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Zinc in PDB 3cqz: Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin

Enzymatic activity of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin

All present enzymatic activity of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin, PDB code: 3cqz was solved by C.D.Kaplan, K.-M.Larsson, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.510, 222.480, 374.230, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin (pdb code 3cqz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin, PDB code: 3cqz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3cqz

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Zinc binding site 1 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:46.7
occ:1.00
 SG A:CYS110 2.2 40.4 1.0
SG A:CYS148 2.3 48.9 1.0
SG A:CYS107 2.5 45.2 1.0
SG A:CYS167 2.6 48.5 1.0
CB A:CYS167 3.0 47.9 1.0
CB A:CYS148 3.1 49.9 1.0
CB A:CYS110 3.2 41.2 1.0
CB A:CYS107 3.3 44.7 1.0
N A:CYS110 3.7 42.0 1.0
CA A:CYS110 3.9 41.2 1.0
CA A:GLY166 4.3 49.1 1.0
CA A:CYS167 4.4 48.1 1.0
CA A:CYS148 4.6 50.5 1.0
C A:CYS110 4.6 40.7 1.0
CA A:CYS107 4.7 44.6 1.0
N A:GLY111 4.8 40.2 1.0
C A:HIS109 4.8 42.7 1.0
CB A:HIS109 4.8 43.6 1.0
C A:GLY166 4.8 48.9 1.0
N A:CYS167 4.8 48.6 1.0
ND1 A:HIS109 4.9 47.9 1.0
CB A:LYS112 4.9 38.3 1.0
O A:CYS148 4.9 51.5 1.0
C A:CYS167 5.0 48.0 1.0

Zinc binding site 2 out of 8 in 3cqz

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Zinc binding site 2 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:77.4
occ:1.00
 NE2 A:HIS80 2.2 44.9 1.0
SG A:CYS70 2.4 60.3 1.0
SG A:CYS77 2.4 47.1 1.0
CB A:CYS70 2.8 60.7 1.0
SG A:CYS67 2.9 61.6 1.0
CD2 A:HIS80 3.1 44.6 1.0
CE1 A:HIS80 3.3 45.5 1.0
CB A:CYS77 3.6 47.6 1.0
CA A:CYS77 4.1 47.5 1.0
CD A:PRO78 4.1 46.3 1.0
CG A:HIS80 4.2 44.6 1.0
ND1 A:HIS80 4.3 45.0 1.0
CA A:CYS70 4.3 60.5 1.0
CB A:CYS67 4.4 62.4 1.0
CB A:THR69 4.4 61.9 1.0
O A:GLU72 4.5 57.8 1.0
N A:PRO78 4.6 46.4 1.0
C A:CYS77 4.6 46.9 1.0
CG2 A:THR69 4.6 61.8 1.0
N A:GLN71 4.7 59.4 1.0
N A:GLY79 4.7 46.0 1.0
N A:THR69 4.8 62.1 1.0
OG A:SER60 4.9 65.5 1.0

Zinc binding site 3 out of 8 in 3cqz

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Zinc binding site 3 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:60.6
occ:1.00
 SG B:CYS1186 2.2 51.8 1.0
SG B:CYS1183 2.3 55.7 1.0
SG B:CYS1163 2.4 38.3 1.0
SG B:CYS1166 2.6 37.4 1.0
CB B:CYS1186 2.9 52.8 1.0
CB B:CYS1163 2.9 37.6 1.0
CB B:CYS1183 3.5 56.1 1.0
CB B:CYS1166 3.8 37.6 1.0
OG1 B:THR1170 4.1 36.7 1.0
N B:CYS1166 4.1 37.2 1.0
CA B:CYS1186 4.3 52.6 1.0
CA B:CYS1163 4.4 37.4 1.0
CA B:CYS1166 4.5 37.6 1.0
CA B:GLY1185 4.7 53.9 1.0
N B:GLY1185 4.9 54.5 1.0
CA B:CYS1183 4.9 56.2 1.0
CB B:ASN1188 4.9 51.0 1.0
N B:CYS1186 5.0 53.3 1.0

Zinc binding site 4 out of 8 in 3cqz

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Zinc binding site 4 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:39.2
occ:1.00
 SG C:CYS88 2.2 19.9 1.0
SG C:CYS86 2.2 18.5 1.0
SG C:CYS92 2.3 22.5 1.0
SG C:CYS95 2.6 21.6 1.0
CB C:CYS88 3.1 20.4 1.0
N C:CYS92 3.2 21.0 1.0
CB C:CYS92 3.3 21.0 1.0
CB C:CYS86 3.3 18.9 1.0
CB C:CYS95 3.6 19.3 1.0
CA C:CYS92 3.7 21.1 1.0
C C:HIS91 4.0 21.1 1.0
N C:CYS95 4.0 19.5 1.0
O C:CYS92 4.0 20.5 1.0
C C:CYS92 4.1 20.6 1.0
CA C:CYS88 4.3 20.6 1.0
CB C:LYS94 4.3 19.8 1.0
N C:CYS88 4.3 20.4 1.0
CA C:HIS91 4.3 21.2 1.0
CA C:CYS95 4.4 19.1 1.0
N C:LYS94 4.5 19.8 1.0
CA C:CYS86 4.6 19.4 1.0
C C:LYS94 4.6 19.7 1.0
CA C:LYS94 4.7 19.9 1.0
O C:HIS91 4.8 20.9 1.0
C C:CYS86 4.9 19.4 1.0
C C:CYS88 5.0 21.0 1.0
O C:ASP90 5.0 22.4 1.0

Zinc binding site 5 out of 8 in 3cqz

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Zinc binding site 5 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:33.8
occ:1.00
 SG I:CYS10 1.9 17.5 1.0
SG I:CYS7 2.1 17.1 1.0
SG I:CYS29 2.3 18.1 1.0
SG I:CYS32 2.3 20.3 1.0
CB I:CYS29 3.1 17.1 1.0
CB I:CYS7 3.1 17.1 1.0
CB I:CYS32 3.4 17.2 1.0
CB I:CYS10 3.5 15.1 1.0
N I:CYS32 3.8 17.8 1.0
N I:CYS10 3.9 15.9 1.0
CB I:TYR34 4.1 13.0 1.0
CA I:CYS32 4.2 17.2 1.0
CA I:CYS10 4.3 15.2 1.0
C I:THR31 4.3 18.1 1.0
CB I:THR31 4.4 18.0 1.0
CA I:CYS7 4.5 16.9 1.0
CA I:CYS29 4.6 16.8 1.0
CB I:ASP9 4.7 15.8 1.0
N I:THR31 4.7 17.3 1.0
CG2 I:THR31 4.7 18.9 1.0
C I:CYS32 4.7 16.5 1.0
CA I:THR31 4.7 17.7 1.0
N I:TYR34 4.9 13.2 1.0
C I:ASP9 4.9 16.1 1.0

Zinc binding site 6 out of 8 in 3cqz

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Zinc binding site 6 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:46.1
occ:1.00
 SG I:CYS103 2.1 22.1 1.0
SG I:CYS106 2.3 24.2 1.0
SG I:CYS78 2.3 34.5 1.0
SG I:CYS75 2.4 31.1 1.0
CB I:CYS106 2.9 23.9 1.0
CB I:CYS103 3.1 20.3 1.0
CB I:CYS75 3.3 32.7 1.0
CB I:CYS78 3.4 34.0 1.0
N I:CYS78 3.8 34.4 1.0
N I:CYS106 3.9 24.6 1.0
CA I:CYS106 3.9 24.2 1.0
CA I:CYS78 4.2 34.1 1.0
CB I:HIS108 4.5 27.1 1.0
CA I:CYS103 4.5 20.4 1.0
CB I:LYS77 4.6 35.2 1.0
C I:CYS106 4.7 24.1 1.0
CA I:CYS75 4.7 32.8 1.0
C I:LYS77 4.8 34.6 1.0
C I:SER105 4.8 25.0 1.0
C I:CYS78 4.9 34.1 1.0
CB I:SER80 4.9 34.5 1.0
CB I:SER105 4.9 25.6 1.0
N I:SER107 4.9 24.3 1.0
N I:HIS108 4.9 26.0 1.0
C I:CYS103 4.9 20.7 1.0
O I:CYS103 4.9 21.2 1.0
N I:HIS79 5.0 34.2 1.0

Zinc binding site 7 out of 8 in 3cqz

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Zinc binding site 7 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:34.4
occ:1.00
 SG J:CYS7 2.1 20.0 1.0
SG J:CYS10 2.2 20.1 1.0
SG J:CYS45 2.2 29.9 1.0
SG J:CYS46 2.3 29.4 1.0
N J:CYS46 2.9 25.5 1.0
CB J:CYS7 3.3 20.4 1.0
CB J:CYS45 3.3 24.9 1.0
CA J:CYS46 3.4 26.0 1.0
CB J:CYS46 3.4 26.0 1.0
C J:CYS45 3.5 25.2 1.0
CB J:CYS10 3.7 20.6 1.0
CA J:CYS45 3.9 25.4 1.0
N J:CYS10 4.1 19.4 1.0
O J:CYS45 4.2 24.9 1.0
NE J:ARG43 4.4 25.2 1.0
CA J:CYS10 4.5 19.8 1.0
CB J:ARG43 4.7 25.1 1.0
N J:CYS45 4.7 24.8 1.0
CA J:CYS7 4.7 20.0 1.0
CB J:SER9 4.8 18.7 1.0
C J:SER9 4.9 19.0 1.0
O J:ARG43 4.9 25.3 1.0
C J:CYS46 4.9 25.5 1.0
CB J:LYS12 5.0 17.4 1.0
NH2 J:ARG43 5.0 22.7 1.0
N J:GLY11 5.0 18.7 1.0

Zinc binding site 8 out of 8 in 3cqz

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Zinc binding site 8 out of 8 in the Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of 10 Subunit Rna Polymerase II in Complex with the Inhibitor Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:73.0
occ:1.00
 SG L:CYS34 2.1 59.8 1.0
SG L:CYS48 2.3 65.0 1.0
SG L:CYS51 2.6 38.0 1.0
SG L:CYS31 2.6 57.5 1.0
CB L:CYS51 2.9 38.3 1.0
CB L:CYS48 3.3 65.8 1.0
O L:GLU33 3.4 61.1 1.0
CB L:CYS34 3.4 60.8 1.0
CB L:CYS31 3.7 57.5 1.0
C L:GLU33 4.3 61.0 1.0
CA L:CYS51 4.3 38.1 1.0
CB L:HIS53 4.4 40.6 1.0
CA L:CYS34 4.5 61.1 1.0
CB L:SER36 4.5 64.5 1.0
CA L:CYS48 4.7 65.9 1.0
C L:CYS34 4.8 61.6 1.0
N L:HIS53 4.8 39.9 1.0
N L:GLY52 4.8 38.5 1.0
N L:CYS34 4.8 61.2 1.0
C L:CYS51 4.9 38.2 1.0
N L:SER36 5.0 63.8 1.0

Reference:

C.D.Kaplan, K.M.Larsson, R.D.Kornberg. The Rna Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted By Alpha-Amanitin. Mol.Cell V. 30 547 2008.
ISSN: ISSN 1097-2765
PubMed: 18538653
DOI: 10.1016/J.MOLCEL.2008.04.023
Page generated: Thu Oct 24 11:56:11 2024

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