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Mercury in PDB 2qfd: Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg

Protein crystallography data

The structure of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg, PDB code: 2qfd was solved by S.Cui, A.Lammens, K.Lammens, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.150, 76.540, 137.900, 90.00, 93.07, 90.00
R / Rfree (%) 24.1 / 27.6

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg (pdb code 2qfd). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 10 binding sites of Mercury where determined in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg, PDB code: 2qfd:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 10 in 2qfd

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Mercury binding site 1 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1001

b:45.9
occ:0.46
SG A:CYS869 2.3 39.1 1.0
SG A:CYS813 2.4 42.0 1.0
SG A:CYS864 2.4 35.9 1.0
SG A:CYS810 2.5 33.0 1.0
CB A:CYS813 3.1 38.4 1.0
CB A:CYS864 3.1 33.1 1.0
CB A:CYS869 3.2 43.1 1.0
CB A:CYS810 3.3 29.0 1.0
N A:CYS813 3.8 41.5 1.0
CA A:CYS813 4.0 40.7 1.0
CB A:ARG866 4.1 50.6 1.0
CA A:CYS864 4.6 32.9 1.0
CB A:HIS871 4.7 35.0 1.0
CA A:CYS869 4.7 44.5 1.0
CZ2 A:TRP873 4.7 26.4 1.0
CA A:CYS810 4.8 30.1 1.0
C A:CYS813 4.8 41.0 1.0
NE1 A:TRP873 4.9 28.6 1.0
CG A:ARG866 4.9 54.3 1.0
N A:LYS814 4.9 41.0 1.0
C A:LYS812 4.9 41.0 1.0
CB A:ALA815 5.0 31.4 1.0
N A:SER870 5.0 39.9 1.0

Mercury binding site 2 out of 10 in 2qfd

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Mercury binding site 2 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1002

b:45.0
occ:0.45
SG B:CYS869 2.3 37.0 1.0
SG B:CYS813 2.4 45.0 1.0
SG B:CYS864 2.4 34.1 1.0
SG B:CYS810 2.4 30.9 1.0
CB B:CYS810 3.1 25.5 1.0
CB B:CYS864 3.1 34.0 1.0
CB B:CYS813 3.3 39.2 1.0
CB B:CYS869 3.4 40.9 1.0
N B:CYS813 3.8 39.8 1.0
CA B:CYS813 4.1 38.6 1.0
CB B:ARG866 4.5 39.3 1.0
CB B:HIS871 4.6 33.0 1.0
CA B:CYS810 4.6 27.1 1.0
CB B:ALA815 4.6 34.7 1.0
CA B:CYS864 4.6 34.7 1.0
CB B:LYS812 4.7 36.4 1.0
CA B:CYS869 4.7 42.9 1.0
C B:CYS813 4.8 38.2 1.0
NE1 B:TRP873 4.8 38.5 1.0
C B:LYS812 4.8 40.0 1.0
CZ2 B:TRP873 4.9 38.1 1.0
N B:LYS814 4.9 38.4 1.0
N B:ALA815 4.9 36.8 1.0

Mercury binding site 3 out of 10 in 2qfd

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Mercury binding site 3 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg1003

b:37.4
occ:0.26
SG C:CYS869 2.3 50.1 1.0
SG C:CYS810 2.3 41.0 1.0
SG C:CYS864 2.4 51.7 1.0
SG C:CYS813 2.4 45.7 1.0
CB C:CYS869 2.8 56.7 1.0
CB C:CYS813 2.9 43.9 1.0
CB C:CYS864 3.1 51.1 1.0
CB C:CYS810 3.1 38.7 1.0
N C:CYS813 3.5 47.8 1.0
CA C:CYS813 3.8 45.6 1.0
CA C:CYS869 4.3 58.8 1.0
CB C:LYS812 4.5 47.7 1.0
CB C:HIS871 4.5 45.8 1.0
CA C:CYS864 4.6 49.8 1.0
CA C:CYS810 4.6 38.9 1.0
N C:LYS814 4.6 44.2 1.0
C C:CYS813 4.6 45.8 1.0
NH1 C:ARG866 4.6 62.2 0.0
CD C:ARG866 4.6 60.3 0.0
C C:LYS812 4.7 48.1 1.0
CZ2 C:TRP873 4.7 42.2 1.0
NE1 C:TRP873 4.8 46.5 1.0
CB C:ALA815 4.9 34.8 1.0
N C:SER870 4.9 55.3 1.0
CB C:ARG866 4.9 59.9 1.0
N C:HIS871 4.9 49.2 1.0
N C:ALA815 5.0 37.9 1.0
C C:CYS869 5.0 57.1 1.0

Mercury binding site 4 out of 10 in 2qfd

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Mercury binding site 4 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1004

b:49.4
occ:0.37
SG D:CYS869 2.2 61.4 1.0
SG D:CYS813 2.2 42.3 1.0
SG D:CYS810 2.3 38.6 1.0
SG D:CYS864 2.3 52.3 1.0
CB D:CYS864 3.0 53.7 1.0
CB D:CYS869 3.3 66.1 1.0
CB D:CYS810 3.3 39.6 1.0
CB D:CYS813 3.4 44.6 1.0
O D:CYS869 3.5 68.7 1.0
N D:CYS813 3.8 46.0 1.0
CB D:ARG866 4.1 61.6 1.0
CA D:CYS813 4.2 45.9 1.0
C D:CYS869 4.4 66.7 1.0
CB D:HIS871 4.4 50.4 1.0
CA D:CYS869 4.5 67.4 1.0
CA D:CYS864 4.5 55.2 1.0
CB D:LYS812 4.6 46.9 1.0
NE1 D:TRP873 4.7 38.9 1.0
CA D:CYS810 4.8 39.7 1.0
C D:LYS812 4.8 45.3 1.0
CZ2 D:TRP873 4.9 36.2 1.0
CG D:ARG866 4.9 61.6 1.0

Mercury binding site 5 out of 10 in 2qfd

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Mercury binding site 5 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg1005

b:59.8
occ:0.39
SG E:CYS864 2.2 60.1 1.0
SG E:CYS813 2.2 53.8 1.0
SG E:CYS869 2.2 72.5 1.0
SG E:CYS810 2.6 45.8 1.0
CB E:CYS813 2.9 49.7 1.0
CB E:CYS864 3.0 61.1 1.0
CB E:CYS810 3.5 37.1 1.0
CB E:CYS869 3.5 75.6 1.0
O E:CYS869 3.7 75.1 1.0
N E:CYS813 3.8 50.6 1.0
CA E:CYS813 4.0 50.9 1.0
CG E:LYS812 4.1 57.3 1.0
CB E:ARG866 4.2 74.8 1.0
CB E:HIS871 4.4 61.0 1.0
C E:CYS869 4.4 74.3 1.0
CA E:CYS864 4.5 62.5 1.0
CA E:CYS869 4.6 75.4 1.0
CG E:ARG866 4.7 76.6 1.0
O E:ARG866 4.8 75.7 1.0
CD E:LYS812 4.8 56.7 0.0
C E:CYS813 4.9 51.2 1.0
N E:HIS871 4.9 66.8 1.0
CA E:CYS810 4.9 38.4 1.0
N E:LYS814 4.9 49.2 1.0
CB E:ALA815 5.0 42.2 1.0
CZ2 E:TRP873 5.0 38.6 1.0
NE1 E:TRP873 5.0 41.5 1.0

Mercury binding site 6 out of 10 in 2qfd

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Mercury binding site 6 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg1006

b:54.6
occ:0.35
SG F:CYS864 2.3 54.9 1.0
SG F:CYS869 2.3 62.3 1.0
SG F:CYS810 2.4 53.7 1.0
SG F:CYS813 2.4 58.3 1.0
CB F:CYS813 3.1 53.7 1.0
CB F:CYS864 3.1 57.8 1.0
CB F:CYS810 3.2 49.7 1.0
N F:CYS813 3.8 55.2 1.0
CA F:CYS813 4.0 54.6 1.0
CB F:CYS869 4.0 68.5 1.0
CG F:LYS812 4.2 56.2 1.0
CB F:HIS871 4.3 50.6 1.0
CZ2 F:TRP873 4.3 42.1 1.0
CA F:CYS864 4.6 59.7 1.0
NE1 F:TRP873 4.6 44.3 1.0
N F:HIS871 4.6 53.6 1.0
CA F:CYS810 4.7 48.4 1.0
C F:CYS813 4.7 54.7 1.0
CB F:ALA815 4.8 47.0 1.0
CE2 F:TRP873 4.8 41.9 1.0
N F:LYS814 4.8 53.9 1.0
C F:LYS812 5.0 55.5 1.0
N F:SER870 5.0 60.4 1.0
CB F:ARG866 5.0 74.2 1.0

Mercury binding site 7 out of 10 in 2qfd

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Mercury binding site 7 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Hg1007

b:51.1
occ:0.42
SG G:CYS813 2.2 52.5 1.0
SG G:CYS864 2.3 41.2 1.0
SG G:CYS869 2.4 42.6 1.0
SG G:CYS810 2.5 41.4 1.0
CB G:CYS864 3.1 39.8 1.0
CB G:CYS813 3.2 49.5 1.0
CB G:CYS810 3.2 41.3 1.0
CB G:CYS869 3.6 47.0 1.0
N G:CYS813 3.7 49.0 1.0
CA G:CYS813 4.0 50.3 1.0
CB G:HIS871 4.5 45.6 1.0
CA G:CYS864 4.5 41.6 1.0
CZ2 G:TRP873 4.6 37.0 1.0
CA G:CYS810 4.7 42.3 1.0
CB G:LYS812 4.7 50.2 1.0
C G:CYS813 4.7 51.3 1.0
NE1 G:TRP873 4.7 38.5 1.0
CB G:ARG866 4.8 51.9 1.0
C G:LYS812 4.8 48.8 1.0
N G:HIS871 4.9 49.2 1.0
CB G:ALA815 4.9 45.7 1.0
N G:LYS814 4.9 51.5 1.0
CA G:CYS869 4.9 50.2 1.0

Mercury binding site 8 out of 10 in 2qfd

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Mercury binding site 8 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Hg1008

b:51.7
occ:0.32
SG H:CYS864 2.2 54.6 1.0
SG H:CYS869 2.2 49.1 1.0
SG H:CYS810 2.4 45.6 1.0
SG H:CYS813 2.5 52.0 1.0
CB H:CYS864 2.9 53.7 1.0
CB H:CYS813 3.1 50.3 1.0
CB H:CYS869 3.3 58.5 1.0
CB H:CYS810 3.3 49.3 1.0
N H:CYS813 3.8 52.0 1.0
CA H:CYS813 4.0 51.6 1.0
CB H:ARG866 4.4 68.3 1.0
CA H:CYS864 4.4 54.5 1.0
CB H:HIS871 4.7 47.2 1.0
CA H:CYS869 4.7 60.5 1.0
CZ2 H:TRP873 4.7 42.9 1.0
CG H:ARG866 4.7 67.8 1.0
CA H:CYS810 4.8 48.4 1.0
CB H:LYS812 4.8 56.1 1.0
NE1 H:TRP873 4.8 42.3 1.0
C H:CYS813 4.9 51.8 1.0
C H:LYS812 4.9 52.5 1.0
N H:SER870 4.9 58.2 1.0
N H:HIS871 4.9 52.5 1.0
N H:LYS814 5.0 50.5 1.0
C H:CYS864 5.0 57.0 1.0

Mercury binding site 9 out of 10 in 2qfd

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Mercury binding site 9 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Hg1009

b:51.6
occ:0.20
SG I:CYS813 2.3 69.9 1.0
SG I:CYS869 2.3 90.0 1.0
SG I:CYS864 2.4 84.3 1.0
SG I:CYS810 2.4 56.2 1.0
CB I:CYS813 2.8 66.4 1.0
CB I:CYS810 3.2 53.9 1.0
CB I:CYS864 3.2 84.2 1.0
CB I:CYS869 3.5 89.2 1.0
N I:CYS813 3.7 66.3 1.0
CA I:CYS813 3.8 66.5 1.0
CB I:HIS871 4.3 78.6 1.0
CB I:ARG866 4.4 91.5 1.0
CG I:ARG866 4.5 93.5 1.0
C I:CYS813 4.6 66.7 1.0
NE1 I:TRP873 4.6 67.3 1.0
CA I:CYS810 4.6 55.7 1.0
CA I:CYS864 4.7 84.5 1.0
CZ2 I:TRP873 4.8 66.9 0.0
N I:HIS871 4.8 81.8 0.0
C I:LYS812 4.8 66.0 1.0
CA I:CYS869 4.9 88.5 1.0

Mercury binding site 10 out of 10 in 2qfd

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Mercury binding site 10 out of 10 in the Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Hg


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 Regulatory Domain of Human Rig-I with Bound Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Hg1010

b:48.2
occ:0.16
SG J:CYS813 2.3 78.9 1.0
SG J:CYS869 2.5 100.0 1.0
SG J:CYS810 2.7 76.4 1.0
SG J:CYS864 2.7 85.1 1.0
CB J:CYS813 2.8 80.1 1.0
CB J:CYS869 3.2 98.1 1.0
CB J:CYS864 3.5 86.6 1.0
N J:CYS813 3.5 80.1 1.0
CB J:CYS810 3.6 74.8 1.0
O J:CYS869 3.7 96.2 1.0
CA J:CYS813 3.7 80.4 1.0
O J:CYS813 4.2 82.2 1.0
CA J:CYS869 4.4 96.5 1.0
C J:CYS869 4.4 96.0 1.0
C J:CYS813 4.5 80.5 1.0
C J:LYS812 4.7 80.5 1.0
CB J:LYS812 4.7 79.3 1.0
CB J:HIS871 4.7 92.0 1.0
NH2 J:ARG866 4.9 92.5 0.0
O J:ARG866 5.0 92.8 1.0
CA J:CYS864 5.0 87.6 1.0

Reference:

S.Cui, K.Eisenacher, A.Kirchhofer, K.Brzozka, A.Lammens, K.Lammens, T.Fujita, K.K.Conzelmann, A.Krug, K.P.Hopfner. The C-Terminal Regulatory Domain Is the Rna 5'-Triphosphate Sensor of Rig-I. Mol.Cell V. 29 169 2008.
ISSN: ISSN 1097-2765
PubMed: 18243112
DOI: 10.1016/J.MOLCEL.2007.10.032
Page generated: Sun Dec 13 19:08:03 2020

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