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Zinc in PDB 2vum: Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex

Enzymatic activity of Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex

All present enzymatic activity of Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex, PDB code: 2vum was solved by F.Brueckner, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.619, 394.234, 283.966, 90.00, 90.00, 90.00
R / Rfree (%) 25.5 / 28.8

Other elements in 2vum:

The structure of Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2vum

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Zinc binding site 1 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:78.9
occ:1.00
 SG A:CYS148 2.6 0.1 1.0
CB A:CYS110 2.6 0.4 1.0
SG A:CYS110 2.9 0.8 1.0
SG A:CYS107 2.9 0.2 1.0
SG A:CYS167 3.1 0.9 1.0
O A:GLY166 3.5 0.2 1.0
CB A:CYS107 3.5 0.6 1.0
O A:CYS167 3.5 0.4 1.0
CB A:CYS148 3.6 0.2 1.0
O A:MET108 3.7 0.3 1.0
CA A:CYS110 4.0 0.6 1.0
N A:CYS110 4.3 0.3 1.0
N A:GLY111 4.4 0.2 1.0
C A:CYS167 4.6 0.2 1.0
CB A:CYS167 4.7 0.3 1.0
C A:GLY166 4.7 0.8 1.0
C A:CYS110 4.7 0.8 1.0
C A:CYS107 4.7 0.1 1.0
CA A:CYS107 4.8 0.9 1.0
C A:MET108 4.8 0.7 1.0
O A:CYS107 4.9 0.2 1.0
N A:MET108 5.0 0.3 1.0
CA A:CYS148 5.0 0.1 1.0

Zinc binding site 2 out of 8 in 2vum

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Zinc binding site 2 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:54.0
occ:1.00
 NE2 A:HIS80 2.3 68.0 1.0
SG A:CYS67 2.5 0.8 1.0
SG A:CYS77 2.7 72.8 1.0
CD2 A:HIS80 2.7 67.0 1.0
SG A:CYS70 2.9 0.3 1.0
CB A:CYS77 3.5 75.3 1.0
CE1 A:HIS80 3.6 68.7 1.0
CB A:CYS67 4.0 1.0 1.0
O A:CYS67 4.0 0.0 1.0
O A:CYS70 4.0 0.5 1.0
CG A:HIS80 4.1 67.4 1.0
CB A:CYS70 4.2 0.7 1.0
O A:PRO78 4.3 75.0 1.0
CA A:CYS77 4.4 75.1 1.0
ND1 A:HIS80 4.4 66.9 1.0
O A:GLN71 4.5 0.7 1.0
C A:CYS70 4.7 0.4 1.0
C A:CYS77 4.8 74.1 1.0
C A:CYS67 4.9 0.1 1.0

Zinc binding site 3 out of 8 in 2vum

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Zinc binding site 3 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:65.8
occ:1.00
 SG B:CYS1166 2.3 65.7 1.0
SG B:CYS1163 2.6 70.9 1.0
CB B:CYS1185 2.6 88.2 1.0
SG B:CYS1182 2.6 79.4 1.0
SG B:CYS1185 2.7 84.3 1.0
CB B:CYS1163 3.3 71.0 1.0
CB B:CYS1166 3.8 67.5 1.0
CB B:CYS1182 3.9 85.2 1.0
O B:CYS1166 4.0 71.0 1.0
N B:CYS1166 4.0 69.4 1.0
CA B:CYS1185 4.1 88.6 1.0
O B:CYS1182 4.3 90.9 1.0
CA B:CYS1166 4.4 68.4 1.0
C B:CYS1166 4.7 70.4 1.0
N B:CYS1185 4.7 89.8 1.0
CA B:CYS1163 4.8 69.6 1.0
C B:CYS1185 4.9 88.9 1.0
OG1 B:THR1170 4.9 64.3 1.0

Zinc binding site 4 out of 8 in 2vum

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Zinc binding site 4 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:67.9
occ:1.00
 SG C:CYS86 2.3 51.9 1.0
SG C:CYS92 2.4 74.3 1.0
SG C:CYS95 2.5 79.1 1.0
SG C:CYS88 2.5 74.8 1.0
CB C:CYS86 3.3 63.2 1.0
N C:CYS92 3.4 79.5 1.0
CB C:CYS92 3.4 78.6 1.0
CB C:CYS88 3.5 73.9 1.0
CB C:CYS95 3.6 75.2 1.0
C C:HIS91 3.7 79.5 1.0
CA C:CYS92 3.9 80.0 1.0
CA C:HIS91 4.1 79.3 1.0
N C:CYS95 4.1 74.5 1.0
O C:HIS91 4.2 79.8 1.0
O C:CYS92 4.3 82.2 1.0
C C:CYS92 4.3 81.9 1.0
CA C:CYS95 4.4 73.7 1.0
CA C:CYS88 4.6 74.0 1.0
N C:CYS88 4.6 70.5 1.0
C C:LYS94 4.6 75.2 1.0
CA C:CYS86 4.7 67.8 1.0
CB C:LYS94 4.8 76.7 1.0
O C:CYS88 4.8 78.3 1.0
N C:HIS91 4.9 81.4 1.0
C C:CYS86 5.0 70.0 1.0
N C:LYS94 5.0 77.5 1.0

Zinc binding site 5 out of 8 in 2vum

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Zinc binding site 5 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:96.2
occ:1.00
 SG I:CYS32 2.3 98.7 1.0
SG I:CYS10 2.5 0.7 1.0
SG I:CYS7 2.6 0.0 1.0
SG I:CYS29 2.8 0.8 1.0
CB I:CYS29 3.5 0.2 1.0
CB I:CYS32 3.7 0.8 1.0
CB I:CYS10 4.0 0.3 1.0
N I:CYS10 4.1 0.2 1.0
O I:ARG8 4.1 0.6 1.0
CB I:CYS7 4.1 0.0 1.0
CB I:TYR34 4.3 83.7 1.0
CA I:CYS10 4.4 0.3 1.0
N I:CYS32 4.5 0.5 1.0
C I:CYS10 4.5 0.5 1.0
O I:CYS10 4.6 0.7 1.0
CA I:CYS32 4.7 0.9 1.0
CB I:ASP9 4.8 0.1 1.0
CB I:ASN12 4.9 0.1 1.0
CB I:THR31 5.0 0.9 1.0
CA I:CYS29 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 2vum

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Zinc binding site 6 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.2
occ:1.00
 SG I:CYS106 2.6 0.2 1.0
SG I:CYS78 2.8 0.1 1.0
SG I:CYS75 2.9 0.9 1.0
CB I:CYS106 2.9 0.2 1.0
CB I:CYS78 3.2 0.1 1.0
CB I:CYS75 3.4 0.1 1.0
N I:CYS78 3.7 0.0 1.0
O I:SER105 3.8 0.3 1.0
CB I:CYS103 4.0 1.0 1.0
SG I:CYS103 4.0 0.8 1.0
CA I:CYS78 4.1 0.9 1.0
CB I:HIS108 4.3 0.3 1.0
CA I:CYS106 4.3 0.6 1.0
C I:SER105 4.4 0.6 1.0
N I:CYS106 4.6 0.9 1.0
CB I:LYS77 4.8 0.0 1.0
C I:LYS77 4.8 0.8 1.0
C I:CYS78 4.9 0.5 1.0
CA I:CYS75 4.9 0.6 1.0

Zinc binding site 7 out of 8 in 2vum

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Zinc binding site 7 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:72.2
occ:1.00
 SG J:CYS10 2.4 63.4 1.0
SG J:CYS7 2.4 79.8 1.0
SG J:CYS45 2.4 54.8 1.0
N J:CYS46 2.7 67.9 1.0
CB J:CYS46 2.7 72.5 1.0
CA J:CYS46 2.9 71.3 1.0
SG J:CYS46 3.1 77.8 1.0
CB J:CYS7 3.1 73.8 1.0
C J:CYS45 3.3 65.8 1.0
CB J:CYS10 3.6 60.3 1.0
CB J:CYS45 3.6 63.0 1.0
N J:CYS10 3.8 63.0 1.0
O J:CYS45 4.0 64.1 1.0
CA J:CYS45 4.0 65.5 1.0
CA J:CYS10 4.2 60.1 1.0
C J:CYS46 4.4 72.9 1.0
NE J:ARG43 4.5 83.9 1.0
CB J:SER9 4.5 63.7 1.0
NH2 J:ARG43 4.5 84.0 1.0
N J:GLY11 4.5 56.4 1.0
CA J:CYS7 4.6 72.2 1.0
CZ J:ARG43 4.7 84.0 1.0
O J:ARG43 4.8 77.9 1.0
N J:CYS45 4.8 68.8 1.0
C J:CYS10 4.8 57.4 1.0
C J:SER9 4.9 64.1 1.0
CE J:MET49 5.0 75.4 1.0
C J:CYS7 5.0 71.0 1.0

Zinc binding site 8 out of 8 in 2vum

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Zinc binding site 8 out of 8 in the Alpha-Amanitin Inhibited Complete 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 Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.9
occ:1.00
 SG L:CYS34 2.5 0.8 1.0
SG L:CYS48 2.6 0.4 1.0
CB L:CYS48 2.7 0.6 1.0
CB L:CYS51 3.1 0.9 1.0
SG L:CYS31 3.1 0.7 1.0
O L:CYS51 3.7 0.7 1.0
CB L:CYS31 3.7 0.6 1.0
SG L:CYS51 3.7 0.9 1.0
N L:CYS51 3.8 0.2 1.0
CA L:CYS51 3.9 0.8 1.0
CA L:CYS48 4.1 0.6 1.0
C L:CYS51 4.2 0.8 1.0
CB L:CYS34 4.3 0.2 1.0
C L:CYS48 4.5 0.2 1.0
C L:ASP50 4.6 0.4 1.0
O L:CYS34 4.6 0.5 1.0
N L:LYS49 4.7 0.9 1.0
N L:ASP50 4.9 0.3 1.0
N L:CYS48 4.9 0.6 1.0
OG L:SER36 5.0 0.5 1.0
CB L:ASP50 5.0 0.7 1.0

Reference:

F.Brueckner, P.Cramer. Structural Basis of Transcription Inhibition By Alpha-Amanitin and Implications For Rna Polymerase II Translocation. Nat.Struct.Mol.Biol. V. 15 811 2008.
ISSN: ISSN 1545-9993
PubMed: 18552824
DOI: 10.1038/NSMB.1458
Page generated: Thu Oct 17 04:34:14 2024

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