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Zinc in PDB 3rzd: Rna Polymerase II Initiation Complex with A 5-Nt Rna

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna, PDB code: 3rzd was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.14 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.538, 221.266, 192.175, 90.00, 97.44, 90.00
R / Rfree (%) 18.8 / 23

Other elements in 3rzd:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 3rzd

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.6
occ:1.00
 SG A:CYS107 2.3 1.0 1.0
SG A:CYS167 2.4 0.0 1.0
SG A:CYS110 2.4 0.5 1.0
SG A:CYS148 2.4 0.0 1.0
CB A:CYS107 3.0 0.5 1.0
CB A:CYS148 3.5 0.2 1.0
CB A:CYS110 3.5 0.8 1.0
N A:CYS110 3.8 0.5 1.0
N A:CYS167 3.8 0.1 1.0
CB A:CYS167 3.9 0.3 1.0
O A:CYS167 4.0 0.6 1.0
CA A:CYS110 4.2 0.0 1.0
CA A:CYS167 4.3 0.3 1.0
CA A:CYS107 4.5 0.9 1.0
C A:CYS167 4.6 0.1 1.0
CB A:HIS109 4.6 0.8 1.0
C A:GLY166 4.8 0.6 1.0
C A:HIS109 4.8 0.5 1.0
N A:HIS109 4.9 0.6 1.0
CA A:GLY166 4.9 0.7 1.0
CA A:CYS148 4.9 1.0 1.0
CA A:HIS109 5.0 0.2 1.0

Zinc binding site 2 out of 8 in 3rzd

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.2
occ:1.00
 CE1 A:HIS80 2.0 0.1 1.0
NE2 A:HIS80 2.2 0.8 1.0
SG A:CYS77 2.4 0.8 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS70 2.4 0.1 1.0
ND1 A:HIS80 3.2 0.8 1.0
CD2 A:HIS80 3.6 0.6 1.0
CG A:GLN68 3.8 0.4 1.0
CB A:CYS77 3.8 0.1 1.0
CB A:CYS67 3.8 0.1 1.0
CB A:CYS70 4.0 0.2 1.0
CG A:HIS80 4.0 0.5 1.0
O A:CYS67 4.1 0.7 1.0
C A:CYS67 4.4 0.2 1.0
CD A:GLN68 4.6 0.0 1.0
CA A:CYS67 4.8 1.0 1.0
O A:GLN71 4.8 0.8 1.0
CB A:GLN68 4.9 0.8 1.0
CA A:CYS77 4.9 0.1 1.0

Zinc binding site 3 out of 8 in 3rzd

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1185 2.3 0.6 1.0
SG B:CYS1166 2.3 0.3 1.0
SG B:CYS1163 2.3 0.8 1.0
SG B:CYS1182 2.4 0.1 1.0
CB B:CYS1185 3.2 0.8 1.0
CB B:CYS1166 3.3 0.9 1.0
N B:CYS1166 3.4 0.7 1.0
CB B:CYS1163 3.6 0.2 1.0
CB B:CYS1182 3.8 0.1 1.0
CA B:CYS1166 3.9 0.4 1.0
CB B:ILE1165 4.3 0.3 1.0
C B:ILE1165 4.5 0.7 1.0
CA B:CYS1185 4.6 0.3 1.0
N B:GLY1167 4.8 0.5 1.0
C B:CYS1166 4.8 0.8 1.0
CA B:ILE1165 4.8 0.4 1.0
N B:CYS1185 4.9 0.3 1.0
CA B:CYS1163 4.9 0.4 1.0
N B:ILE1165 4.9 0.6 1.0

Zinc binding site 4 out of 8 in 3rzd

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:64.5
occ:1.00
 SG C:CYS92 2.3 75.7 1.0
SG C:CYS95 2.3 69.6 1.0
SG C:CYS86 2.4 68.8 1.0
SG C:CYS88 2.4 63.0 1.0
CB C:CYS86 3.3 63.4 1.0
CB C:CYS88 3.4 60.7 1.0
CB C:CYS92 3.4 72.5 1.0
N C:CYS92 3.4 70.7 1.0
CB C:CYS95 3.5 65.9 1.0
C C:HIS91 3.9 74.1 1.0
CA C:CYS92 4.0 71.8 1.0
N C:CYS95 4.1 68.5 1.0
CA C:HIS91 4.1 69.7 1.0
CA C:CYS95 4.4 66.7 1.0
N C:CYS88 4.5 60.7 1.0
CA C:CYS88 4.5 60.7 1.0
O C:HIS91 4.6 73.9 1.0
C C:CYS92 4.7 76.0 1.0
CA C:CYS86 4.7 63.0 1.0
CB C:LYS94 4.8 72.3 1.0
C C:LYS94 4.9 73.3 1.0
N C:LYS94 4.9 70.1 1.0
C C:CYS86 5.0 66.2 1.0
N C:HIS91 5.0 69.9 1.0

Zinc binding site 5 out of 8 in 3rzd

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:94.9
occ:1.00
 SG I:CYS32 2.3 0.5 1.0
SG I:CYS7 2.3 0.3 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS29 2.4 0.5 1.0
CB I:CYS10 2.8 0.3 1.0
CB I:CYS7 3.1 97.6 1.0
OG1 I:THR31 3.3 0.2 1.0
CB I:CYS29 3.5 0.7 1.0
CB I:CYS32 3.5 0.2 1.0
N I:CYS10 3.7 0.0 1.0
CA I:CYS10 3.9 0.9 1.0
N I:CYS32 4.1 0.3 1.0
CB I:TYR34 4.3 0.2 1.0
CA I:CYS32 4.3 0.9 1.0
CA I:CYS7 4.5 96.9 1.0
CB I:THR31 4.6 0.1 1.0
C I:THR31 4.6 0.4 1.0
CA I:CYS29 4.9 0.3 1.0
CB I:ASP9 4.9 0.6 1.0
C I:ASP9 4.9 0.2 1.0
C I:CYS32 5.0 0.3 1.0
C I:CYS10 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 3rzd

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Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:67.8
occ:1.00
 SG I:CYS78 2.3 78.2 1.0
SG I:CYS106 2.3 79.8 1.0
SG I:CYS75 2.4 71.3 1.0
SG I:CYS103 2.4 81.0 1.0
CB I:CYS103 3.1 75.5 1.0
CB I:CYS75 3.2 66.8 1.0
CB I:CYS78 3.5 76.4 1.0
CB I:CYS106 3.6 77.7 1.0
N I:CYS78 3.7 75.5 1.0
O I:CYS78 3.9 79.7 1.0
N I:CYS106 4.0 77.1 1.0
CA I:CYS78 4.0 76.2 1.0
C I:CYS78 4.3 80.6 1.0
CA I:CYS106 4.3 77.2 1.0
CB I:HIS108 4.5 72.5 1.0
CB I:LYS77 4.5 75.8 1.0
CB I:SER80 4.6 77.0 1.0
CA I:CYS103 4.6 73.8 1.0
CA I:CYS75 4.7 66.2 1.0
C I:LYS77 4.8 79.4 1.0
CB I:SER105 4.8 82.2 1.0
C I:SER105 4.9 82.3 1.0
C I:CYS106 5.0 80.8 1.0
N I:SER80 5.0 75.5 1.0
N I:HIS108 5.0 72.1 1.0

Zinc binding site 7 out of 8 in 3rzd

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:63.1
occ:1.00
 SG J:CYS10 2.3 58.4 1.0
SG J:CYS7 2.3 60.3 1.0
SG J:CYS45 2.4 56.4 1.0
SG J:CYS46 2.4 63.0 1.0
CB J:CYS7 3.2 57.4 1.0
N J:CYS46 3.3 56.6 1.0
CB J:CYS10 3.4 53.5 1.0
CB J:CYS45 3.6 51.5 1.0
CB J:CYS46 3.6 59.2 1.0
CA J:CYS46 3.7 57.3 1.0
C J:CYS45 3.7 58.5 1.0
N J:CYS10 3.7 51.5 1.0
NE J:ARG43 4.1 77.7 1.0
CA J:CYS10 4.1 52.1 1.0
CD J:ARG43 4.1 70.6 1.0
CA J:CYS45 4.2 52.3 1.0
CG J:ARG43 4.2 65.6 1.0
O J:CYS45 4.4 58.1 1.0
CA J:CYS7 4.6 56.3 1.0
N J:GLY11 4.7 52.9 1.0
CB J:SER9 4.7 54.8 1.0
CB J:LYS12 4.7 64.4 1.0
C J:CYS10 4.8 56.3 1.0
C J:SER9 4.9 55.0 1.0
N J:LYS12 4.9 59.4 1.0
N J:CYS45 4.9 53.9 1.0
O J:CYS7 4.9 57.5 1.0

Zinc binding site 8 out of 8 in 3rzd

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Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Initiation Complex with A 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:96.9
occ:1.00
 SG L:CYS51 2.3 0.0 1.0
SG L:CYS34 2.3 0.0 1.0
SG L:CYS48 2.3 0.1 1.0
SG L:CYS31 2.4 0.1 1.0
CB L:CYS48 3.1 0.9 1.0
CB L:CYS31 3.1 0.8 1.0
CB L:CYS51 3.1 0.6 1.0
CB L:CYS34 3.5 0.5 1.0
N L:CYS51 3.6 0.1 1.0
N L:CYS34 3.8 0.8 1.0
CA L:CYS51 3.9 0.6 1.0
CA L:CYS34 4.2 0.9 1.0
N L:GLY52 4.5 0.8 1.0
C L:CYS51 4.6 0.5 1.0
CA L:CYS48 4.6 0.4 1.0
CA L:CYS31 4.6 0.2 1.0
C L:ASP50 4.7 0.8 1.0
CB L:ASP50 4.8 0.6 1.0
C L:CYS34 4.8 0.7 1.0
N L:HIS53 4.9 0.9 1.0
N L:ASP50 5.0 0.2 1.0

Reference:

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629
Page generated: Wed Aug 20 13:43:05 2025

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