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Zinc in PDB 2qfb: Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn

Protein crystallography data

The structure of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn, PDB code: 2qfb 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) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.900, 76.600, 139.400, 90.00, 93.30, 90.00
R / Rfree (%) 24.8 / 28.5

Zinc Binding Sites:

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

Zinc binding site 1 out of 10 in 2qfb

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:28.1
occ:1.00
 SG A:CYS869 2.0 28.1 1.0
SG A:CYS810 2.2 18.6 1.0
SG A:CYS864 2.2 19.9 1.0
SG A:CYS813 2.3 28.6 1.0
CB A:CYS813 2.8 23.8 1.0
CB A:CYS864 3.0 23.4 1.0
CB A:CYS810 3.2 14.8 1.0
CB A:CYS869 3.2 31.8 1.0
N A:CYS813 3.6 23.9 1.0
CA A:CYS813 3.7 24.6 1.0
CB A:ARG866 4.3 38.0 1.0
CB A:HIS871 4.4 16.8 1.0
C A:CYS813 4.5 25.4 1.0
CA A:CYS864 4.5 22.0 1.0
CA A:CYS869 4.6 31.5 1.0
CA A:CYS810 4.7 15.7 1.0
NE1 A:TRP873 4.7 18.5 1.0
CZ2 A:TRP873 4.8 16.7 1.0
N A:LYS814 4.8 26.0 1.0
C A:LYS812 4.8 22.9 1.0
N A:HIS871 4.9 20.1 1.0
CB A:ALA815 4.9 17.3 1.0
N A:SER870 4.9 25.1 1.0

Zinc binding site 2 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:30.5
occ:1.00
 SG B:CYS813 2.1 32.1 1.0
SG B:CYS810 2.2 12.7 1.0
SG B:CYS869 2.2 23.5 1.0
SG B:CYS864 2.2 28.7 1.0
CB B:CYS810 3.0 13.6 1.0
CB B:CYS864 3.0 26.4 1.0
CB B:CYS813 3.3 30.0 1.0
CB B:CYS869 3.3 30.7 1.0
N B:CYS813 3.7 29.2 1.0
CA B:CYS813 4.0 28.6 1.0
CA B:CYS810 4.4 14.8 1.0
CA B:CYS864 4.5 25.3 1.0
CB B:ARG866 4.5 28.8 1.0
NE1 B:TRP873 4.5 31.2 1.0
CZ2 B:TRP873 4.6 31.9 1.0
CB B:ALA815 4.6 24.0 1.0
CB B:HIS871 4.6 21.0 1.0
C B:CYS813 4.6 28.1 1.0
CA B:CYS869 4.7 32.9 1.0
CB B:LYS812 4.7 24.7 1.0
C B:LYS812 4.9 28.0 1.0
CE2 B:TRP873 4.9 31.5 1.0
N B:LYS814 5.0 28.2 1.0
N B:ALA815 5.0 26.3 1.0
C B:CYS810 5.0 16.5 1.0

Zinc binding site 3 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:47.2
occ:1.00
 SG C:CYS869 2.1 59.9 1.0
SG C:CYS864 2.2 59.0 1.0
SG C:CYS813 2.2 37.8 1.0
SG C:CYS810 2.3 32.3 1.0
CB C:CYS869 2.7 62.6 1.0
CB C:CYS864 3.0 57.3 1.0
CB C:CYS813 3.1 39.5 1.0
CB C:CYS810 3.1 30.9 1.0
N C:CYS813 3.6 41.4 1.0
CA C:CYS813 3.9 40.3 1.0
CA C:CYS869 4.2 63.4 1.0
CZ2 C:TRP873 4.3 44.4 1.0
CA C:CYS864 4.4 56.6 1.0
CB C:HIS871 4.5 53.2 1.0
CA C:CYS810 4.5 31.7 1.0
CB C:LYS812 4.6 42.4 1.0
NE1 C:TRP873 4.6 47.2 1.0
CD C:ARG866 4.7 61.0 0.0
N C:SER870 4.7 62.4 1.0
C C:CYS813 4.7 40.8 1.0
C C:CYS869 4.8 62.8 1.0
C C:LYS812 4.8 42.4 1.0
N C:LYS814 4.8 40.9 1.0
CE2 C:TRP873 4.8 45.7 1.0
N C:HIS871 4.8 58.5 1.0
CB C:ALA815 4.9 35.2 1.0
NH1 C:ARG866 5.0 60.8 0.0

Zinc binding site 4 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:47.1
occ:1.00
 SG D:CYS869 1.8 63.0 1.0
SG D:CYS813 2.3 31.0 1.0
SG D:CYS810 2.4 32.5 1.0
SG D:CYS864 2.4 50.5 1.0
CB D:CYS869 2.7 65.6 1.0
CB D:CYS864 3.0 55.7 1.0
O D:CYS869 3.2 67.3 1.0
CB D:CYS813 3.2 33.8 1.0
CB D:CYS810 3.6 30.8 1.0
N D:CYS813 3.8 34.4 1.0
C D:CYS869 3.9 66.2 1.0
CA D:CYS869 3.9 66.8 1.0
CA D:CYS813 4.1 34.1 1.0
CB D:ARG866 4.2 59.4 1.0
CA D:CYS864 4.5 57.2 1.0
CB D:HIS871 4.5 48.6 1.0
CB D:LYS812 4.5 37.3 1.0
C D:LYS812 4.9 34.6 1.0
C D:CYS864 4.9 58.3 1.0
O D:CYS864 4.9 58.4 1.0
N D:CYS869 5.0 69.0 1.0
CA D:CYS810 5.0 31.5 1.0
N D:HIS871 5.0 54.8 1.0

Zinc binding site 5 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1005

b:50.6
occ:1.00
 SG E:CYS813 2.0 44.7 1.0
SG E:CYS869 2.1 83.2 1.0
SG E:CYS864 2.1 74.6 1.0
CB E:CYS813 2.8 40.2 1.0
SG E:CYS810 2.9 42.4 1.0
CB E:CYS864 3.0 77.4 1.0
CB E:CYS869 3.3 85.7 1.0
CB E:CYS810 3.5 36.4 1.0
N E:CYS813 3.8 41.9 1.0
CA E:CYS813 3.9 40.3 1.0
O E:CYS869 3.9 84.4 1.0
CG E:LYS812 4.0 43.8 1.0
CB E:HIS871 4.4 69.9 1.0
CB E:ARG866 4.4 89.0 1.0
CA E:CYS864 4.4 78.4 1.0
CA E:CYS869 4.5 85.0 1.0
C E:CYS869 4.5 83.7 1.0
CG E:ARG866 4.7 90.2 1.0
CD E:LYS812 4.7 43.5 0.0
C E:CYS813 4.7 39.5 1.0
NE1 E:TRP873 4.9 43.4 1.0
C E:LYS812 5.0 43.4 1.0

Zinc binding site 6 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1006

b:44.1
occ:1.00
 SG F:CYS813 2.1 53.1 1.0
SG F:CYS864 2.3 53.6 1.0
SG F:CYS810 2.3 44.0 1.0
SG F:CYS869 2.4 59.7 1.0
CB F:CYS813 2.7 49.2 1.0
CB F:CYS864 3.0 58.6 1.0
CB F:CYS869 3.1 63.6 1.0
CB F:CYS810 3.2 43.2 1.0
N F:CYS813 3.8 48.4 1.0
CA F:CYS813 3.8 49.1 1.0
CB F:HIS871 4.4 51.5 1.0
CG F:LYS812 4.5 50.7 1.0
CA F:CYS864 4.5 59.7 1.0
CZ2 F:TRP873 4.6 39.4 1.0
CA F:CYS869 4.6 63.2 1.0
N F:HIS871 4.6 54.5 1.0
C F:CYS813 4.6 49.2 1.0
N F:SER870 4.6 59.8 1.0
CA F:CYS810 4.7 44.1 1.0
N F:LYS814 4.7 48.1 1.0
NE1 F:TRP873 4.7 40.6 1.0
CB F:ARG866 4.8 70.7 1.0
CB F:ALA815 4.8 40.4 1.0
N F:ALA815 5.0 41.1 1.0

Zinc binding site 7 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1007

b:52.3
occ:1.00
 SG G:CYS869 2.2 54.3 1.0
SG G:CYS813 2.2 40.8 1.0
SG G:CYS864 2.3 39.6 1.0
SG G:CYS810 2.5 53.5 1.0
CB G:CYS864 2.9 41.6 1.0
CB G:CYS813 2.9 42.8 1.0
CB G:CYS869 3.3 56.0 1.0
N G:CYS813 3.5 45.9 1.0
CB G:CYS810 3.7 49.9 1.0
CA G:CYS813 3.8 44.7 1.0
CB G:LYS812 4.4 49.7 1.0
CA G:CYS864 4.4 42.3 1.0
CB G:HIS871 4.4 48.6 1.0
C G:LYS812 4.6 47.5 1.0
CA G:CYS869 4.7 57.2 1.0
C G:CYS813 4.8 44.6 1.0
N G:HIS871 4.8 50.9 1.0
N G:SER870 4.9 54.7 1.0
NE1 G:TRP873 4.9 36.2 1.0
CD G:LYS812 4.9 56.7 1.0
CG G:LYS812 4.9 52.6 1.0
CA G:LYS812 5.0 48.8 1.0

Zinc binding site 8 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1008

b:57.9
occ:1.00
 SG H:CYS864 2.1 48.9 1.0
SG H:CYS869 2.1 51.4 1.0
SG H:CYS813 2.3 48.3 1.0
SG H:CYS810 2.4 51.0 1.0
CB H:CYS864 2.8 52.0 1.0
CB H:CYS869 3.1 61.1 1.0
CB H:CYS810 3.1 49.5 1.0
CB H:CYS813 3.2 50.1 1.0
N H:CYS813 3.8 51.5 1.0
CA H:CYS813 4.1 51.0 1.0
CA H:CYS864 4.3 53.1 1.0
CB H:HIS871 4.4 53.1 1.0
CB H:ARG866 4.4 67.8 1.0
CA H:CYS869 4.5 63.1 1.0
N H:SER870 4.5 63.0 1.0
N H:HIS871 4.6 57.3 1.0
CG H:ARG866 4.6 68.7 1.0
CA H:CYS810 4.6 49.1 1.0
CB H:LYS812 4.7 54.6 1.0
C H:CYS869 4.8 63.3 1.0
NE1 H:TRP873 4.8 44.3 1.0
C H:CYS813 4.9 50.7 1.0
C H:CYS864 4.9 54.3 1.0
C H:LYS812 4.9 51.3 1.0
N H:LYS814 5.0 50.5 1.0

Zinc binding site 9 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1009

b:88.9
occ:1.00
 SG I:CYS813 2.1 71.7 1.0
SG I:CYS810 2.4 49.5 1.0
SG I:CYS864 2.4 79.2 1.0
SG I:CYS869 2.8 97.4 1.0
CB I:CYS864 2.9 78.8 1.0
CB I:CYS810 3.2 51.7 1.0
CB I:CYS813 3.3 67.7 1.0
N I:CYS813 3.8 65.9 1.0
CB I:CYS869 3.8 96.3 1.0
NE1 I:TRP873 4.1 71.4 1.0
CB I:HIS871 4.1 83.8 1.0
CA I:CYS813 4.1 67.1 1.0
CA I:CYS864 4.4 79.5 1.0
CG I:ARG866 4.5 90.9 0.0
CB I:ARG866 4.5 90.8 1.0
CZ2 I:TRP873 4.5 70.9 0.0
CA I:CYS810 4.6 54.6 1.0
CE2 I:TRP873 4.7 70.7 1.0
N I:HIS871 4.7 86.9 0.0
CB I:LYS812 4.8 63.0 1.0
C I:CYS813 4.9 67.4 1.0
C I:LYS812 4.9 64.5 1.0

Zinc binding site 10 out of 10 in 2qfb

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Regulatory Domain of Human Rig-I with Bound Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1010

b:86.9
occ:1.00
 SG J:CYS869 2.4 86.1 0.0
SG J:CYS813 2.7 69.1 1.0
SG J:CYS810 3.0 78.9 1.0
O J:CYS869 3.1 85.5 0.0
CB J:CYS813 3.1 74.5 1.0
SG J:CYS864 3.2 85.2 1.0
CB J:CYS869 3.2 86.1 0.0
N J:CYS813 3.4 76.2 1.0
CB J:CYS864 3.7 86.9 1.0
CA J:CYS813 3.8 76.8 1.0
C J:CYS869 3.9 85.6 0.0
CB J:HIS871 4.0 82.4 0.0
CB J:CYS810 4.1 76.0 1.0
CA J:CYS869 4.2 86.1 0.0
CB J:LYS812 4.2 76.9 1.0
N J:HIS871 4.4 83.0 0.0
C J:LYS812 4.5 76.7 1.0
O J:CYS813 4.6 81.1 1.0
C J:CYS813 4.7 79.1 1.0
CA J:LYS812 4.8 76.5 1.0
CA J:HIS871 4.9 82.3 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: Wed Dec 16 03:50:15 2020

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