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Zinc in PDB 1nik: Wild Type Rna Polymerase II

Enzymatic activity of Wild Type Rna Polymerase II

All present enzymatic activity of Wild Type Rna Polymerase II:
2.7.7.6;

Protein crystallography data

The structure of Wild Type Rna Polymerase II, PDB code: 1nik was solved by D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 4.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 224.098, 394.462, 284.343, 90.00, 90.00, 90.00
R / Rfree (%) 33.4 / 36

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 1nik

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Zinc binding site 1 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

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

Zinc binding site 2 out of 7 in 1nik

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Zinc binding site 2 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

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

Zinc binding site 3 out of 7 in 1nik

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Zinc binding site 3 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG B:CYS1166 2.0 97.6 1.0
SG B:CYS1182 2.2 95.8 1.0
SG B:CYS1163 2.7 0.3 1.0
SG B:CYS1185 2.9 0.6 1.0
CB B:CYS1185 3.1 0.6 1.0
CB B:CYS1163 3.2 0.3 1.0
CB B:CYS1166 3.7 97.6 1.0
CB B:CYS1182 4.0 95.8 1.0
O B:CYS1166 4.1 0.9 1.0
N B:CYS1166 4.4 0.9 1.0
O B:CYS1182 4.4 0.3 1.0
CA B:CYS1185 4.5 0.0 1.0
CA B:CYS1166 4.6 0.9 1.0
CA B:CYS1163 4.7 0.7 1.0
N B:CYS1185 4.7 0.0 1.0
C B:CYS1166 4.8 0.9 1.0
CB B:THR1170 4.9 0.0 1.0
C B:CYS1182 4.9 0.3 1.0
CA B:CYS1182 5.0 0.3 1.0

Zinc binding site 4 out of 7 in 1nik

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Zinc binding site 4 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG C:CYS86 1.9 0.5 1.0
SG C:CYS92 2.2 71.7 1.0
SG C:CYS95 2.2 96.2 1.0
SG C:CYS88 2.3 76.3 1.0
CB C:CYS86 2.8 0.5 1.0
CB C:CYS88 3.3 76.3 1.0
CB C:CYS95 3.4 96.2 1.0
CB C:CYS92 3.5 71.7 1.0
N C:CYS92 3.6 0.3 1.0
C C:HIS91 3.9 84.6 1.0
CA C:CYS92 4.1 0.3 1.0
N C:CYS95 4.1 0.9 1.0
CA C:CYS86 4.2 0.8 1.0
N C:CYS88 4.2 0.0 1.0
CA C:HIS91 4.2 84.6 1.0
CA C:CYS88 4.3 0.0 1.0
O C:ASP90 4.4 0.2 1.0
CA C:CYS95 4.4 0.9 1.0
CB C:LYS94 4.5 0.1 1.0
C C:CYS86 4.5 0.8 1.0
O C:HIS91 4.6 84.6 1.0
C C:CYS92 4.6 0.3 1.0
C C:LYS94 4.8 0.6 1.0
O C:CYS86 4.8 0.8 1.0
O C:CYS92 4.8 0.3 1.0
N C:LYS94 4.9 0.6 1.0
N C:PHE87 5.0 0.5 1.0

Zinc binding site 5 out of 7 in 1nik

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Zinc binding site 5 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG I:CYS32 1.9 0.1 1.0
SG I:CYS10 1.9 0.7 1.0
SG I:CYS29 1.9 0.2 1.0
SG I:CYS7 2.8 0.0 1.0
CB I:CYS29 3.0 0.2 1.0
CB I:CYS32 3.1 0.1 1.0
CG2 I:THR31 3.5 0.5 1.0
CB I:CYS10 3.7 0.7 1.0
N I:CYS32 3.7 0.3 1.0
CB I:CYS7 3.8 0.0 1.0
CA I:CYS32 4.0 0.3 1.0
O I:CYS29 4.0 0.7 1.0
CB I:TYR34 4.1 0.8 1.0
CA I:CYS29 4.3 0.7 1.0
CB I:THR31 4.4 0.5 1.0
N I:SER33 4.4 0.1 1.0
N I:TYR34 4.5 0.9 1.0
C I:CYS29 4.5 0.7 1.0
C I:THR31 4.6 0.1 1.0
N I:CYS10 4.6 0.5 1.0
CA I:CYS10 4.7 0.5 1.0
C I:CYS32 4.7 0.3 1.0
N I:THR31 4.9 0.1 1.0
CA I:THR31 4.9 0.1 1.0
O I:ARG8 5.0 0.9 1.0
CA I:TYR34 5.0 0.9 1.0

Zinc binding site 6 out of 7 in 1nik

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Zinc binding site 6 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG I:CYS75 1.8 0.2 1.0
SG I:CYS106 1.9 0.6 1.0
SG I:CYS103 2.1 0.2 1.0
SG I:CYS78 2.4 0.8 1.0
CB I:CYS103 2.5 0.2 1.0
CB I:CYS75 2.6 0.2 1.0
CB I:CYS106 3.5 0.6 1.0
CB I:HIS108 3.9 0.8 1.0
N I:CYS106 3.9 1.0 1.0
CB I:CYS78 3.9 0.8 1.0
N I:CYS78 3.9 0.7 1.0
CA I:CYS75 4.0 0.9 1.0
CA I:CYS103 4.0 0.8 1.0
CA I:CYS106 4.3 1.0 1.0
CA I:CYS78 4.4 0.7 1.0
OG I:SER80 4.5 0.2 1.0
N I:CYS75 4.6 0.9 1.0
N I:HIS108 4.6 0.3 1.0
CB I:LYS77 4.6 0.1 1.0
C I:CYS103 4.7 0.8 1.0
CG I:HIS108 4.7 0.8 1.0
CB I:SER80 4.8 0.2 1.0
C I:CYS78 4.8 0.7 1.0
C I:CYS75 4.8 0.9 1.0
C I:CYS106 4.8 1.0 1.0
CD2 I:HIS108 4.8 0.8 1.0
CA I:HIS108 4.8 0.3 1.0
N I:SER107 4.9 0.3 1.0
C I:SER105 4.9 0.3 1.0
N I:CYS103 4.9 0.8 1.0
CB I:SER105 5.0 0.2 1.0
O I:CYS75 5.0 0.9 1.0
O I:CYS103 5.0 0.8 1.0

Zinc binding site 7 out of 7 in 1nik

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Zinc binding site 7 out of 7 in the Wild Type Rna Polymerase II


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG J:CYS46 1.8 0.8 1.0
SG J:CYS45 1.9 0.7 1.0
SG J:CYS10 2.1 0.4 1.0
SG J:CYS7 2.5 0.1 1.0
N J:CYS46 3.0 87.2 1.0
CB J:CYS46 3.1 0.8 1.0
CB J:CYS45 3.3 0.7 1.0
CA J:CYS46 3.3 87.2 1.0
C J:CYS45 3.3 0.8 1.0
CB J:CYS10 3.5 0.4 1.0
CB J:CYS7 3.5 0.1 1.0
N J:CYS10 3.7 0.9 1.0
O J:CYS45 3.8 0.8 1.0
CA J:CYS45 3.9 0.8 1.0
CA J:CYS10 4.1 0.9 1.0
CB J:SER9 4.3 0.1 1.0
NE J:ARG43 4.3 0.1 1.0
CG J:ARG43 4.4 0.1 1.0
N J:CYS45 4.6 0.8 1.0
CD J:ARG43 4.6 0.1 1.0
N J:GLY11 4.8 0.3 1.0
C J:CYS46 4.8 87.2 1.0
C J:CYS10 4.8 0.9 1.0
C J:SER9 4.8 95.7 1.0
CB J:LYS12 4.9 0.3 1.0
CA J:CYS7 5.0 0.1 1.0

Reference:

D.A.Bushnell, R.D.Kornberg. Complete, 12-Subunit Rna Polymerase II at 4.1-A Resolution: Implications For the Initiation of Transcription. Proc.Natl.Acad.Sci.Usa V. 100 6969 2003.
ISSN: ISSN 0027-8424
PubMed: 12746498
DOI: 10.1073/PNAS.1130601100
Page generated: Wed Oct 16 17:15:46 2024

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