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Zinc in PDB 3fki: 12-Subunit Rna Polymerase II Refined with Zn-Sad Data

Enzymatic activity of 12-Subunit Rna Polymerase II Refined with Zn-Sad Data

All present enzymatic activity of 12-Subunit Rna Polymerase II Refined with Zn-Sad Data:
2.7.7.6;

Protein crystallography data

The structure of 12-Subunit Rna Polymerase II Refined with Zn-Sad Data, PDB code: 3fki was solved by P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, J.Fu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.22 / 3.88
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.581, 391.537, 280.734, 90.00, 90.00, 90.00
R / Rfree (%) 28.2 / 30.1

Other elements in 3fki:

The structure of 12-Subunit Rna Polymerase II Refined with Zn-Sad Data also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data (pdb code 3fki). 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 Refined with Zn-Sad Data, PDB code: 3fki:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3fki

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Zinc binding site 1 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:0.95
 SG A:CYS110 1.9 0.5 1.0
SG A:CYS148 2.6 0.8 1.0
CB A:CYS148 3.2 0.7 1.0
CB A:CYS167 3.3 0.2 1.0
O A:CYS167 3.3 0.4 1.0
CB A:CYS110 3.4 0.1 1.0
SG A:CYS167 3.5 0.1 1.0
O A:MET108 3.6 0.9 1.0
O A:GLY166 3.7 0.3 1.0
SG A:CYS107 3.7 0.5 1.0
CB A:CYS107 4.2 0.1 1.0
N A:CYS110 4.2 0.6 1.0
C A:CYS167 4.2 0.2 1.0
CA A:CYS167 4.3 0.6 1.0
CA A:CYS110 4.4 0.1 1.0
C A:GLY166 4.6 0.1 1.0
N A:GLY111 4.7 0.5 1.0
CA A:CYS148 4.7 0.5 1.0
C A:MET108 4.9 0.3 1.0
N A:CYS167 4.9 0.7 1.0

Zinc binding site 2 out of 8 in 3fki

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Zinc binding site 2 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.0
occ:1.00
 SG A:CYS77 2.4 0.2 1.0
CE1 A:HIS80 2.6 0.1 1.0
SG A:CYS67 2.6 0.9 1.0
SG A:CYS70 2.7 0.5 1.0
CB A:CYS67 3.2 0.0 1.0
CB A:CYS70 3.2 0.5 1.0
O A:CYS67 3.2 0.8 1.0
NE2 A:HIS80 3.3 0.7 1.0
ND1 A:HIS80 3.7 0.3 1.0
CB A:CYS77 3.9 0.1 1.0
C A:CYS67 4.1 0.2 1.0
CA A:CYS67 4.3 0.9 1.0
O A:GLN71 4.5 0.9 1.0
CA A:CYS70 4.5 0.5 1.0
CD2 A:HIS80 4.6 0.2 1.0
O A:PRO78 4.7 0.5 1.0
CA A:CYS77 4.7 99.5 1.0
C A:CYS70 4.8 0.8 1.0
CG A:HIS80 4.8 0.0 1.0
N A:GLN71 4.8 0.0 1.0
CD A:PRO78 5.0 0.2 1.0

Zinc binding site 3 out of 8 in 3fki

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Zinc binding site 3 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1225

b:0.0
occ:1.00
 SG B:CYS1166 1.9 0.3 1.0
SG B:CYS1163 2.5 0.4 1.0
SG B:CYS1185 2.6 0.1 1.0
SG B:CYS1182 2.6 0.9 1.0
CB B:CYS1185 3.1 0.1 1.0
CB B:CYS1163 3.2 0.5 1.0
CB B:CYS1166 3.2 0.8 1.0
N B:CYS1166 3.4 0.5 1.0
CA B:CYS1166 3.8 0.4 1.0
CB B:CYS1182 3.8 0.7 1.0
O B:CYS1166 4.1 0.9 1.0
C B:CYS1166 4.4 0.5 1.0
CB B:ILE1165 4.5 0.3 1.0
CA B:CYS1185 4.5 0.8 1.0
C B:ILE1165 4.6 0.5 1.0
O B:CYS1182 4.6 0.3 1.0
CA B:CYS1163 4.6 0.7 1.0
N B:CYS1185 4.7 0.8 1.0
N B:ILE1165 4.8 0.7 1.0
CA B:ILE1165 4.8 0.5 1.0

Zinc binding site 4 out of 8 in 3fki

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Zinc binding site 4 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.0
occ:1.00
 SG C:CYS88 1.9 97.3 1.0
SG C:CYS95 2.2 97.1 1.0
SG C:CYS86 2.4 97.7 1.0
SG C:CYS92 2.5 0.3 1.0
N C:CYS92 3.0 98.7 1.0
CB C:CYS86 3.1 96.0 1.0
CB C:CYS92 3.3 0.6 1.0
CB C:CYS88 3.4 98.3 1.0
C C:HIS91 3.6 98.1 1.0
CA C:CYS92 3.6 0.2 1.0
CB C:CYS95 3.6 96.8 1.0
CA C:HIS91 4.0 96.6 1.0
C C:CYS92 4.2 0.8 1.0
N C:CYS95 4.3 99.1 1.0
O C:HIS91 4.4 98.6 1.0
N C:HIS91 4.4 95.8 1.0
N C:CYS88 4.5 97.1 1.0
CA C:CYS88 4.5 97.6 1.0
O C:CYS92 4.5 0.2 1.0
CA C:CYS86 4.5 95.5 1.0
CA C:CYS95 4.6 97.8 1.0
C C:LYS94 4.7 99.6 1.0
N C:LYS94 4.7 0.5 1.0
C C:CYS86 4.8 95.4 1.0
CB C:LYS94 4.9 0.0 1.0
N C:ASP93 4.9 0.1 1.0
CA C:LYS94 5.0 0.0 1.0
O C:CYS88 5.0 95.5 1.0

Zinc binding site 5 out of 8 in 3fki

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Zinc binding site 5 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn123

b:0.0
occ:1.00
 SG I:CYS32 2.1 0.2 1.0
SG I:CYS29 2.5 0.1 1.0
SG I:CYS7 3.1 0.1 1.0
SG I:CYS10 3.2 0.6 1.0
CB I:CYS32 3.3 0.6 1.0
N I:CYS32 3.3 0.9 1.0
CB I:CYS29 3.5 0.1 1.0
OD1 I:ASN12 3.5 0.4 1.0
CB I:THR31 3.8 0.4 1.0
O I:CYS10 3.8 0.4 1.0
CA I:CYS32 3.9 0.9 1.0
OD2 I:ASP9 4.0 0.2 1.0
C I:THR31 4.1 0.2 1.0
CG I:ASN12 4.2 0.7 1.0
CB I:ASN12 4.2 0.1 1.0
CA I:THR31 4.3 0.2 1.0
OG1 I:THR31 4.4 0.4 1.0
N I:THR31 4.4 0.6 1.0
CB I:CYS7 4.6 0.1 1.0
CG2 I:THR31 4.7 1.0 1.0
CB I:CYS10 4.7 0.1 1.0
C I:CYS32 4.8 0.1 1.0
C I:CYS10 4.9 0.5 1.0
CA I:CYS29 4.9 0.0 1.0
O I:ARG8 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 3fki

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Zinc binding site 6 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn124

b:0.0
occ:0.93
 SG I:CYS78 2.2 0.1 1.0
O I:SER105 3.1 0.4 1.0
SG I:CYS75 3.2 0.2 1.0
CB I:CYS106 3.3 0.2 1.0
CB I:CYS75 3.6 0.1 1.0
CB I:CYS78 3.6 0.3 1.0
SG I:CYS106 3.6 0.7 1.0
CB I:CYS103 3.7 0.9 1.0
N I:SER107 3.9 0.3 1.0
N I:HIS108 3.9 0.9 1.0
SG I:CYS103 4.0 0.3 1.0
CB I:HIS108 4.1 1.0 1.0
C I:SER105 4.2 0.7 1.0
CA I:CYS106 4.3 0.9 1.0
C I:CYS106 4.3 0.9 1.0
CA I:HIS108 4.6 0.0 1.0
CA I:SER107 4.7 0.3 1.0
N I:CYS106 4.7 0.5 1.0
C I:SER107 4.7 0.5 1.0
CA I:CYS78 4.8 0.7 1.0
OG I:SER80 4.9 1.0 1.0
N I:CYS78 4.9 0.3 1.0

Zinc binding site 7 out of 8 in 3fki

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Zinc binding site 7 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn71

b:0.0
occ:1.00
 SG J:CYS10 2.0 95.9 1.0
SG J:CYS45 2.2 95.9 1.0
SG J:CYS7 2.6 94.1 1.0
N J:CYS46 2.9 96.9 1.0
CB J:CYS10 3.1 94.9 1.0
CB J:CYS46 3.1 98.2 1.0
CA J:CYS46 3.2 97.4 1.0
C J:CYS45 3.2 95.8 1.0
CB J:CYS45 3.3 95.1 1.0
CB J:CYS7 3.4 95.0 1.0
SG J:CYS46 3.4 99.1 1.0
N J:CYS10 3.6 92.9 1.0
OG J:SER9 3.7 92.7 1.0
O J:CYS45 3.7 95.1 1.0
CA J:CYS45 3.9 95.6 1.0
CA J:CYS10 3.9 93.6 1.0
N J:GLY11 4.5 94.1 1.0
NE J:ARG43 4.5 99.1 1.0
CB J:SER9 4.7 91.8 1.0
N J:CYS45 4.7 96.8 1.0
C J:SER9 4.7 91.8 1.0
C J:CYS46 4.7 98.2 1.0
NH2 J:ARG43 4.8 98.8 1.0
C J:CYS10 4.8 93.6 1.0
CA J:CYS7 4.8 94.3 1.0

Zinc binding site 8 out of 8 in 3fki

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Zinc binding site 8 out of 8 in the 12-Subunit Rna Polymerase II Refined with Zn-Sad Data


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 Refined with Zn-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn71

b:0.0
occ:1.00
 SG L:CYS48 2.0 0.9 1.0
SG L:CYS34 2.5 0.1 1.0
SG L:CYS31 2.7 0.4 1.0
CB L:CYS48 3.3 0.5 1.0
O L:CYS34 3.5 0.9 1.0
SG L:CYS51 3.9 0.6 1.0
CB L:CYS34 4.0 0.7 1.0
CB L:CYS31 4.1 0.6 1.0
O L:LYS49 4.1 0.6 1.0
N L:LYS49 4.1 0.6 1.0
OG L:SER36 4.3 0.1 1.0
C L:CYS34 4.4 0.3 1.0
CA L:CYS48 4.5 0.8 1.0
C L:CYS48 4.6 1.0 1.0
CA L:CYS34 4.7 0.0 1.0
O L:CYS51 4.8 0.8 1.0
CA L:LYS49 4.8 0.7 1.0
C L:LYS49 4.9 0.5 1.0
CB L:LYS49 4.9 1.0 1.0

Reference:

P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, J.Fu. Structure of the 12-Subunit Rna Polymerase II Refined with the Aid of Anomalous Diffraction Data J.Biol.Chem. V. 284 12933 2009.
ISSN: ISSN 0021-9258
PubMed: 19289466
DOI: 10.1074/JBC.M809199200
Page generated: Thu Oct 24 13:17:25 2024

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