Zinc in PDB 5sva: Mediator-Rna Polymerase II Pre-Initiation Complex

Enzymatic activity of Mediator-Rna Polymerase II Pre-Initiation Complex

All present enzymatic activity of Mediator-Rna Polymerase II Pre-Initiation Complex:
2.7.7.6; 3.6.4.12;

Other elements in 5sva:

The structure of Mediator-Rna Polymerase II Pre-Initiation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mediator-Rna Polymerase II Pre-Initiation Complex (pdb code 5sva). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Mediator-Rna Polymerase II Pre-Initiation Complex, PDB code: 5sva:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5sva

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Zinc binding site 1 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:1.0
occ:1.00
 SG A:CYS148 2.3 1.0 1.0
SG A:CYS110 2.3 1.0 1.0
SG A:CYS167 2.4 1.0 1.0
SG A:CYS107 2.4 1.0 1.0
CB A:CYS167 2.6 1.0 1.0
CB A:CYS110 3.1 1.0 1.0
CB A:CYS148 3.1 1.0 1.0
CB A:CYS107 3.3 1.0 1.0
N A:CYS110 3.7 1.0 1.0
CA A:CYS110 4.0 1.0 1.0
CA A:CYS167 4.0 1.0 1.0
O A:CYS167 4.2 1.0 1.0
O A:GLY166 4.2 1.0 1.0
C A:CYS167 4.3 1.0 1.0
CA A:CYS148 4.6 1.0 1.0
CA A:CYS107 4.7 1.0 1.0
N A:CYS167 4.8 1.0 1.0
C A:HIS109 4.8 1.0 1.0
C A:CYS110 4.8 1.0 1.0
C A:GLY166 4.9 1.0 1.0
CB A:HIS109 4.9 1.0 1.0
NE2 A:GLN171 4.9 1.0 1.0
CD2 A:HIS109 4.9 1.0 1.0
N A:GLY111 5.0 1.0 1.0

Zinc binding site 2 out of 8 in 5sva

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Zinc binding site 2 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:1.0
occ:1.00
 NE2 A:HIS80 1.9 1.0 1.0
SG A:CYS70 2.2 1.0 1.0
CE1 A:HIS80 2.3 1.0 1.0
SG A:CYS67 2.5 1.0 1.0
SG A:CYS77 2.7 1.0 1.0
CB A:CYS70 3.1 1.0 1.0
CD2 A:HIS80 3.3 1.0 1.0
ND1 A:HIS80 3.6 1.0 1.0
O A:CYS67 3.7 1.0 1.0
CB A:CYS67 3.8 1.0 1.0
CB A:CYS77 3.8 1.0 1.0
CG A:HIS80 4.1 1.0 1.0
NE2 A:GLN68 4.2 1.0 1.0
CD A:GLN68 4.4 1.0 1.0
OE1 A:GLN68 4.4 1.0 1.0
CA A:CYS70 4.5 1.0 1.0
CA A:CYS77 4.6 1.0 1.0
O A:GLN71 4.6 1.0 1.0
C A:CYS67 4.6 1.0 1.0
C A:CYS70 4.7 1.0 1.0
CA A:CYS67 4.8 1.0 1.0
CD A:PRO78 4.8 1.0 1.0
N A:GLN71 4.9 1.0 1.0

Zinc binding site 3 out of 8 in 5sva

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Zinc binding site 3 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:1.0
occ:1.00
 SG B:CYS1166 2.2 1.0 1.0
SG B:CYS1182 2.4 1.0 1.0
SG B:CYS1163 2.4 1.0 1.0
SG B:CYS1185 2.4 1.0 1.0
CB B:CYS1163 2.9 1.0 1.0
CB B:CYS1185 3.4 1.0 1.0
O B:CYS1166 3.5 1.0 1.0
N B:CYS1166 3.7 1.0 1.0
CB B:CYS1166 3.7 1.0 1.0
CB B:CYS1182 3.8 1.0 1.0
CA B:CYS1166 4.1 1.0 1.0
C B:CYS1166 4.2 1.0 1.0
CA B:CYS1163 4.4 1.0 1.0
OG1 B:THR1170 4.5 1.0 1.0
CA B:CYS1185 4.7 1.0 1.0
CB B:THR1170 4.7 1.0 1.0
CD D:LYS17 4.7 1.0 1.0
CG2 B:THR1170 4.8 1.0 1.0
CB B:ILE1165 4.8 1.0 1.0
C B:ILE1165 4.8 1.0 1.0
O B:CYS1182 4.9 1.0 1.0
N B:ILE1165 4.9 1.0 1.0
CD1 B:ILE1165 4.9 1.0 1.0
C B:CYS1163 5.0 1.0 1.0
N B:CYS1185 5.0 1.0 1.0

Zinc binding site 4 out of 8 in 5sva

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Zinc binding site 4 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:1.0
occ:1.00
 SG C:CYS95 2.2 1.0 1.0
SG C:CYS92 2.2 1.0 1.0
SG C:CYS86 2.3 1.0 1.0
SG C:CYS88 2.3 1.0 1.0
CB C:CYS92 3.2 1.0 1.0
CB C:CYS86 3.3 1.0 1.0
CB C:CYS95 3.3 1.0 1.0
N C:CYS92 3.5 1.0 1.0
CB C:CYS88 3.7 1.0 1.0
CA C:CYS92 3.9 1.0 1.0
C C:HIS91 4.0 1.0 1.0
N C:CYS95 4.0 1.0 1.0
CA C:CYS95 4.3 1.0 1.0
CA C:HIS91 4.3 1.0 1.0
N C:CYS88 4.3 1.0 1.0
C C:CYS92 4.4 1.0 1.0
O C:ASP90 4.5 1.0 1.0
CA C:CYS86 4.6 1.0 1.0
O C:HIS91 4.6 1.0 1.0
CA C:CYS88 4.6 1.0 1.0
CB C:LYS94 4.7 1.0 1.0
C C:LYS94 4.7 1.0 1.0
O C:CYS92 4.8 1.0 1.0
N C:PHE87 4.8 1.0 1.0
C C:CYS86 4.9 1.0 1.0
N C:LYS94 4.9 1.0 1.0

Zinc binding site 5 out of 8 in 5sva

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Zinc binding site 5 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:1.0
occ:1.00
 SG I:CYS7 2.2 1.0 1.0
SG I:CYS29 2.3 1.0 1.0
SG I:CYS10 2.3 1.0 1.0
SG I:CYS32 2.3 1.0 1.0
CB I:CYS10 2.6 1.0 1.0
CB I:CYS29 3.2 1.0 1.0
CB I:CYS7 3.3 1.0 1.0
CB I:CYS32 3.4 1.0 1.0
N I:CYS10 3.7 1.0 1.0
CA I:CYS10 3.7 1.0 1.0
N I:CYS32 3.8 1.0 1.0
CA I:CYS32 4.1 1.0 1.0
CB I:TYR34 4.3 1.0 1.0
OG1 I:THR31 4.3 1.0 1.0
C I:THR31 4.7 1.0 1.0
CA I:CYS29 4.7 1.0 1.0
CA I:CYS7 4.7 1.0 1.0
C I:CYS32 4.7 1.0 1.0
O I:ARG8 4.8 1.0 1.0
C I:ASP9 4.8 1.0 1.0
CB I:ASP9 4.8 1.0 1.0
C I:CYS10 4.9 1.0 1.0
CB I:THR31 5.0 1.0 1.0

Zinc binding site 6 out of 8 in 5sva

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Zinc binding site 6 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:1.0
occ:1.00
 SG I:CYS106 2.3 1.0 1.0
SG I:CYS78 2.3 1.0 1.0
SG I:CYS75 2.4 1.0 1.0
SG I:CYS103 2.4 1.0 1.0
CB I:CYS106 3.1 1.0 1.0
CB I:CYS75 3.2 1.0 1.0
CB I:CYS103 3.2 1.0 1.0
CB I:CYS78 3.5 1.0 1.0
N I:CYS78 3.6 1.0 1.0
N I:CYS106 3.8 1.0 1.0
CA I:CYS106 3.9 1.0 1.0
CA I:CYS78 4.0 1.0 1.0
OG I:SER105 4.1 1.0 1.0
CB I:SER80 4.6 1.0 1.0
C I:CYS78 4.6 1.0 1.0
C I:CYS106 4.6 1.0 1.0
CB I:LYS77 4.6 1.0 1.0
N I:HIS79 4.6 1.0 1.0
CA I:CYS103 4.6 1.0 1.0
CA I:CYS75 4.7 1.0 1.0
N I:SER80 4.7 1.0 1.0
C I:LYS77 4.7 1.0 1.0
N I:SER107 4.7 1.0 1.0
CB I:HIS108 5.0 1.0 1.0
CA I:LYS77 5.0 1.0 1.0
N I:LYS77 5.0 1.0 1.0
C I:SER105 5.0 1.0 1.0

Zinc binding site 7 out of 8 in 5sva

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Zinc binding site 7 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:1.0
occ:1.00
 SG J:CYS7 2.2 1.0 1.0
SG J:CYS46 2.3 1.0 1.0
SG J:CYS45 2.4 1.0 1.0
SG J:CYS10 2.5 1.0 1.0
CB J:CYS7 3.2 1.0 1.0
N J:CYS46 3.3 1.0 1.0
CB J:CYS45 3.5 1.0 1.0
CB J:CYS10 3.5 1.0 1.0
CB J:CYS46 3.6 1.0 1.0
N J:CYS10 3.6 1.0 1.0
CA J:CYS46 3.6 1.0 1.0
C J:CYS45 3.7 1.0 1.0
CA J:CYS10 4.0 1.0 1.0
CA J:CYS45 4.2 1.0 1.0
O J:CYS45 4.2 1.0 1.0
NE J:ARG43 4.3 1.0 1.0
NH2 J:ARG43 4.5 1.0 1.0
C J:SER9 4.6 1.0 1.0
N J:GLY11 4.6 1.0 1.0
CA J:CYS7 4.6 1.0 1.0
CB J:SER9 4.6 1.0 1.0
C J:CYS10 4.7 1.0 1.0
CA J:SER9 4.9 1.0 1.0
C J:CYS7 4.9 1.0 1.0
N J:LYS12 4.9 1.0 1.0
N J:CYS45 4.9 1.0 1.0
N J:SER9 4.9 1.0 1.0
CZ J:ARG43 4.9 1.0 1.0
CB J:LYS12 5.0 1.0 1.0
CB J:ARG43 5.0 1.0 1.0

Zinc binding site 8 out of 8 in 5sva

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Zinc binding site 8 out of 8 in the Mediator-Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mediator-Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.3
occ:1.00
 SG L:CYS48 2.4 0.8 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS34 2.6 0.7 1.0
SG L:CYS51 2.7 0.2 1.0
CB L:CYS48 3.0 0.4 1.0
CB L:CYS31 3.2 0.8 1.0
O L:CYS51 3.6 0.4 1.0
CA L:CYS31 4.0 0.1 1.0
CB L:CYS51 4.1 0.3 1.0
CB L:CYS34 4.3 0.1 1.0
CA L:CYS48 4.4 0.4 1.0
C L:CYS51 4.5 0.2 1.0
OG L:SER36 4.7 0.3 1.0
CA L:CYS51 4.9 0.2 1.0
N L:CYS34 4.9 1.0 1.0

Reference:

P.J.Robinson, M.J.Trnka, D.A.Bushnell, R.E.Davis, P.J.Mattei, A.L.Burlingame, R.D.Kornberg. Structure of A Complete Mediator-Rna Polymerase II Pre-Initiation Complex. Cell V. 166 1411 2016.
ISSN: ISSN 1097-4172
PubMed: 27610567
DOI: 10.1016/J.CELL.2016.08.050
Page generated: Wed Dec 16 08:37:20 2020

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