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Zinc in PDB 4iqr: Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna

Protein crystallography data

The structure of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna, PDB code: 4iqr was solved by V.Chandra, P.Huang, Y.Kim, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.81 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 119.786, 57.596, 166.305, 90.00, 96.30, 90.00
R / Rfree (%) 23.9 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna (pdb code 4iqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna, PDB code: 4iqr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4iqr

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Zinc binding site 1 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:74.1
occ:1.00
 SG A:CYS54 2.1 78.5 1.0
SG A:CYS71 2.4 61.9 1.0
SG A:CYS68 2.5 87.0 1.0
SG A:CYS51 2.5 79.0 1.0
CB A:CYS54 3.1 68.5 1.0
N A:CYS54 3.4 74.6 1.0
CB A:CYS71 3.4 63.3 1.0
CB A:CYS51 3.4 84.8 1.0
CB A:CYS68 3.5 78.0 1.0
N A:CYS68 3.7 83.7 1.0
CA A:CYS54 3.7 74.7 1.0
CA A:CYS68 4.2 77.7 1.0
CB A:ILE53 4.3 68.4 1.0
N A:CYS71 4.3 74.7 1.0
N A:GLY55 4.4 78.5 1.0
C A:CYS54 4.5 76.5 1.0
CA A:CYS71 4.5 61.8 1.0
C A:ILE53 4.5 74.0 1.0
CB A:ASP56 4.7 91.2 1.0
CB A:SER67 4.7 78.5 1.0
N A:ASP56 4.7 85.3 1.0
C A:SER67 4.7 84.6 1.0
NH1 A:ARG100 4.8 88.2 1.0
CA A:SER67 4.8 78.0 1.0
CG2 A:ILE53 4.8 66.5 1.0
CA A:CYS51 4.8 79.5 1.0
CA A:ILE53 4.9 68.5 1.0
C A:CYS68 4.9 76.7 1.0
O A:CYS68 5.0 78.0 1.0

Zinc binding site 2 out of 8 in 4iqr

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Zinc binding site 2 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:77.4
occ:1.00
 SG A:CYS103 2.2 63.8 1.0
SG A:CYS93 2.3 75.5 1.0
SG A:CYS87 2.3 68.3 1.0
SG A:CYS106 2.5 66.4 1.0
CB A:CYS87 3.1 62.0 1.0
CB A:CYS93 3.4 69.2 1.0
CB A:CYS103 3.5 64.8 1.0
CB A:CYS106 3.7 61.9 1.0
CA A:CYS87 3.8 60.9 1.0
N A:CYS106 4.0 56.9 1.0
N A:CYS93 4.2 78.3 1.0
CA A:ARG91 4.3 72.7 1.0
CB A:TYR105 4.4 66.4 1.0
CD2 A:TYR105 4.4 69.3 1.0
CA A:CYS93 4.4 74.2 1.0
CA A:CYS106 4.4 62.7 1.0
N A:ARG91 4.6 73.7 1.0
N A:ARG88 4.7 69.5 1.0
N A:GLN92 4.7 76.9 1.0
C A:ARG91 4.8 78.3 1.0
C A:CYS87 4.8 68.2 1.0
CG A:TYR105 4.9 65.9 1.0
N A:CYS87 4.9 60.8 1.0
CA A:CYS103 4.9 67.2 1.0

Zinc binding site 3 out of 8 in 4iqr

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Zinc binding site 3 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:98.4
occ:1.00
 SG B:CYS54 2.3 98.6 1.0
SG B:CYS71 2.3 82.1 1.0
SG B:CYS51 2.5 89.5 1.0
SG B:CYS68 2.5 81.3 1.0
CB B:CYS71 3.2 89.6 1.0
CB B:CYS51 3.6 92.9 1.0
CB B:CYS54 3.8 94.4 1.0
CB B:CYS68 3.9 93.5 1.0
N B:CYS68 3.9 88.3 1.0
N B:CYS71 4.1 83.5 1.0
NH1 B:ARG100 4.1 87.5 1.0
N B:CYS54 4.1 92.3 1.0
CA B:CYS71 4.3 88.4 1.0
CA B:CYS68 4.4 91.2 1.0
CB B:ASP56 4.5 90.7 1.0
CA B:CYS54 4.5 92.5 1.0
CB B:SER67 4.6 86.4 1.0
O B:CYS68 4.6 87.1 1.0
CB B:ILE53 4.6 94.7 1.0
N B:ASP56 4.7 96.1 1.0
C B:CYS68 4.9 89.7 1.0
CD B:ARG100 4.9 80.4 1.0
C B:SER67 4.9 86.8 1.0
N B:GLY55 4.9 94.3 1.0
CA B:SER67 5.0 87.7 1.0
CA B:CYS51 5.0 92.7 1.0

Zinc binding site 4 out of 8 in 4iqr

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Zinc binding site 4 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:98.7
occ:1.00
 SG B:CYS87 2.2 0.9 1.0
SG B:CYS93 2.3 0.3 1.0
SG B:CYS106 2.4 93.2 1.0
SG B:CYS103 2.6 0.7 1.0
CB B:CYS93 3.0 0.8 1.0
CB B:CYS103 3.1 94.8 1.0
CB B:CYS106 3.4 0.8 1.0
CB B:CYS87 3.5 0.3 1.0
N B:CYS93 4.0 0.2 1.0
CA B:CYS93 4.2 0.3 1.0
CA B:CYS87 4.2 0.9 1.0
N B:CYS106 4.2 93.6 1.0
CA B:CYS106 4.4 0.5 1.0
CA B:ARG91 4.6 0.1 1.0
CA B:CYS103 4.6 97.4 1.0
N B:GLN92 4.8 0.1 1.0
CD2 B:PHE89 4.8 0.1 1.0
CD2 B:TYR105 4.9 0.3 1.0
C B:ARG91 4.9 1.0 1.0
N B:ARG91 5.0 0.4 1.0
C B:CYS87 5.0 1.0 1.0
O B:CYS103 5.0 86.0 1.0

Zinc binding site 5 out of 8 in 4iqr

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Zinc binding site 5 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:88.0
occ:1.00
 SG E:CYS54 2.2 88.5 1.0
SG E:CYS71 2.2 63.4 1.0
SG E:CYS51 2.3 86.0 1.0
SG E:CYS68 2.3 86.9 1.0
CB E:CYS54 3.3 85.5 1.0
CB E:CYS71 3.3 74.3 1.0
CB E:CYS51 3.3 88.3 1.0
N E:CYS54 3.5 90.8 1.0
CB E:CYS68 3.7 86.8 1.0
CA E:CYS54 4.0 86.2 1.0
N E:CYS68 4.0 95.2 1.0
CB E:ILE53 4.2 87.9 1.0
N E:CYS71 4.4 74.9 1.0
CA E:CYS68 4.4 84.4 1.0
CA E:CYS71 4.4 67.6 1.0
NH1 E:ARG100 4.5 80.7 1.0
N E:GLY55 4.5 87.0 1.0
C E:ILE53 4.6 92.5 1.0
CA E:CYS51 4.8 89.1 1.0
C E:CYS54 4.8 87.0 1.0
CG2 E:ILE53 4.8 84.7 1.0
CA E:ILE53 4.8 85.4 1.0
N E:ILE53 4.9 92.4 1.0
CB E:ASP56 4.9 99.5 1.0
N E:ASP56 4.9 95.8 1.0

Zinc binding site 6 out of 8 in 4iqr

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Zinc binding site 6 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:95.4
occ:1.00
 SG E:CYS93 2.2 0.4 1.0
SG E:CYS106 2.2 85.0 1.0
SG E:CYS87 2.2 88.4 1.0
SG E:CYS103 2.3 75.8 1.0
CB E:CYS93 3.0 90.6 1.0
CB E:CYS103 3.3 75.4 1.0
CB E:CYS106 3.4 77.6 1.0
CB E:CYS87 3.5 83.9 1.0
N E:CYS93 3.8 0.3 1.0
CA E:CYS93 4.0 90.4 1.0
N E:CYS106 4.1 73.3 1.0
CA E:CYS106 4.4 77.4 1.0
CA E:CYS87 4.4 86.4 1.0
CA E:ARG91 4.5 0.4 1.0
N E:GLN92 4.5 99.3 1.0
N E:ARG91 4.7 0.4 1.0
CA E:CYS103 4.7 74.4 1.0
CD2 E:TYR105 4.8 79.1 1.0
C E:ARG91 4.8 0.2 1.0
CB E:TYR105 4.8 72.8 1.0

Zinc binding site 7 out of 8 in 4iqr

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Zinc binding site 7 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:0.2
occ:1.00
 SG F:CYS54 2.3 99.5 1.0
SG F:CYS71 2.4 90.4 1.0
SG F:CYS51 2.4 95.0 1.0
SG F:CYS68 2.8 86.2 1.0
CB F:CYS51 3.3 97.3 1.0
CB F:CYS54 3.4 0.7 1.0
CB F:CYS71 3.5 87.1 1.0
N F:CYS54 3.9 0.7 1.0
CB F:CYS68 3.9 87.9 1.0
N F:CYS71 4.0 84.8 1.0
N F:CYS68 4.1 88.8 1.0
CA F:CYS54 4.2 0.5 1.0
CA F:CYS71 4.4 86.1 1.0
CB F:ILE53 4.4 95.3 1.0
NH2 F:ARG100 4.4 0.4 1.0
CZ F:ARG100 4.5 99.6 1.0
CA F:CYS68 4.6 89.5 1.0
CB F:ASP56 4.7 0.8 1.0
C F:ILE53 4.8 0.3 1.0
CA F:CYS51 4.8 96.9 1.0
NH1 F:ARG107 4.8 71.3 1.0
NE F:ARG100 4.8 95.6 1.0
N F:GLY55 4.8 0.1 1.0
CB F:SER67 4.9 93.2 1.0
O F:CYS68 4.9 80.9 1.0
N F:ASP56 4.9 0.0 1.0
NH1 F:ARG100 5.0 93.7 1.0
C F:CYS54 5.0 0.4 1.0

Zinc binding site 8 out of 8 in 4iqr

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Zinc binding site 8 out of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn403

b:0.3
occ:1.00
 SG F:CYS87 2.2 0.8 1.0
SG F:CYS93 2.4 86.8 1.0
SG F:CYS106 2.4 90.9 1.0
SG F:CYS103 2.5 0.1 1.0
CB F:CYS87 3.3 0.9 1.0
CB F:CYS93 3.4 97.6 1.0
CB F:CYS106 3.5 96.8 1.0
CB F:CYS103 3.5 0.4 1.0
N F:CYS106 4.0 99.1 1.0
CA F:CYS87 4.1 0.2 1.0
CA F:ARG91 4.2 0.7 1.0
CA F:CYS106 4.3 98.2 1.0
N F:CYS93 4.3 0.8 1.0
CD2 F:TYR105 4.5 0.6 1.0
CA F:CYS93 4.5 96.2 1.0
N F:ARG91 4.5 0.9 1.0
CB F:TYR105 4.6 0.4 1.0
C F:ARG91 4.7 0.8 1.0
N F:GLN92 4.8 0.5 1.0
N F:ARG88 4.9 0.3 1.0
CA F:CYS103 4.9 0.1 1.0
C F:TYR105 5.0 0.1 1.0

Reference:

V.Chandra, P.Huang, N.Potluri, D.Wu, Y.Kim, F.Rastinejad. Multidomain Integration in the Structure of the Hnf-4 Alpha Nuclear Receptor Complex. Nature V. 495 394 2013.
ISSN: ISSN 0028-0836
PubMed: 23485969
DOI: 10.1038/NATURE11966
Page generated: Wed Dec 16 05:24:29 2020

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