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Zinc in PDB 3m3y: Rna Polymerase II Elongation Complex C

Enzymatic activity of Rna Polymerase II Elongation Complex C

All present enzymatic activity of Rna Polymerase II Elongation Complex C:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex C, PDB code: 3m3y was solved by D.Wang, G.Zhu, X.Huang, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.481, 223.119, 193.806, 90.00, 101.47, 90.00
R / Rfree (%) 20.7 / 25.5

Other elements in 3m3y:

The structure of Rna Polymerase II Elongation Complex C also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Platinum (Pt) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex C (pdb code 3m3y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex C, PDB code: 3m3y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3m3y

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

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

b:0.4
occ:0.99
SG A:CYS110 2.5 0.3 1.0
SG A:CYS167 2.8 0.0 1.0
N A:CYS110 3.6 0.7 1.0
CB A:CYS110 3.6 1.0 1.0
SG A:CYS107 3.7 0.6 1.0
SG A:CYS148 3.9 0.5 1.0
CB A:CYS107 4.0 0.9 1.0
CA A:CYS110 4.0 0.5 1.0
CB A:CYS167 4.2 0.5 1.0
N A:CYS167 4.3 0.6 1.0
CB A:HIS109 4.3 0.5 1.0
N A:GLY111 4.4 0.5 1.0
ND2 A:ASN169 4.5 0.9 1.0
CA A:CYS167 4.6 0.2 1.0
C A:CYS110 4.6 0.9 1.0
O A:GLY168 4.7 0.5 1.0
C A:HIS109 4.7 0.9 1.0
O A:MET108 4.7 0.2 1.0
O A:CYS107 4.8 0.5 1.0
C A:CYS167 4.8 0.3 1.0
CA A:HIS109 4.9 0.5 1.0

Zinc binding site 2 out of 8 in 3m3y

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:92.3
occ:1.00
SG B:CYS1166 2.0 0.4 1.0
SG B:CYS1163 2.3 0.7 1.0
SG B:CYS1185 2.5 0.2 1.0
CB B:CYS1163 2.9 0.2 1.0
SG B:CYS1182 3.0 0.1 1.0
CB B:CYS1185 3.3 0.8 1.0
CB B:CYS1166 3.4 0.8 1.0
N B:CYS1166 3.5 0.9 1.0
CA B:CYS1166 4.0 0.8 1.0
CB B:CYS1182 4.2 0.5 1.0
CB B:ILE1165 4.3 0.6 1.0
CA B:CYS1163 4.4 1.0 1.0
C B:ILE1165 4.6 0.5 1.0
O B:GLY1184 4.6 0.7 1.0
N B:GLY1167 4.7 0.3 1.0
CA B:ILE1165 4.8 0.0 1.0
CA B:CYS1185 4.8 0.8 1.0
N B:ILE1165 4.8 0.4 1.0
C B:CYS1166 4.9 0.1 1.0
C B:CYS1163 4.9 0.9 1.0
CG1 B:ILE1165 5.0 0.4 1.0

Zinc binding site 3 out of 8 in 3m3y

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:83.8
occ:1.00
SG A:CYS67 1.9 0.0 1.0
SG A:CYS77 2.2 0.5 1.0
CE1 A:HIS80 2.4 0.6 1.0
NE2 A:HIS80 2.5 0.8 1.0
SG A:CYS70 2.8 0.9 1.0
CB A:CYS77 3.0 0.8 1.0
CB A:CYS67 3.1 1.0 1.0
ND1 A:HIS80 3.7 0.1 1.0
CA A:CYS77 3.7 0.4 1.0
CD2 A:HIS80 3.8 0.7 1.0
O A:CYS67 4.0 0.7 1.0
CB A:CYS70 4.2 0.6 1.0
CG A:GLN68 4.3 0.0 1.0
CA A:CYS67 4.4 0.4 1.0
CG A:HIS80 4.4 0.6 1.0
C A:CYS67 4.5 0.2 1.0
C A:CYS77 4.6 0.3 1.0
CD A:GLN68 4.6 0.4 1.0
CD A:PRO78 4.8 0.9 1.0
NE2 A:GLN68 4.9 0.1 1.0
N A:CYS77 4.9 0.2 1.0

Zinc binding site 4 out of 8 in 3m3y

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:74.5
occ:1.00
SG I:CYS7 2.1 0.8 1.0
SG I:CYS10 2.1 0.1 1.0
SG I:CYS29 2.3 0.4 1.0
SG I:CYS32 2.3 0.6 1.0
CB I:CYS10 2.8 0.5 1.0
CB I:CYS7 3.2 0.2 1.0
CB I:CYS29 3.3 0.5 1.0
CB I:CYS32 3.7 0.3 1.0
N I:CYS32 3.7 0.9 1.0
N I:CYS10 3.9 0.8 1.0
CA I:CYS10 3.9 0.8 1.0
CB I:THR31 4.2 0.1 1.0
CA I:CYS32 4.2 0.4 1.0
CB I:TYR34 4.3 0.8 1.0
C I:CYS32 4.6 0.4 1.0
CA I:CYS7 4.6 0.6 1.0
C I:THR31 4.6 0.8 1.0
O I:CYS32 4.7 0.3 1.0
O I:ARG8 4.7 0.3 1.0
OG1 I:THR31 4.7 0.4 1.0
CA I:CYS29 4.8 0.7 1.0
N I:THR31 4.8 0.7 1.0
CA I:THR31 4.8 0.7 1.0
C I:ASP9 4.9 0.7 1.0
C I:CYS10 4.9 0.1 1.0
CB I:ASP9 4.9 0.1 1.0

Zinc binding site 5 out of 8 in 3m3y

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:63.2
occ:1.00
SG C:CYS88 1.9 96.6 1.0
SG C:CYS92 2.1 99.1 1.0
SG C:CYS86 2.2 96.3 1.0
SG C:CYS95 2.5 90.0 1.0
N C:CYS92 3.2 96.5 1.0
CB C:CYS88 3.2 98.5 1.0
CB C:CYS92 3.2 0.7 1.0
CB C:CYS86 3.4 95.3 1.0
CB C:CYS95 3.5 88.2 1.0
CA C:CYS92 3.7 98.9 1.0
C C:HIS91 3.8 96.4 1.0
N C:CYS95 4.3 92.7 1.0
C C:CYS92 4.3 99.4 1.0
N C:CYS88 4.3 98.7 1.0
CA C:HIS91 4.3 93.9 1.0
CA C:CYS88 4.3 99.2 1.0
O C:CYS92 4.4 98.0 1.0
CA C:CYS95 4.5 88.9 1.0
O C:HIS91 4.5 98.3 1.0
CB C:LYS94 4.6 0.6 1.0
CA C:CYS86 4.7 95.8 1.0
C C:CYS86 4.8 96.0 1.0
O C:ASP90 4.9 92.7 1.0
C C:LYS94 4.9 96.0 1.0
N C:LYS94 4.9 0.6 1.0

Zinc binding site 6 out of 8 in 3m3y

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

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

b:59.9
occ:1.00
SG I:CYS106 1.9 0.2 1.0
SG I:CYS78 1.9 0.6 1.0
SG I:CYS103 2.3 0.0 1.0
SG I:CYS75 2.4 0.1 1.0
CB I:CYS78 2.4 0.8 1.0
CB I:CYS103 3.1 0.0 1.0
CB I:CYS75 3.2 0.5 1.0
N I:CYS78 3.6 0.7 1.0
CA I:CYS78 3.6 1.0 1.0
CB I:CYS106 3.6 0.7 1.0
N I:CYS106 3.7 0.5 1.0
CA I:CYS106 4.2 0.9 1.0
CB I:SER80 4.3 0.7 1.0
C I:CYS78 4.5 0.1 1.0
CA I:CYS103 4.5 98.1 1.0
N I:SER80 4.5 0.4 1.0
N I:HIS79 4.6 0.1 1.0
CB I:SER105 4.6 0.3 1.0
CA I:CYS75 4.6 0.3 1.0
C I:SER105 4.7 0.7 1.0
CB I:HIS108 4.7 0.1 1.0
C I:LYS77 4.8 0.9 1.0
N I:SER105 4.8 0.6 1.0
CA I:SER105 4.9 0.9 1.0
CA I:SER80 5.0 0.8 1.0

Zinc binding site 7 out of 8 in 3m3y

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

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

b:61.4
occ:1.00
SG J:CYS46 1.9 66.2 1.0
SG J:CYS45 2.2 67.6 1.0
SG J:CYS10 2.3 65.2 1.0
SG J:CYS7 2.4 64.9 1.0
N J:CYS46 2.7 63.5 1.0
CB J:CYS46 3.0 64.8 1.0
CA J:CYS46 3.2 63.6 1.0
CB J:CYS10 3.2 65.5 1.0
C J:CYS45 3.4 63.0 1.0
CB J:CYS45 3.5 63.3 1.0
CB J:CYS7 3.6 62.9 1.0
CA J:CYS45 4.0 63.1 1.0
N J:CYS10 4.0 63.7 1.0
CA J:CYS10 4.1 64.8 1.0
O J:CYS45 4.2 62.5 1.0
OG J:SER9 4.3 63.7 1.0
NE J:ARG43 4.3 71.8 1.0
CG J:ARG43 4.3 71.1 1.0
N J:CYS45 4.6 64.5 1.0
CD J:ARG43 4.6 71.1 1.0
C J:CYS46 4.7 64.1 1.0
O J:ARG43 4.7 70.5 1.0
N J:GLY11 4.7 65.4 1.0
C J:CYS10 4.8 66.0 1.0
CB J:LYS12 4.9 70.2 1.0

Zinc binding site 8 out of 8 in 3m3y

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:0.84
SG L:CYS51 1.9 0.6 1.0
CB L:CYS51 2.2 0.9 1.0
SG L:CYS34 2.7 0.9 0.7
SG L:CYS48 3.0 0.7 1.0
SG L:CYS31 3.1 0.6 1.0
CA L:CYS51 3.7 1.0 1.0
CB L:SER36 3.8 0.1 1.0
CB L:CYS34 4.2 0.1 1.0
CB L:CYS31 4.2 0.5 1.0
N L:CYS51 4.3 0.7 1.0
CB L:CYS48 4.5 0.7 1.0
OG L:SER36 4.5 0.1 1.0
C L:CYS51 4.5 0.8 1.0
N L:CYS34 4.6 0.7 1.0
N L:SER36 4.8 0.3 1.0
CA L:SER36 4.9 0.7 1.0
CA L:CYS34 5.0 0.9 1.0

Reference:

D.Wang, G.Zhu, X.Huang, S.J.Lippard. X-Ray Structure and Mechanism of Rna Polymerase II Stalled at An Antineoplastic Monofunctional Platinum-Dna Adduct. Proc.Natl.Acad.Sci.Usa V. 107 9584 2010.
ISSN: ISSN 0027-8424
PubMed: 20448203
DOI: 10.1073/PNAS.1002565107
Page generated: Wed Dec 16 04:34:07 2020

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