CB A:CYS77 2.9 78.7 1.0
CD2 A:TYR145 3.1 42.8 1.0
CB A:CYS154 3.4 41.2 1.0
CB A:CYS83 3.5 33.5 1.0
CE2 A:TYR145 3.5 49.6 1.0
SG A:CYS77 3.6 0.9 1.0
HG A:HG1001 3.6 81.4 0.5
CA A:CYS77 4.0 59.6 1.0
O A:TYR143 4.0 42.6 1.0
CG A:TYR145 4.2 47.8 1.0
CG A:MET101 4.4 30.1 1.0
CB A:TYR143 4.5 32.5 1.0
N A:CYS77 4.5 52.7 1.0
C A:TYR143 4.5 34.3 1.0
CB A:TYR145 4.6 43.0 1.0
CA A:CYS83 4.6 34.5 1.0
CA A:CYS154 4.7 38.0 1.0
N A:CYS154 4.8 36.0 1.0
N A:TYR145 4.8 38.6 1.0
CG2 A:VAL81 4.8 26.6 1.0
CZ A:TYR145 4.9 43.8 1.0
C A:VAL144 4.9 32.5 1.0

Mercury binding site 3 out of 8 in 1wqs

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Mercury binding site 3 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1003

b:69.3
occ:0.44
SG B:CYS169 2.3 58.3 1.0
SG B:CYS154 2.6 98.6 1.0
HG B:HG1004 3.2 0.2 0.5
O B:CYS154 3.4 77.9 1.0
CB B:TYR143 3.4 39.6 1.0
C B:CYS154 3.5 67.6 1.0
CD1 B:TYR143 3.6 49.7 1.0
CB B:CYS154 3.6 70.8 1.0
CG B:TYR143 3.6 39.2 1.0
N B:GLY155 3.9 61.2 1.0
CB B:CYS169 4.0 58.9 1.0
CA B:GLY155 4.0 53.6 1.0
CE B:MET101 4.1 43.3 1.0
SG B:CYS77 4.1 81.8 1.0
CA B:CYS154 4.1 69.4 1.0
CG B:GLN117 4.2 56.5 1.0
SD B:MET101 4.6 61.1 1.0
CG1 B:VAL171 4.6 55.4 1.0
CE1 B:TYR143 4.6 56.2 1.0
O B:TYR143 4.6 49.8 1.0
CD2 B:TYR143 4.6 40.2 1.0
CG B:MET101 4.7 43.4 1.0
C B:GLY155 4.8 53.4 1.0
CB B:GLN117 4.9 60.9 1.0
CA B:TYR143 4.9 40.8 1.0

Mercury binding site 4 out of 8 in 1wqs

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Mercury binding site 4 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1004

b:0.2
occ:0.48
SG B:CYS77 2.2 81.8 1.0
SG B:CYS83 2.4 82.4 1.0
SG B:CYS154 2.5 98.6 1.0
CB B:CYS83 2.5 50.5 1.0
HG B:HG1003 3.2 69.3 0.4
CB B:CYS154 3.3 70.8 1.0
CB B:TYR143 3.4 39.6 1.0
O B:TYR143 3.6 49.8 1.0
CG B:MET101 3.6 43.4 1.0
SD B:MET101 4.0 61.1 1.0
CB B:CYS77 4.0 66.1 1.0
CD1 B:TYR143 4.0 49.7 1.0
C B:TYR143 4.1 50.3 1.0
CG B:TYR143 4.2 39.2 1.0
CA B:CYS83 4.2 49.0 1.0
CA B:TYR143 4.3 40.8 1.0
O B:VAL144 4.5 67.0 1.0
CA B:CYS154 4.7 69.4 1.0
CD2 B:TYR145 4.7 79.9 1.0
CE B:MET101 4.8 43.3 1.0
N B:CYS83 4.9 53.2 1.0
N B:VAL144 4.9 55.2 1.0

Mercury binding site 5 out of 8 in 1wqs

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Mercury binding site 5 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg1005

b:60.3
occ:0.36
SG C:CYS169 2.5 37.6 1.0
SG C:CYS154 2.6 75.0 1.0
CE C:MET101 3.0 26.4 1.0
CB C:CYS169 3.6 19.7 1.0
C C:CYS154 3.7 36.4 1.0
O C:CYS154 3.8 38.1 1.0
CB C:TYR143 3.9 37.2 1.0
CD1 C:TYR143 3.9 44.2 1.0
N C:CYS77 4.0 76.1 1.0
CB C:CYS154 4.0 32.5 1.0
OE1 C:GLN117 4.0 63.8 1.0
N C:GLY155 4.0 30.0 1.0
CG C:TYR143 4.1 48.4 1.0
CA C:GLY155 4.2 32.5 1.0
CG1 C:VAL171 4.3 28.6 1.0
CA C:CYS154 4.4 38.8 1.0
HG C:HG1006 4.5 75.2 0.4
CA C:GLY76 4.6 72.3 1.0
C C:GLY76 4.6 72.9 1.0
SG C:CYS77 4.6 0.8 1.0
CD C:GLN117 4.7 57.2 1.0
CE1 C:TYR143 4.7 41.2 1.0
CB C:GLN117 4.7 30.4 1.0
SD C:MET101 4.8 45.8 1.0
C C:GLY155 4.9 25.8 1.0
CG C:GLN117 4.9 38.6 1.0
O C:TYR143 5.0 38.9 1.0

Mercury binding site 6 out of 8 in 1wqs

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Mercury binding site 6 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg1006

b:75.2
occ:0.41
SG C:CYS154 2.1 75.0 1.0
SG C:CYS83 2.2 58.2 1.0
CB C:CYS154 2.9 32.5 1.0
CD2 C:TYR145 3.0 73.1 1.0
CB C:CYS77 3.4 88.2 1.0
CE2 C:TYR145 3.5 77.8 1.0
CB C:CYS83 3.6 43.1 1.0
CG C:TYR145 3.6 52.1 1.0
O C:TYR143 3.7 38.9 1.0
SG C:CYS77 3.9 0.8 1.0
CB C:TYR145 3.9 49.2 1.0
O C:VAL144 4.0 46.2 1.0
C C:VAL144 4.1 45.2 1.0
C C:TYR143 4.3 34.0 1.0
CA C:CYS154 4.3 38.8 1.0
N C:TYR145 4.4 46.8 1.0
CA C:CYS77 4.4 80.4 1.0
N C:CYS154 4.4 37.8 1.0
HG C:HG1005 4.5 60.3 0.4
CZ C:TYR145 4.5 65.0 1.0
N C:CYS77 4.6 76.1 1.0
CA C:VAL144 4.6 42.8 1.0
CB C:TYR143 4.6 37.2 1.0
CD1 C:TYR145 4.6 49.3 1.0
CA C:CYS83 4.6 39.7 1.0
N C:VAL144 4.6 36.9 1.0
CA C:TYR145 4.7 48.5 1.0

Mercury binding site 7 out of 8 in 1wqs

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Mercury binding site 7 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1007

b:64.7
occ:0.48
SG D:CYS169 2.5 59.1 1.0
HG D:HG1008 2.9 96.2 0.3
SG D:CYS154 3.0 77.6 1.0
CE D:MET101 3.4 37.6 1.0
CB D:CYS169 3.5 51.2 1.0
CB D:CYS154 3.6 58.6 1.0
O D:CYS154 3.7 58.6 1.0
C D:CYS154 3.7 51.7 1.0
CD1 D:TYR143 3.9 26.6 1.0
CB D:TYR143 3.9 40.5 1.0
CG D:TYR143 4.0 29.1 1.0
N D:GLY155 4.1 42.6 1.0
CA D:CYS154 4.2 57.0 1.0
CA D:GLY155 4.4 33.1 1.0
NE2 D:GLN117 4.4 61.6 1.0
SG D:CYS83 4.6 76.6 1.0
CE1 D:TYR143 4.8 20.2 1.0
CG D:GLN117 4.8 62.4 1.0
SD D:MET101 4.8 54.2 1.0
SG D:CYS77 4.9 79.5 1.0
CG1 D:VAL171 4.9 46.6 1.0
CA D:GLY76 4.9 89.2 1.0
CD D:GLN117 4.9 66.3 1.0
CA D:CYS169 4.9 54.4 1.0
CG D:MET101 4.9 50.5 1.0
N D:CYS77 4.9 77.2 1.0

Mercury binding site 8 out of 8 in 1wqs

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Mercury binding site 8 out of 8 in the Crystal Structure of Norovirus 3C-Like Protease


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1008

b:96.2
occ:0.34
SG D:CYS154 1.8 77.6 1.0
SG D:CYS83 1.9 76.6 1.0
SG D:CYS77 2.7 79.5 1.0
HG D:HG1007 2.9 64.7 0.5
CB D:CYS83 3.1 60.7 1.0
CG D:MET101 3.2 50.5 1.0
CB D:CYS77 3.5 72.2 1.0
CB D:CYS154 3.5 58.6 1.0
CE D:MET101 3.6 37.6 1.0
SD D:MET101 4.0 54.2 1.0
CB D:MET101 4.3 47.3 1.0
CB D:TYR143 4.3 40.5 1.0
CD1 D:TYR143 4.4 26.6 1.0
CA D:CYS83 4.7 50.3 1.0
CA D:CYS77 4.7 72.9 1.0
N D:CYS77 4.7 77.2 1.0
CG D:TYR143 4.8 29.1 1.0
N D:CYS83 4.9 49.7 1.0

Reference:

K.Nakamura, Y.Someya, T.Kumasaka, G.Ueno, M.Yamamoto, T.Sato, N.Takeda, T.Miyamura, N.Tanaka. A Norovirus Protease Structure Provides Insights Into Active and Substrate Binding Site Integrity J.Virol. V. 79 13685 2005.
ISSN: ISSN 0022-538X
PubMed: 16227288
DOI: 10.1128/JVI.79.21.13685-13693.2005
Page generated: Wed Oct 28 18:40:47 2020

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