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Zinc in PDB 2b8k: 12-Subunit Rna Polymerase II

Enzymatic activity of 12-Subunit Rna Polymerase II

All present enzymatic activity of 12-Subunit Rna Polymerase II:
2.7.7.6;

Protein crystallography data

The structure of 12-Subunit Rna Polymerase II, PDB code: 2b8k was solved by P.A.Meyer, P.Ye, M.Zhang, M.H.Suh, J.Fu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 158.11 / 4.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.690, 394.330, 281.310, 90.00, 90.00, 90.00
R / Rfree (%) 38.7 / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the 12-Subunit Rna Polymerase II (pdb code 2b8k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 12-Subunit Rna Polymerase II, PDB code: 2b8k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2b8k

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Zinc binding site 1 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:20.0
occ:1.00
 SG A:CYS167 2.5 0.2 1.0
SG A:CYS148 2.9 0.3 1.0
O A:CYS167 3.1 0.0 1.0
O A:MET108 3.3 0.4 1.0
SG A:CYS110 3.3 0.3 1.0
CB A:CYS148 3.4 0.9 1.0
CB A:CYS107 4.0 0.1 1.0
CB A:CYS167 4.1 0.1 1.0
C A:CYS167 4.2 0.9 1.0
CB A:CYS110 4.2 0.0 1.0
N A:CYS110 4.3 0.9 1.0
SG A:CYS107 4.3 0.8 1.0
O A:CYS107 4.4 0.5 1.0
C A:MET108 4.5 0.6 1.0
C A:CYS107 4.6 0.9 1.0
CB A:HIS109 4.7 0.8 1.0
CA A:CYS167 4.7 0.5 1.0
O A:GLY166 4.8 0.8 1.0
CA A:CYS110 4.8 0.4 1.0
CA A:CYS148 4.9 0.4 1.0
O A:ASN169 4.9 0.9 1.0
CA A:CYS107 4.9 0.4 1.0

Zinc binding site 2 out of 8 in 2b8k

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Zinc binding site 2 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:20.0
occ:1.00
 O A:CYS67 1.7 0.1 1.0
NE2 A:HIS80 2.4 0.0 1.0
C A:CYS67 2.7 0.1 1.0
CB A:CYS70 2.7 0.3 1.0
CD2 A:HIS80 2.8 0.5 1.0
CB A:CYS67 3.0 0.7 1.0
SG A:CYS70 3.1 0.7 1.0
CE1 A:HIS80 3.3 1.0 1.0
CA A:CYS67 3.3 0.9 1.0
SG A:CYS77 3.5 0.9 1.0
SG A:CYS67 3.7 0.6 1.0
NE2 A:GLN68 3.7 0.1 1.0
CB A:GLN68 3.8 0.6 1.0
CD A:GLN68 3.8 0.0 1.0
CG A:HIS80 3.8 0.9 1.0
N A:GLN68 3.9 0.0 1.0
CG A:GLN68 4.0 0.8 1.0
ND1 A:HIS80 4.0 0.7 1.0
CA A:CYS70 4.1 0.3 1.0
OE1 A:GLN68 4.4 0.4 1.0
CA A:GLN68 4.4 0.6 1.0
N A:CYS70 4.4 0.9 1.0
N A:CYS67 4.5 0.9 1.0
O A:GLN68 4.6 0.3 1.0
C A:GLN68 4.7 0.8 1.0
C A:CYS70 4.8 0.1 1.0
CB A:CYS77 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 2b8k

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Zinc binding site 3 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1225

b:20.0
occ:1.00
 SG B:CYS1166 1.3 0.2 1.0
SG B:CYS1185 2.5 0.8 1.0
CB B:CYS1163 2.8 0.5 1.0
O B:CYS1166 2.9 0.6 1.0
CB B:CYS1166 3.1 0.8 1.0
SG B:CYS1163 3.1 0.9 1.0
SG B:CYS1182 3.2 0.4 1.0
CB B:CYS1185 3.5 0.8 1.0
OG1 B:THR1170 3.6 0.2 1.0
C B:CYS1166 3.7 0.7 1.0
CA B:CYS1166 3.8 0.3 1.0
N B:CYS1166 3.8 0.0 1.0
CB B:THR1170 4.3 0.2 1.0
CA B:CYS1163 4.3 0.5 1.0
CD1 B:LEU1168 4.4 1.0 1.0
N B:LEU1168 4.7 0.7 1.0
CB B:LEU1168 4.8 0.5 1.0
N B:CYS1163 4.8 0.5 1.0
CB B:CYS1182 4.8 0.3 1.0
CA B:CYS1185 4.8 0.5 1.0
CG B:LEU1168 4.9 0.8 1.0
O B:CYS1182 4.9 0.8 1.0
CG2 B:THR1170 4.9 0.4 1.0

Zinc binding site 4 out of 8 in 2b8k

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Zinc binding site 4 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:20.0
occ:1.00
 SG C:CYS86 1.3 0.3 1.0
SG C:CYS88 2.1 0.1 1.0
CB C:CYS86 2.2 0.9 1.0
SG C:CYS92 2.6 0.8 1.0
SG C:CYS95 3.3 0.8 1.0
CA C:CYS86 3.4 0.4 1.0
CB C:CYS88 3.4 0.2 1.0
C C:CYS86 3.5 0.1 1.0
O C:CYS86 3.5 0.3 1.0
N C:CYS88 3.6 0.2 1.0
CB C:CYS95 3.8 0.5 1.0
N C:CYS92 4.0 0.9 1.0
CB C:CYS92 4.0 0.1 1.0
CA C:CYS88 4.1 0.7 1.0
N C:PHE87 4.2 0.9 1.0
C C:HIS91 4.4 0.7 1.0
N C:CYS86 4.4 0.1 1.0
CA C:HIS91 4.5 0.4 1.0
O C:CYS88 4.5 0.8 1.0
CA C:CYS92 4.5 0.3 1.0
N C:CYS95 4.7 1.0 1.0
O C:CYS92 4.7 1.0 1.0
C C:PHE87 4.7 0.7 1.0
CB C:LYS94 4.7 0.4 1.0
C C:CYS88 4.8 0.0 1.0
N C:HIS91 4.9 0.3 1.0
C C:LYS94 4.9 0.4 1.0
CA C:CYS95 4.9 0.1 1.0
C C:CYS92 5.0 0.2 1.0
CA C:PHE87 5.0 0.6 1.0

Zinc binding site 5 out of 8 in 2b8k

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Zinc binding site 5 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn123

b:20.0
occ:1.00
 SG I:CYS10 1.9 0.3 1.0
SG I:CYS32 2.0 0.0 1.0
SG I:CYS29 2.4 0.3 1.0
CB I:CYS32 2.8 0.1 1.0
CB I:CYS29 3.1 0.1 1.0
SG I:CYS7 3.3 0.2 1.0
N I:CYS32 3.4 0.5 1.0
CB I:CYS10 3.5 0.6 1.0
CA I:CYS32 3.7 0.5 1.0
CA I:CYS10 4.3 1.0 1.0
N I:CYS10 4.4 0.5 1.0
C I:CYS32 4.4 0.5 1.0
CB I:THR31 4.4 0.3 1.0
OD2 I:ASP9 4.6 0.6 1.0
C I:THR31 4.6 0.4 1.0
CA I:CYS29 4.6 0.8 1.0
O I:ARG8 4.6 0.4 1.0
N I:SER33 4.6 0.9 1.0
CB I:CYS7 4.7 0.3 1.0
CB I:TYR34 4.7 0.6 1.0
C I:CYS10 4.7 0.0 1.0
CA I:THR31 4.9 0.1 1.0
N I:TYR34 5.0 0.5 1.0
OG1 I:THR31 5.0 0.2 1.0
N I:ASN11 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 2b8k

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Zinc binding site 6 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn124

b:20.0
occ:1.00
 SG I:CYS106 2.2 0.5 1.0
SG I:CYS78 3.4 0.4 1.0
CB I:HIS108 3.4 0.9 1.0
CB I:CYS75 3.5 0.1 1.0
CB I:CYS106 3.6 0.1 1.0
CB I:CYS78 3.6 0.9 1.0
SG I:CYS75 4.1 0.3 1.0
CG I:HIS108 4.3 0.3 1.0
N I:CYS78 4.5 0.8 1.0
N I:HIS108 4.6 0.4 1.0
CB I:CYS103 4.6 0.8 1.0
CA I:HIS108 4.6 0.3 1.0
CD2 I:HIS108 4.7 1.0 1.0
SG I:CYS103 4.7 0.3 1.0
CA I:CYS78 4.8 0.9 1.0
CA I:CYS75 4.8 0.1 1.0
CD I:PRO76 4.9 0.8 1.0
N I:PRO76 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 2b8k

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Zinc binding site 7 out of 8 in the 12-Subunit 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 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn71

b:20.0
occ:1.00
 N J:CYS46 2.0 0.6 1.0
CB J:CYS46 2.2 0.3 1.0
CA J:CYS46 2.2 0.3 1.0
SG J:CYS46 2.3 0.5 1.0
SG J:CYS7 2.5 0.3 1.0
SG J:CYS45 2.7 0.3 1.0
SG J:CYS10 2.7 0.8 1.0
C J:CYS45 2.8 0.8 1.0
CB J:CYS10 2.9 0.9 1.0
CB J:CYS45 3.2 0.0 1.0
CB J:CYS7 3.3 0.1 1.0
O J:CYS45 3.5 0.1 1.0
CA J:CYS45 3.6 0.7 1.0
C J:CYS46 3.7 1.0 1.0
N J:CYS10 3.9 0.2 1.0
CA J:CYS10 4.0 0.6 1.0
OG J:SER9 4.1 0.3 1.0
N J:ARG47 4.4 0.5 1.0
N J:CYS45 4.5 0.3 1.0
O J:CYS46 4.5 0.5 1.0
N J:GLY11 4.6 0.3 1.0
O J:ARG43 4.7 0.8 1.0
CA J:CYS7 4.7 0.9 1.0
CE J:MET49 4.8 0.9 1.0
C J:CYS10 4.8 0.2 1.0
CB J:SER9 4.8 0.5 1.0
NE J:ARG43 4.9 0.3 1.0
CG J:ARG43 4.9 0.4 1.0

Zinc binding site 8 out of 8 in 2b8k

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Zinc binding site 8 out of 8 in the 12-Subunit Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 12-Subunit Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn71

b:20.0
occ:1.00
 SG L:CYS51 1.5 1.0 1.0
SG L:CYS34 2.2 0.5 1.0
SG L:CYS48 2.6 0.5 1.0
SG L:CYS31 2.9 0.9 1.0
CB L:CYS51 3.2 0.1 1.0
O L:CYS51 3.3 0.2 1.0
CB L:CYS48 3.4 0.2 1.0
CB L:CYS34 3.9 0.9 1.0
C L:CYS51 4.0 0.0 1.0
CA L:CYS51 4.0 0.0 1.0
CB L:CYS31 4.1 0.6 1.0
N L:CYS51 4.2 0.4 1.0
O L:LYS49 4.6 0.8 1.0
CA L:CYS48 4.8 0.2 1.0
OG L:SER36 4.9 0.1 1.0
N L:LYS49 5.0 0.3 1.0

Reference:

P.A.Meyer, P.Ye, M.Zhang, M.H.Suh, J.Fu. Phasing Rna Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model. Structure V. 14 973 2006.
ISSN: ISSN 0969-2126
PubMed: 16765890
DOI: 10.1016/J.STR.2006.04.003
Page generated: Wed Oct 16 21:56:04 2024

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