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Zinc in PDB 1i6h: Rna Polymerase II Elongation Complex

Enzymatic activity of Rna Polymerase II Elongation Complex

All present enzymatic activity of Rna Polymerase II Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex, PDB code: 1i6h was solved by A.L.Gnatt, P.Cramer, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.300, 220.700, 191.300, 90.00, 97.50, 90.00
R / Rfree (%) 25 / 29.8

Other elements in 1i6h:

The structure of Rna Polymerase II Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex (pdb code 1i6h). 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 Elongation Complex, PDB code: 1i6h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1i6h

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.8
occ:1.00
 SG A:CYS167 2.2 0.2 1.0
SG A:CYS110 2.3 0.9 1.0
CB A:CYS110 3.3 0.1 1.0
N A:CYS110 3.5 0.9 1.0
O A:MET108 3.8 0.5 1.0
SG A:CYS148 3.8 0.0 1.0
CA A:CYS110 3.8 0.4 1.0
CB A:CYS167 3.9 0.5 1.0
C A:CYS110 4.3 0.6 1.0
O A:CYS167 4.3 0.9 1.0
SG A:CYS107 4.3 0.2 1.0
CB A:CYS107 4.4 0.7 1.0
N A:GLY111 4.5 0.2 1.0
CB A:CYS148 4.6 0.5 1.0
CB A:HIS109 4.6 1.0 1.0
C A:HIS109 4.7 0.9 1.0
O A:CYS107 4.7 0.5 1.0
C A:MET108 4.8 0.7 1.0
ND2 A:ASN169 4.8 0.8 1.0
O A:CYS110 4.9 0.4 1.0
CA A:CYS167 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 1i6h

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:79.0
occ:1.00
 SG A:CYS67 2.0 0.5 1.0
SG A:CYS70 2.1 0.5 1.0
NE2 A:HIS80 2.3 93.4 1.0
CB A:CYS67 3.0 0.1 1.0
O A:CYS67 3.1 0.3 1.0
CD2 A:HIS80 3.2 94.2 1.0
CE1 A:HIS80 3.4 94.2 1.0
CB A:CYS70 3.4 0.8 1.0
SG A:CYS77 3.5 98.5 1.0
C A:CYS67 3.6 0.2 1.0
CA A:CYS67 3.9 0.9 1.0
O A:GLN71 4.3 0.7 1.0
CB A:CYS77 4.4 98.4 1.0
CG A:HIS80 4.4 96.0 1.0
ND1 A:HIS80 4.4 94.0 1.0
CA A:CYS70 4.5 0.8 1.0
CA A:CYS77 4.5 98.7 1.0
N A:GLN68 4.6 1.0 1.0
C A:CYS70 4.6 0.1 1.0
CB A:GLN68 4.6 0.8 1.0
N A:CYS70 4.9 0.2 1.0
C A:CYS77 4.9 99.1 1.0
O A:CYS70 5.0 0.2 1.0
N A:GLN71 5.0 0.6 1.0

Zinc binding site 3 out of 8 in 1i6h

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:83.8
occ:1.00
 SG B:CYS1166 2.0 90.1 1.0
SG B:CYS1182 2.2 0.4 1.0
SG B:CYS1163 2.7 74.0 1.0
SG B:CYS1185 2.9 0.4 1.0
CB B:CYS1185 3.1 0.5 1.0
CB B:CYS1163 3.2 82.7 1.0
CB B:CYS1166 3.7 91.9 1.0
CB B:CYS1182 4.0 0.1 1.0
O B:CYS1166 4.1 94.9 1.0
N B:CYS1166 4.4 93.4 1.0
O B:CYS1182 4.4 0.3 1.0
CA B:CYS1185 4.5 0.5 1.0
CA B:CYS1166 4.6 92.8 1.0
CA B:CYS1163 4.7 83.5 1.0
N B:CYS1185 4.7 0.4 1.0
C B:CYS1166 4.8 93.6 1.0
CB B:THR1170 4.9 89.7 1.0
C B:CYS1182 4.9 0.8 1.0
CA B:CYS1182 5.0 0.1 1.0

Zinc binding site 4 out of 8 in 1i6h

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:56.8
occ:1.00
 SG C:CYS86 1.9 28.3 1.0
SG C:CYS92 2.2 18.2 1.0
SG C:CYS95 2.2 28.4 1.0
SG C:CYS88 2.3 22.5 1.0
CB C:CYS86 2.8 32.3 1.0
CB C:CYS88 3.3 26.7 1.0
CB C:CYS95 3.4 32.6 1.0
CB C:CYS92 3.5 32.1 1.0
N C:CYS92 3.6 39.5 1.0
C C:HIS91 3.9 41.5 1.0
CA C:CYS92 4.1 37.3 1.0
N C:CYS95 4.1 37.9 1.0
CA C:CYS86 4.2 31.0 1.0
N C:CYS88 4.2 27.9 1.0
CA C:HIS91 4.2 42.2 1.0
CA C:CYS88 4.3 29.9 1.0
O C:ASP90 4.4 44.1 1.0
CA C:CYS95 4.4 33.5 1.0
CB C:LYS94 4.5 34.1 1.0
C C:CYS86 4.5 31.1 1.0
O C:HIS91 4.6 41.7 1.0
C C:CYS92 4.7 38.9 1.0
C C:LYS94 4.8 37.5 1.0
O C:CYS86 4.8 32.9 1.0
O C:CYS92 4.8 39.9 1.0
N C:LYS94 4.9 35.7 1.0
N C:PHE87 5.0 30.6 1.0

Zinc binding site 5 out of 8 in 1i6h

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:76.0
occ:1.00
 SG I:CYS32 1.9 71.5 1.0
SG I:CYS10 1.9 62.0 1.0
SG I:CYS29 1.9 59.0 1.0
SG I:CYS7 2.8 78.9 1.0
CB I:CYS29 3.0 61.3 1.0
CB I:CYS32 3.1 74.4 1.0
CG2 I:THR31 3.5 74.0 1.0
CB I:CYS10 3.7 71.5 1.0
N I:CYS32 3.7 76.9 1.0
CB I:CYS7 3.8 81.5 1.0
CA I:CYS32 4.0 76.8 1.0
O I:CYS29 4.0 69.6 1.0
CB I:TYR34 4.1 71.8 1.0
CA I:CYS29 4.3 65.6 1.0
CB I:THR31 4.4 75.3 1.0
N I:SER33 4.4 78.0 1.0
N I:TYR34 4.5 75.0 1.0
C I:CYS29 4.5 67.7 1.0
C I:THR31 4.6 76.1 1.0
N I:CYS10 4.6 77.1 1.0
CA I:CYS10 4.7 73.9 1.0
C I:CYS32 4.7 78.1 1.0
N I:THR31 4.9 71.2 1.0
CA I:THR31 4.9 74.3 1.0
O I:ARG8 5.0 76.0 1.0
CA I:TYR34 5.0 73.0 1.0
CG I:TYR34 5.0 70.4 1.0

Zinc binding site 6 out of 8 in 1i6h

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:45.1
occ:1.00
 SG I:CYS75 1.8 53.4 1.0
SG I:CYS106 1.9 33.6 1.0
SG I:CYS103 2.1 24.4 1.0
SG I:CYS78 2.4 31.9 1.0
CB I:CYS103 2.5 32.3 1.0
CB I:CYS75 2.6 47.6 1.0
CB I:CYS106 3.5 40.9 1.0
CB I:HIS108 3.9 28.7 1.0
N I:CYS106 3.9 44.3 1.0
CB I:CYS78 3.9 37.5 1.0
N I:CYS78 3.9 41.0 1.0
CA I:CYS75 4.0 51.2 1.0
CA I:CYS103 4.0 33.0 1.0
CA I:CYS106 4.3 42.7 1.0
CA I:CYS78 4.4 38.2 1.0
OG I:SER80 4.5 54.8 1.0
N I:CYS75 4.6 52.9 1.0
N I:HIS108 4.6 34.8 1.0
CB I:LYS77 4.6 47.6 1.0
C I:CYS103 4.7 35.4 1.0
CG I:HIS108 4.7 32.3 1.0
CB I:SER80 4.8 47.8 1.0
C I:CYS78 4.8 38.0 1.0
C I:CYS75 4.8 51.4 1.0
C I:CYS106 4.8 44.2 1.0
CD2 I:HIS108 4.8 34.4 1.0
CA I:HIS108 4.8 31.6 1.0
N I:SER107 4.9 44.1 1.0
C I:SER105 4.9 46.5 1.0
N I:CYS103 4.9 30.9 1.0
CB I:SER105 5.0 46.9 1.0
O I:CYS75 5.0 52.2 1.0
O I:CYS103 5.0 35.0 1.0

Zinc binding site 7 out of 8 in 1i6h

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:49.0
occ:1.00
 SG J:CYS46 1.8 35.6 1.0
SG J:CYS45 1.9 25.7 1.0
SG J:CYS10 2.1 15.0 1.0
SG J:CYS7 2.5 29.3 1.0
N J:CYS46 3.0 31.8 1.0
CB J:CYS46 3.1 28.7 1.0
CB J:CYS45 3.3 30.8 1.0
CA J:CYS46 3.3 30.5 1.0
C J:CYS45 3.3 31.9 1.0
CB J:CYS10 3.5 20.8 1.0
CB J:CYS7 3.5 25.3 1.0
N J:CYS10 3.7 21.9 1.0
O J:CYS45 3.8 34.2 1.0
CA J:CYS45 3.9 29.3 1.0
CA J:CYS10 4.1 21.6 1.0
CB J:SER9 4.3 15.0 1.0
NE J:ARG43 4.3 30.4 1.0
CG J:ARG43 4.4 31.7 1.0
N J:CYS45 4.6 28.9 1.0
CD J:ARG43 4.6 27.9 1.0
N J:GLY11 4.8 21.3 1.0
C J:CYS46 4.8 30.0 1.0
C J:CYS10 4.8 21.3 1.0
C J:SER9 4.8 20.7 1.0
CB J:LYS12 4.9 30.8 1.0
CA J:CYS7 5.0 24.3 1.0

Zinc binding site 8 out of 8 in 1i6h

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:79.8
occ:1.00
 SG L:CYS34 1.7 76.4 1.0
SG L:CYS51 1.8 0.1 1.0
SG L:CYS31 2.5 76.1 1.0
SG L:CYS48 2.5 63.7 1.0
CB L:CYS48 3.4 80.3 1.0
CB L:CYS31 3.4 72.4 1.0
CB L:CYS34 3.5 80.2 1.0
CB L:CYS51 3.6 0.2 1.0
O L:CYS51 4.0 0.0 1.0
N L:CYS34 4.0 82.6 1.0
CA L:CYS34 4.3 83.3 1.0
CA L:CYS51 4.5 0.9 1.0
CD2 L:HIS53 4.5 0.3 1.0
N L:CYS51 4.7 0.4 1.0
C L:CYS51 4.7 0.3 1.0
O L:LYS49 4.8 0.8 1.0
N L:LYS49 4.8 99.5 1.0
CA L:CYS48 4.8 87.4 1.0
CA L:CYS31 4.9 71.2 1.0
C L:CYS34 5.0 84.7 1.0

Reference:

A.L.Gnatt, P.Cramer, J.Fu, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: An Rna Polymerase II Elongation Complex at 3.3 A Resolution. Science V. 292 1876 2001.
ISSN: ISSN 0036-8075
PubMed: 11313499
DOI: 10.1126/SCIENCE.1059495
Page generated: Sun Oct 13 02:52:02 2024

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