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Zinc in PDB 3j0k: Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly

Enzymatic activity of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly

All present enzymatic activity of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly:
2.7.7.6;

Other elements in 3j0k:

The structure of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly (pdb code 3j0k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly, PDB code: 3j0k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3j0k

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Zinc binding site 1 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1506

b:58.5
occ:1.00
 SG A:CYS107 2.5 0.8 1.0
SG A:CYS167 2.6 0.4 1.0
SG A:CYS110 2.7 97.9 1.0
SG A:CYS148 2.7 0.2 1.0
O A:CYS167 3.4 0.2 1.0
CB A:CYS148 3.4 0.7 1.0
O A:GLY166 3.6 0.6 1.0
CB A:CYS110 3.7 0.9 1.0
O A:MET108 3.9 92.0 1.0
CB A:CYS107 4.2 93.4 1.0
N A:CYS110 4.3 0.8 1.0
CB A:CYS167 4.3 0.4 1.0
C A:CYS167 4.4 0.7 1.0
CA A:CYS110 4.5 0.1 1.0
O A:CYS107 4.7 90.4 1.0
N A:GLY111 4.8 97.4 1.0
C A:GLY166 4.8 1.0 1.0
CA A:CYS167 4.9 0.7 1.0
CA A:CYS148 4.9 0.8 1.0
C A:CYS110 4.9 99.8 1.0

Zinc binding site 2 out of 9 in 3j0k

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Zinc binding site 2 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1508

b:15.2
occ:1.00
 SG A:CYS67 2.3 0.6 1.0
SG A:CYS77 2.4 40.2 1.0
NE2 A:HIS80 2.4 33.6 1.0
SG A:CYS70 2.7 68.8 1.0
CB A:CYS67 3.0 98.9 1.0
CE1 A:HIS80 3.3 35.2 1.0
O A:CYS67 3.4 99.3 1.0
CD2 A:HIS80 3.4 32.3 1.0
CB A:CYS70 3.4 75.4 1.0
CB A:CYS77 3.7 41.5 1.0
CA A:CYS67 4.1 0.7 1.0
C A:CYS67 4.2 0.9 1.0
O A:GLN71 4.4 83.9 1.0
ND1 A:HIS80 4.4 32.2 1.0
CG A:HIS80 4.5 34.8 1.0
O A:PRO78 4.6 40.2 1.0
OE1 A:GLN68 4.7 0.9 1.0
CA A:CYS77 4.7 42.5 1.0
CA A:CYS70 4.8 81.5 1.0
C A:CYS70 4.9 81.3 1.0
NE2 A:GLN68 4.9 0.6 1.0
CD A:GLN68 5.0 0.2 1.0

Zinc binding site 3 out of 9 in 3j0k

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Zinc binding site 3 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:

Zinc binding site 4 out of 9 in 3j0k

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Zinc binding site 4 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:15.1
occ:1.00
 CB B:CYS1185 2.2 53.4 1.0
SG B:CYS1166 2.3 27.2 1.0
SG B:CYS1163 2.3 26.2 1.0
SG B:CYS1185 2.4 62.5 1.0
SG B:CYS1182 2.6 22.4 1.0
CB B:CYS1163 2.9 23.4 1.0
N B:CYS1166 3.4 33.6 1.0
CA B:CYS1185 3.6 53.6 1.0
CB B:CYS1166 3.7 29.0 1.0
CB B:CYS1182 3.8 37.9 1.0
CG2 B:ILE1165 3.8 29.6 1.0
CB B:ILE1165 4.0 31.7 1.0
O B:CYS1185 4.0 52.8 1.0
C B:CYS1185 4.1 51.7 1.0
CA B:CYS1166 4.1 31.8 1.0
O B:CYS1182 4.2 48.0 1.0
O B:CYS1166 4.2 37.6 1.0
N B:CYS1185 4.2 54.7 1.0
CA B:CYS1163 4.3 24.0 1.0
C B:ILE1165 4.5 34.0 1.0
C B:CYS1166 4.5 34.4 1.0
CA B:ILE1165 4.6 32.2 1.0
N B:ILE1165 4.7 32.6 1.0
OG1 B:THR1170 4.9 33.0 1.0
C B:CYS1163 4.9 23.4 1.0
N B:ASP1186 5.0 51.2 1.0

Zinc binding site 5 out of 9 in 3j0k

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Zinc binding site 5 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:20.5
occ:1.00
 SG C:CYS88 2.2 48.1 1.0
CB C:CYS86 2.4 49.7 1.0
SG C:CYS92 2.5 43.7 1.0
SG C:CYS86 2.7 52.5 1.0
O C:CYS86 2.7 43.5 1.0
CB C:CYS92 2.8 51.9 1.0
CB C:CYS88 2.8 42.7 1.0
N C:CYS92 2.9 54.4 1.0
SG C:CYS95 3.1 28.6 1.0
C C:CYS86 3.3 44.0 1.0
CA C:CYS86 3.4 49.0 1.0
CA C:CYS92 3.4 55.4 1.0
C C:HIS91 3.5 54.6 1.0
N C:CYS88 3.7 36.4 1.0
CA C:CYS88 3.8 39.9 1.0
CA C:HIS91 3.8 55.5 1.0
O C:CYS88 3.9 45.1 1.0
N C:HIS91 4.1 57.6 1.0
CB C:CYS95 4.2 36.1 1.0
C C:CYS88 4.2 42.0 1.0
O C:HIS91 4.3 52.5 1.0
N C:CYS86 4.4 55.7 1.0
C C:CYS92 4.5 58.2 1.0
N C:PHE87 4.5 38.7 1.0
O C:CYS92 4.7 59.5 1.0
C C:PHE87 4.8 33.7 1.0

Zinc binding site 6 out of 9 in 3j0k

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Zinc binding site 6 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:63.8
occ:1.00
 SG I:CYS32 2.1 51.7 1.0
SG I:CYS7 2.2 81.9 1.0
SG I:CYS29 2.7 77.5 1.0
SG I:CYS10 2.9 78.3 1.0
CB I:CYS7 3.0 86.9 1.0
CB I:CYS29 3.1 77.8 1.0
CB I:CYS10 3.8 91.3 1.0
CB I:CYS32 3.8 68.9 1.0
O I:ARG8 3.9 92.9 1.0
C I:CYS10 4.0 93.0 1.0
O I:CYS10 4.2 93.8 1.0
CA I:CYS10 4.2 94.2 1.0
CB I:TYR34 4.3 47.8 1.0
N I:CYS10 4.3 98.6 1.0
CA I:CYS7 4.4 90.2 1.0
N I:ASN11 4.5 89.7 1.0
CA I:CYS29 4.5 77.0 1.0
OD2 I:ASP9 4.6 0.9 1.0
N I:CYS32 4.6 80.7 1.0
N I:ARG8 4.7 89.9 1.0
CA I:CYS32 4.8 73.5 1.0
N I:CYS7 4.9 92.8 1.0
N I:ASN12 4.9 88.9 1.0
C I:CYS7 4.9 90.7 1.0
CG I:TYR34 5.0 43.3 1.0

Zinc binding site 7 out of 9 in 3j0k

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Zinc binding site 7 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:97.5
occ:1.00
 SG I:CYS103 2.6 0.8 1.0
SG I:CYS106 2.6 0.9 1.0
CB I:CYS78 2.7 0.2 1.0
SG I:CYS78 2.9 0.2 1.0
SG I:CYS75 2.9 0.3 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS106 3.2 0.1 1.0
CB I:CYS75 3.3 0.7 1.0
CA I:CYS78 3.8 0.6 1.0
N I:CYS78 3.8 0.4 1.0
O I:SER105 4.4 0.5 1.0
C I:CYS78 4.5 0.5 1.0
CA I:CYS103 4.5 0.6 1.0
N I:HIS79 4.6 0.1 1.0
CA I:CYS106 4.6 0.5 1.0
CB I:HIS108 4.6 1.0 1.0
C I:SER105 4.7 0.5 1.0
N I:CYS106 4.8 0.2 1.0
CA I:CYS75 4.8 0.5 1.0

Zinc binding site 8 out of 9 in 3j0k

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Zinc binding site 8 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:16.4
occ:1.00
 SG J:CYS10 2.3 47.6 1.0
SG J:CYS7 2.4 49.5 1.0
SG J:CYS46 2.6 47.6 1.0
SG J:CYS45 2.7 28.7 1.0
N J:CYS46 3.0 31.1 1.0
CB J:CYS46 3.1 37.4 1.0
CB J:CYS7 3.1 40.7 1.0
OG J:SER9 3.2 52.6 1.0
CA J:CYS46 3.2 34.3 1.0
CB J:CYS10 3.5 47.1 1.0
N J:CYS10 3.5 46.1 1.0
CB J:CYS45 3.6 33.4 1.0
C J:CYS45 3.6 32.0 1.0
CA J:CYS10 3.9 47.2 1.0
O J:CYS7 4.1 36.6 1.0
CA J:CYS45 4.2 33.4 1.0
O J:CYS45 4.2 31.5 1.0
N J:GLY11 4.3 44.0 1.0
CB J:SER9 4.5 46.4 1.0
CA J:CYS7 4.5 38.8 1.0
C J:CYS10 4.5 45.2 1.0
NE J:ARG43 4.5 61.5 1.0
C J:CYS7 4.6 39.1 1.0
C J:SER9 4.6 44.8 1.0
C J:CYS46 4.7 34.7 1.0
CG J:ARG43 4.7 60.4 1.0
CA J:SER9 4.9 44.1 1.0

Zinc binding site 9 out of 9 in 3j0k

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Zinc binding site 9 out of 9 in the Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Orientation of Rna Polymerase II Within the Human VP16-Mediator-Pol II-Tfiif Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:68.3
occ:1.00
 SG L:CYS34 2.4 92.8 1.0
O L:CYS51 2.5 0.1 1.0
SG L:CYS51 2.5 0.4 1.0
SG L:CYS31 2.5 0.4 1.0
CB L:CYS51 2.7 0.7 1.0
CB L:CYS48 2.7 0.6 1.0
SG L:CYS48 2.9 0.2 1.0
C L:CYS51 3.3 0.1 1.0
CA L:CYS51 3.4 0.7 1.0
CB L:CYS31 3.7 0.4 1.0
N L:CYS51 3.9 0.6 1.0
CB L:CYS34 4.1 0.4 1.0
CA L:CYS48 4.1 0.2 1.0
CA L:CYS31 4.5 0.5 1.0
C L:CYS48 4.5 0.2 1.0
N L:GLY52 4.6 0.9 1.0
O L:CYS34 4.8 0.3 1.0
C L:ASP50 4.8 0.7 1.0
N L:LYS49 4.9 0.4 1.0
N L:CYS48 4.9 0.4 1.0
O L:CYS48 4.9 0.9 1.0

Reference:

C.Bernecky, P.Grob, C.C.Ebmeier, E.Nogales, D.J.Taatjes. Molecular Architecture of the Human Mediator-Rna Polymerase II-Tfiif Assembly. Plos Biol. V. 9 00603 2011.
ISSN: ISSN 1544-9173
PubMed: 21468301
DOI: 10.1371/JOURNAL.PBIO.1000603
Page generated: Sat Oct 26 07:23:44 2024

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