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

Protein crystallography data

The structure of Crystal Structure of the Oligomerization Domain of VP35 From Reston Virus, Mercury Derivative, PDB code: 6gbr 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) 29.58 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.933, 91.901, 104.193, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 31.1

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of the Oligomerization Domain of VP35 From Reston Virus, Mercury Derivative (pdb code 6gbr). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Crystal Structure of the Oligomerization Domain of VP35 From Reston Virus, Mercury Derivative, PDB code: 6gbr:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 6gbr

Go back to Mercury Binding Sites List in 6gbr
Mercury binding site 1 out of 2 in the Crystal Structure of the Oligomerization Domain of VP35 From Reston 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 Reston Virus, Mercury Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg201

b:0.4
occ:1.00
HG A:MBO201 0.0 0.4 1.0
CE1 A:MBO201 2.8 0.3 1.0
SG B:CYS124 2.9 37.4 1.0
SG A:CYS124 3.0 79.5 1.0
HD11 B:LEU120 3.3 63.6 1.0
HD12 B:LEU120 3.4 63.6 1.0
HE2 A:MBO201 3.6 0.4 1.0
HB3 A:CYS124 3.6 71.8 1.0
HE6 A:MBO201 3.6 0.9 1.0
CE2 A:MBO201 3.7 98.7 1.0
CE6 A:MBO201 3.7 100.0 1.0
HG21 A:VAL128 3.7 0.9 1.0
CD1 B:LEU120 3.8 53.0 1.0
O A:CYS124 3.8 69.7 1.0
CB A:CYS124 3.9 59.8 1.0
HG23 A:VAL128 3.9 0.9 1.0
HA B:CYS124 4.1 82.9 1.0
HD13 B:LEU120 4.2 63.6 1.0
C A:CYS124 4.2 66.5 1.0
SD C:MET127 4.2 60.0 1.0
HB3 B:SER123 4.2 85.0 1.0
CG2 A:VAL128 4.2 0.6 1.0
HB2 B:SER123 4.3 85.0 1.0
CB B:CYS124 4.4 76.7 1.0
HE1 C:MET127 4.5 82.7 1.0
O B:LEU120 4.5 47.9 1.0
CA B:CYS124 4.6 69.1 1.0
N B:CYS124 4.6 70.3 1.0
HB2 A:CYS124 4.7 71.8 1.0
HG22 A:VAL128 4.7 0.9 1.0
CA A:CYS124 4.7 61.8 1.0
CB B:SER123 4.8 70.8 1.0
HA A:ALA125 4.8 72.7 1.0
N A:ALA125 4.8 65.1 1.0
C B:SER123 4.8 64.5 1.0
H B:CYS124 4.9 84.4 1.0
O B:SER123 4.9 66.4 1.0
HG3 B:MET127 4.9 75.6 1.0
CE C:MET127 4.9 68.9 1.0
HA A:CYS124 4.9 74.2 1.0
HG B:LEU120 5.0 68.8 1.0
HE2 A:MET127 5.0 85.2 1.0
CE3 A:MBO201 5.0 0.3 1.0
HB2 B:CYS124 5.0 92.0 1.0
CE5 A:MBO201 5.0 0.0 1.0

Mercury binding site 2 out of 2 in 6gbr

Go back to Mercury Binding Sites List in 6gbr
Mercury binding site 2 out of 2 in the Crystal Structure of the Oligomerization Domain of VP35 From Reston 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 Reston Virus, Mercury Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg201

b:0.1
occ:1.00
HG D:MBO201 0.0 0.1 1.0
CE1 D:MBO201 2.8 0.9 1.0
SG C:CYS124 2.9 89.1 1.0
SG D:CYS124 3.0 62.1 1.0
HE1 A:MET127 3.3 85.2 1.0
HE2 D:MBO201 3.6 0.3 1.0
CE2 D:MBO201 3.7 0.3 1.0
HG D:LEU120 3.7 63.8 1.0
HE6 D:MBO201 3.7 0.3 1.0
HB2 D:SER123 3.7 0.1 1.0
CE6 D:MBO201 3.7 0.1 1.0
HB3 C:CYS124 3.9 99.3 1.0
HA D:CYS124 4.0 93.4 1.0
HG11 C:VAL128 4.0 0.5 1.0
CB C:CYS124 4.1 82.7 1.0
HD11 D:LEU120 4.1 61.2 1.0
CE A:MET127 4.1 71.0 1.0
HG13 C:VAL128 4.2 0.5 1.0
HD12 D:LEU120 4.3 61.2 1.0
O D:LEU120 4.3 58.0 1.0
HE2 A:MET127 4.5 85.2 1.0
O C:CYS124 4.5 87.3 1.0
SD A:MET127 4.5 57.4 1.0
CB D:CYS124 4.5 80.1 1.0
CG D:LEU120 4.5 53.2 1.0
CD1 D:LEU120 4.5 51.0 1.0
CA D:CYS124 4.5 77.8 1.0
N D:CYS124 4.5 79.7 1.0
CG1 C:VAL128 4.6 93.8 1.0
CB D:SER123 4.6 86.0 1.0
C C:CYS124 4.6 80.7 1.0
HA C:ALA125 4.7 70.8 1.0
C D:SER123 4.7 82.2 1.0
HB2 C:CYS124 4.7 99.3 1.0
H D:CYS124 4.8 95.6 1.0
O D:SER123 4.8 81.0 1.0
HG21 C:VAL128 4.8 0.0 1.0
HB3 D:SER123 4.8 0.1 1.0
HA D:LEU120 4.9 81.6 1.0
HE3 A:MET127 4.9 85.2 1.0
CA C:CYS124 5.0 79.2 1.0
HG22 C:VAL128 5.0 0.0 1.0

Reference:

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
Page generated: Sun Dec 13 19:14:42 2020

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