Mercury in PDB 6gbp: Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative

The structure of Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative, PDB code: 6gbp was solved by L.Zinzula, I.Nagy, M.Orsini, E.Weyher-Stingl, W.Baumeister, A.Bracher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.421, 103.923, 186.287, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 28.1

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>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative (pdb code 6gbp). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 11 binding sites of Mercury where determined in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative, PDB code: 6gbp:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg201 b:0.8 occ:1.00 SG A:CYS135 2.0 82.3 1.0 CB A:CYS135 3.0 79.8 1.0 O A:CYS135 3.3 76.3 1.0 C A:CYS135 3.3 77.8 1.0 OD1 F:ASN132 3.7 99.6 1.0 CA A:CYS135 3.8 77.1 1.0 N A:ALA136 3.8 80.3 1.0 CD2 D:LEU131 4.1 0.4 1.0 CA A:ALA136 4.3 81.5 1.0 CG F:ASN132 4.4 91.8 1.0 CA F:ASN132 4.7 78.8 1.0 CB F:ASN132 4.7 84.7 1.0 CB A:ALA136 4.7 81.0 1.0 HG F:HG201 4.7 0.5 1.0 CD1 D:LEU131 4.8 0.8 1.0 O A:ASN132 4.8 72.1 1.0 N A:CYS135 5.0 73.8 1.0 CG D:LEU131 5.0 0.9 1.0

Mercury binding site 2 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg202 b:0.5 occ:1.00 SG D:CYS135 2.2 87.2 1.0 OG A:SER129 3.1 86.7 1.0 CB D:CYS135 3.5 93.2 1.0 O A:SER129 3.5 88.4 1.0 CB A:ASN132 3.6 73.2 1.0 CA A:SER129 3.9 82.7 1.0 CB A:SER129 4.0 84.1 1.0 C A:SER129 4.1 86.5 1.0 CG A:ASN132 4.4 71.8 1.0 CA D:CYS135 4.8 95.3 1.0 C D:CYS135 4.8 97.1 1.0 CA A:ASN132 4.9 73.2 1.0 ND2 A:ASN132 4.9 72.5 1.0 C A:ASN132 4.9 73.8 1.0 N A:ARG133 5.0 75.2 1.0 O D:ASN132 5.0 0.4 1.0

Mercury binding site 3 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg201 b:0.1 occ:1.00 SG B:CYS135 3.2 93.4 1.0 CB B:CYS135 3.3 87.7 1.0 CB C:LEU131 3.5 0.2 1.0 N B:ALA136 3.8 87.3 1.0 CD1 C:LEU131 3.9 0.2 1.0 OD1 E:ASN132 3.9 94.3 1.0 OD1 B:ASN132 4.0 66.8 1.0 O C:LEU131 4.0 0.1 1.0 C B:CYS135 4.0 87.4 1.0 O B:ASN132 4.1 80.1 1.0 CG C:LEU131 4.1 0.0 1.0 CA B:CYS135 4.3 85.8 1.0 CA B:ALA136 4.4 87.1 1.0 CB B:ALA136 4.6 88.4 1.0 CD2 C:LEU131 4.6 0.7 1.0 O B:CYS135 4.6 87.9 1.0 CA C:LEU131 4.7 0.7 1.0 CA B:ASN132 4.7 77.5 1.0 C C:LEU131 4.7 0.5 1.0 CG E:ASN132 4.7 92.5 1.0 CG B:ASN132 4.8 74.3 1.0 CA E:ASN132 4.8 87.7 1.0 C B:ASN132 4.8 80.2 1.0 CB E:ASN132 4.8 89.9 1.0 SG C:CYS135 4.9 1.0 1.0 SG E:CYS135 4.9 85.3 1.0 CB B:ASN132 5.0 76.8 1.0

Mercury binding site 4 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg201 b:0.2 occ:1.00 CB C:CYS135 3.0 0.1 1.0 ND2 E:ASN132 3.2 93.7 1.0 C C:CYS135 3.8 98.5 1.0 CA E:SER129 4.0 76.3 1.0 O C:CYS135 4.0 99.8 1.0 OG E:SER129 4.0 83.7 1.0 CA C:CYS135 4.0 0.1 1.0 CB E:SER129 4.0 79.6 1.0 CG E:ASN132 4.2 92.5 1.0 N C:ALA136 4.2 93.6 1.0 SG C:CYS135 4.2 1.0 1.0 O E:SER129 4.3 72.7 1.0 CB E:ASN132 4.3 89.9 1.0 CG2 C:VAL139 4.6 82.4 1.0 C E:SER129 4.6 73.9 1.0 CA C:ALA136 4.9 91.1 1.0 O C:ASN132 4.9 94.9 1.0

Mercury binding site 5 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ F:Hg201 b:0.5 occ:1.00 SG F:CYS135 2.7 74.7 1.0 ND2 A:ASN132 3.2 72.5 1.0 CB F:CYS135 3.4 77.3 1.0 C F:CYS135 3.4 77.8 1.0 N F:ALA136 3.4 78.3 1.0 O F:CYS135 3.5 79.3 1.0 OD1 A:ASN132 3.7 68.5 1.0 CG A:ASN132 3.7 71.8 1.0 CA F:ALA136 3.8 78.1 1.0 CA F:CYS135 4.0 76.3 1.0 CB F:ALA136 4.4 77.7 1.0 CG2 F:VAL139 4.6 66.3 1.0 O F:ASN132 4.7 70.7 1.0 HG A:HG201 4.7 0.8 1.0 SG A:CYS135 4.8 82.3 1.0 CB A:ASN132 4.9 73.2 1.0

Mercury binding site 6 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Hg201 b:0.7 occ:1.00 SG H:CYS135 1.8 99.6 1.0 CB H:CYS135 3.1 94.2 1.0 C H:CYS135 3.4 88.3 1.0 O H:CYS135 3.4 87.7 1.0 OD1 K:ASN132 3.6 76.2 1.0 N H:ALA136 3.7 86.1 1.0 CG K:ASN132 3.8 75.0 1.0 ND2 K:ASN132 3.8 76.5 1.0 CA H:CYS135 3.8 88.8 1.0 CA H:ALA136 4.2 83.1 1.0 CB K:ASN132 4.6 73.4 1.0 CG2 H:VAL139 4.7 82.3 1.0 SG K:CYS135 4.8 85.1 1.0 HG H:HG202 4.8 0.8 1.0 CB H:ALA136 4.8 81.6 1.0 O H:ASN132 4.9 79.5 1.0 CA K:ASN132 5.0 71.5 1.0

Mercury binding site 7 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Hg202 b:0.8 occ:1.00 SG K:CYS135 2.3 85.1 1.0 OD1 H:ASN132 2.6 90.4 1.0 CB K:CYS135 3.4 79.7 1.0 O K:CYS135 3.5 74.9 1.0 C K:CYS135 3.6 75.8 1.0 CG H:ASN132 3.8 86.1 1.0 N K:ALA136 3.9 75.3 1.0 CA K:CYS135 4.1 76.4 1.0 CA K:ALA136 4.3 74.4 1.0 SG H:CYS135 4.5 99.6 1.0 ND2 H:ASN132 4.6 88.6 1.0 CG2 K:VAL139 4.7 69.0 1.0 HG H:HG201 4.8 0.7 1.0 CB H:ASN132 4.8 81.3 1.0 CA H:ASN132 4.9 78.0 1.0 CB K:ALA136 5.0 75.6 1.0

Mercury binding site 8 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


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 the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ J:Hg201 b:0.2 occ:1.00 SG J:CYS135 2.5 0.7 1.0 CB J:CYS135 3.2 99.2 1.0 CB G:SER129 3.7 75.7 1.0 ND2 G:ASN132 3.9 98.6 1.0 C J:CYS135 4.0 95.5 1.0 CG2 J:VAL139 4.1 75.7 1.0 CA G:SER129 4.1 73.6 1.0 N J:ALA136 4.2 91.9 1.0 CA J:CYS135 4.2 97.4 1.0 O J:CYS135 4.2 96.6 1.0 O G:SER129 4.5 72.3 1.0 CA J:ALA136 4.8 90.2 1.0 CB G:ASN132 4.8 85.6 1.0 C G:SER129 4.8 72.6 1.0 CG G:ASN132 4.8 93.0 1.0 OG G:SER129 5.0 79.9 1.0

Mercury binding site 9 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ K:Hg201 b:0.7 occ:1.00 SG I:CYS135 2.0 0.4 1.0 OG K:SER129 2.9 85.3 1.0 O K:SER129 3.1 82.7 1.0 CB I:CYS135 3.6 99.5 1.0 CA K:SER129 3.7 80.5 1.0 CB K:ASN132 3.8 73.4 1.0 C K:SER129 3.8 79.5 1.0 CB K:SER129 3.9 82.4 1.0 ND2 K:ASN132 4.4 76.5 1.0 CG K:ASN132 4.5 75.0 1.0 N K:ARG133 4.6 70.8 1.0 CA I:CYS135 4.8 95.8 1.0 C I:CYS135 4.8 93.2 1.0 CA K:ASN132 4.8 71.5 1.0 C K:ASN132 4.9 70.9 1.0 O I:CYS135 5.0 89.2 1.0

Mercury binding site 10 out of 11 in the Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of the Oligomerization Domain of VP35 From Ebola Virus, Mercury Derivative within 5.0Å range: probe atom residue distance (Å) B Occ L:Hg201 b:0.7 occ:1.00 SG L:CYS135 3.1 92.4 1.0 OD1 G:ASN132 3.3 97.1 1.0 CB L:CYS135 3.3 86.5 1.0 N L:ALA136 3.4 84.4 1.0 C L:CYS135 3.5 84.0 1.0 CA L:ALA136 3.7 82.7 1.0 O L:CYS135 3.8 85.7 1.0 CA L:CYS135 4.0 82.8 1.0 O L:ASN132 4.1 82.9 1.0 CB L:ALA136 4.2 83.2 1.0 CG G:ASN132 4.2 93.0 1.0 CG2 L:VAL139 4.7 72.9 1.0 CB G:ASN132 4.7 85.6 1.0 CB J:LEU131 4.7 0.6 1.0 SG G:CYS135 4.9 93.6 1.0 CA J:LEU131 4.9 0.8 1.0 CA G:ASN132 4.9 80.4 1.0

L.Zinzula, I.Nagy, M.Orsini, E.Weyher-Stingl, A.Bracher, W.Baumeister. Structures of Ebola and Reston Virus VP35 Oligomerization Domains and Comparative Biophysical Characterization in All Ebolavirus Species. Structure V. 27 39 2019.
ISSN: ISSN 1878-4186
PubMed: 30482729
DOI: 10.1016/J.STR.2018.09.009