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Zinc in PDB 3rzo: Rna Polymerase II Initiation Complex with A 4-Nt Rna

Enzymatic activity of Rna Polymerase II Initiation Complex with A 4-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 4-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 4-Nt Rna, PDB code: 3rzo 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) 40.01 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.038, 221.149, 192.875, 90.00, 98.34, 90.00
R / Rfree (%) 18.8 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Initiation Complex with A 4-Nt Rna (pdb code 3rzo). 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 4-Nt Rna, PDB code: 3rzo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3rzo

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS107 2.3 0.4 1.0
SG A:CYS110 2.3 0.7 1.0
SG A:CYS167 2.3 0.9 1.0
SG A:CYS148 2.4 0.2 1.0
CB A:CYS148 3.3 0.9 1.0
CB A:CYS107 3.4 0.9 1.0
CB A:CYS167 3.6 0.9 1.0
CB A:CYS110 3.6 0.3 1.0
N A:CYS167 3.8 0.4 1.0
CA A:CYS167 4.1 0.9 1.0
N A:CYS110 4.3 0.6 1.0
C A:CYS167 4.4 0.4 1.0
CA A:CYS110 4.4 0.6 1.0
O A:CYS167 4.5 0.7 1.0
O A:MET108 4.5 0.8 1.0
CA A:CYS148 4.7 0.8 1.0
CA A:CYS107 4.8 0.0 1.0
C A:GLY166 4.9 0.3 1.0
N A:GLY111 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 3rzo

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.2
occ:1.00
 NE2 A:HIS80 2.1 0.4 1.0
SG A:CYS77 2.3 0.9 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS70 2.5 0.2 1.0
CD2 A:HIS80 3.0 0.9 1.0
CE1 A:HIS80 3.2 0.4 1.0
CB A:CYS67 3.4 0.2 1.0
NE2 A:GLN68 3.6 0.4 1.0
CB A:CYS77 3.7 0.6 1.0
O A:CYS67 3.9 0.8 1.0
CB A:CYS70 4.1 0.9 1.0
CG A:HIS80 4.1 0.6 1.0
ND1 A:HIS80 4.2 0.8 1.0
CA A:CYS67 4.6 0.3 1.0
C A:CYS67 4.6 0.4 1.0
O A:GLN71 4.7 0.3 1.0
CA A:CYS77 4.7 0.6 1.0
CD A:GLN68 4.8 0.3 1.0
O A:LEU58 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 3rzo

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.9
occ:1.00
 SG B:CYS1166 2.3 0.0 1.0
SG B:CYS1163 2.4 0.8 1.0
SG B:CYS1185 2.5 0.8 1.0
SG B:CYS1182 2.5 0.0 1.0
CB B:CYS1185 2.8 0.8 1.0
CB B:CYS1163 3.0 0.3 1.0
CB B:CYS1166 3.4 0.5 1.0
CB B:CYS1182 3.4 1.0 1.0
N B:CYS1166 3.7 0.8 1.0
CA B:CYS1166 4.1 0.8 1.0
CA B:CYS1185 4.3 0.1 1.0
CA B:CYS1163 4.5 0.3 1.0
CB B:ILE1165 4.7 0.1 1.0
CA B:CYS1182 4.9 0.4 1.0
CB B:ASN1187 4.9 0.3 1.0
C B:ILE1165 4.9 0.7 1.0

Zinc binding site 4 out of 8 in 3rzo

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:79.6
occ:1.00
 SG C:CYS92 2.2 92.6 1.0
SG C:CYS86 2.3 87.3 1.0
SG C:CYS88 2.4 81.5 1.0
SG C:CYS95 2.4 84.6 1.0
CB C:CYS86 3.2 81.8 1.0
CB C:CYS88 3.3 79.1 1.0
CB C:CYS95 3.3 81.2 1.0
N C:CYS92 3.4 86.3 1.0
CB C:CYS92 3.4 88.6 1.0
C C:HIS91 3.8 88.4 1.0
CA C:CYS92 3.9 87.5 1.0
N C:CYS95 4.0 83.3 1.0
CA C:HIS91 4.1 83.6 1.0
CA C:CYS95 4.3 81.3 1.0
C C:CYS92 4.4 92.3 1.0
N C:CYS88 4.5 80.3 1.0
CA C:CYS88 4.5 79.9 1.0
CB C:LYS94 4.5 89.0 1.0
CA C:CYS86 4.6 81.4 1.0
O C:HIS91 4.6 87.2 1.0
C C:LYS94 4.6 90.6 1.0
O C:CYS92 4.6 90.9 1.0
O C:ASP90 4.7 92.0 1.0
N C:LYS94 4.8 89.6 1.0
CA C:LYS94 4.9 87.9 1.0
C C:CYS86 4.9 83.1 1.0
N C:HIS91 4.9 84.1 1.0

Zinc binding site 5 out of 8 in 3rzo

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.6
occ:1.00
 SG I:CYS29 2.2 1.0 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS32 2.4 0.2 1.0
SG I:CYS7 2.4 0.6 1.0
CB I:CYS10 2.8 0.0 1.0
CB I:CYS7 3.0 0.5 1.0
CB I:CYS29 3.2 0.4 1.0
CB I:CYS32 3.6 0.7 1.0
N I:CYS10 3.8 0.1 1.0
N I:CYS32 3.9 0.3 1.0
CA I:CYS10 3.9 0.7 1.0
CA I:CYS32 4.2 0.3 1.0
CB I:THR31 4.2 0.5 1.0
CB I:TYR34 4.3 0.8 1.0
CA I:CYS7 4.5 0.7 1.0
CA I:CYS29 4.7 0.6 1.0
C I:THR31 4.7 0.6 1.0
OG1 I:THR31 4.7 0.3 1.0
C I:CYS32 4.8 0.7 1.0
N I:THR31 4.9 0.0 1.0
CA I:THR31 4.9 0.8 1.0
C I:ASP9 5.0 0.8 1.0

Zinc binding site 6 out of 8 in 3rzo

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Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:90.8
occ:1.00
 SG I:CYS106 2.2 93.6 1.0
SG I:CYS103 2.3 95.1 1.0
SG I:CYS75 2.3 97.9 1.0
SG I:CYS78 2.3 94.0 1.0
CB I:CYS103 3.1 89.1 1.0
CB I:CYS75 3.2 93.4 1.0
CB I:CYS106 3.4 91.2 1.0
CB I:CYS78 3.6 92.5 1.0
N I:CYS78 3.7 94.3 1.0
N I:CYS106 4.1 90.4 1.0
CA I:CYS78 4.1 93.7 1.0
CA I:CYS106 4.3 90.7 1.0
CB I:HIS108 4.3 87.6 1.0
O I:CYS78 4.4 98.8 1.0
CB I:SER80 4.4 93.2 1.0
C I:CYS78 4.4 99.3 1.0
CB I:LYS77 4.4 96.5 1.0
CA I:CYS103 4.6 85.8 1.0
CA I:CYS75 4.6 93.6 1.0
C I:SER105 4.8 94.3 1.0
N I:SER80 4.8 93.7 1.0
C I:LYS77 4.8 98.6 1.0
CB I:SER105 4.9 92.1 1.0
C I:CYS106 4.9 94.5 1.0
N I:HIS108 5.0 87.7 1.0
C I:CYS103 5.0 87.7 1.0

Zinc binding site 7 out of 8 in 3rzo

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:88.8
occ:1.00
 SG J:CYS10 2.3 80.5 1.0
SG J:CYS46 2.3 82.3 1.0
SG J:CYS45 2.3 83.1 1.0
SG J:CYS7 2.4 70.9 1.0
CB J:CYS10 3.2 76.4 1.0
CB J:CYS7 3.2 67.7 1.0
N J:CYS46 3.4 77.6 1.0
CB J:CYS45 3.6 77.6 1.0
CB J:CYS46 3.6 78.2 1.0
C J:CYS45 3.7 81.5 1.0
CA J:CYS46 3.8 77.0 1.0
N J:CYS10 3.9 73.5 1.0
CA J:CYS10 4.0 74.9 1.0
CG J:ARG43 4.2 80.7 1.0
CA J:CYS45 4.2 77.0 1.0
O J:CYS45 4.3 82.0 1.0
CZ J:ARG43 4.5 96.6 1.0
CB J:LYS12 4.6 76.8 1.0
NH1 J:ARG43 4.6 84.8 1.0
N J:GLY11 4.6 73.2 1.0
CA J:CYS7 4.7 67.2 1.0
C J:CYS10 4.7 77.2 1.0
NE J:ARG43 4.8 80.1 1.0
NH2 J:ARG43 4.8 84.3 1.0
N J:CYS45 4.8 78.2 1.0
N J:LYS12 4.9 75.4 1.0
CB J:SER9 5.0 67.8 1.0

Zinc binding site 8 out of 8 in 3rzo

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Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.7
occ:1.00
 CB L:CYS51 2.3 0.7 1.0
SG L:CYS48 2.3 0.8 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS51 2.4 0.8 1.0
SG L:CYS34 2.4 0.9 1.0
CB L:CYS48 3.2 0.2 1.0
CB L:CYS31 3.2 0.4 1.0
CB L:CYS34 3.7 0.7 1.0
CA L:CYS51 3.8 0.7 1.0
N L:CYS34 3.9 0.2 1.0
CB L:SER36 4.3 0.9 1.0
CA L:CYS34 4.3 0.4 1.0
O L:ASP50 4.5 0.4 1.0
N L:CYS51 4.5 0.5 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 1.0 1.0
N L:GLY52 4.8 0.6 1.0
C L:ASP50 4.9 0.9 1.0
O L:CYS48 4.9 0.2 1.0
CB L:HIS53 4.9 0.6 1.0
C L:CYS48 4.9 0.1 1.0
CB L:GLU33 5.0 0.3 1.0
C L:CYS34 5.0 0.6 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 13:43:06 2025

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