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Zinc in PDB 3m4o: Rna Polymerase II Elongation Complex B

Enzymatic activity of Rna Polymerase II Elongation Complex B

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex B, PDB code: 3m4o 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 / 3.57
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.114, 222.131, 191.782, 90.00, 100.99, 90.00
R / Rfree (%) 24.1 / 29.2

Other elements in 3m4o:

The structure of Rna Polymerase II Elongation Complex B 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 B (pdb code 3m4o). 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 B, PDB code: 3m4o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:90.1
occ:0.76
 SG A:CYS148 2.9 0.7 1.0
SG A:CYS110 3.1 0.8 1.0
N A:CYS167 3.5 0.3 1.0
CA A:GLY166 3.6 0.2 1.0
C A:GLY166 4.0 0.9 1.0
SG A:CYS167 4.2 0.6 1.0
N A:GLY166 4.2 0.1 1.0
CB A:CYS110 4.2 0.7 1.0
O A:MET108 4.5 0.9 1.0
CB A:CYS148 4.6 0.2 1.0
CA A:CYS167 4.6 0.7 1.0
CB A:CYS167 4.8 0.4 1.0
CB A:LYS112 4.9 0.9 1.0
O A:CYS167 4.9 0.6 1.0
N A:GLY111 5.0 0.3 1.0
CB A:CYS107 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.1
occ:0.84
 SG A:CYS77 1.9 0.5 1.0
CE1 A:HIS80 2.3 0.3 1.0
SG A:CYS70 2.5 0.6 1.0
SG A:CYS67 2.6 0.9 1.0
CB A:CYS67 2.9 0.8 1.0
ND1 A:HIS80 3.0 0.5 1.0
NE2 A:HIS80 3.0 0.8 1.0
CB A:CYS77 3.2 0.1 1.0
O A:CYS67 3.3 0.2 1.0
CB A:CYS70 3.5 0.8 1.0
CD2 A:HIS80 4.0 0.9 1.0
CG A:HIS80 4.0 0.2 1.0
CA A:CYS67 4.0 0.3 1.0
C A:CYS67 4.0 0.4 1.0
CA A:CYS77 4.0 0.5 1.0
NE2 A:GLN68 4.4 0.6 1.0
CD A:PRO78 4.5 0.8 1.0
C A:CYS77 4.8 0.4 1.0
O A:PRO78 4.8 0.2 1.0
CA A:CYS70 4.8 0.6 1.0
N A:PRO78 4.9 1.0 1.0

Zinc binding site 3 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:95.1
occ:0.85
 SG B:CYS1166 2.1 0.1 1.0
SG B:CYS1163 2.3 0.9 1.0
SG B:CYS1185 2.6 0.8 1.0
CB B:CYS1166 3.0 0.2 1.0
CB B:CYS1163 3.1 0.7 1.0
CB B:CYS1185 3.2 0.6 1.0
N B:CYS1166 3.4 0.5 1.0
SG B:CYS1182 3.4 0.3 1.0
CA B:CYS1166 3.8 0.0 1.0
CB B:ILE1165 4.0 0.2 1.0
CB B:CYS1182 4.2 0.9 1.0
C B:ILE1165 4.3 0.5 1.0
N B:GLY1167 4.4 0.8 1.0
CA B:CYS1163 4.6 0.6 1.0
CA B:ILE1165 4.6 0.8 1.0
C B:CYS1166 4.6 0.4 1.0
CG2 B:ILE1165 4.7 0.7 1.0
CA B:CYS1185 4.7 0.0 1.0
O B:CYS1163 4.7 0.6 1.0
N B:ILE1165 4.8 0.8 1.0
CG1 B:ILE1165 4.8 1.0 1.0
C B:CYS1163 4.9 0.0 1.0
OE2 A:GLU26 4.9 0.6 1.0

Zinc binding site 4 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:83.1
occ:0.94
 SG C:CYS95 2.0 99.5 1.0
SG C:CYS88 2.1 0.8 1.0
SG C:CYS86 2.6 0.3 1.0
SG C:CYS92 2.9 0.7 1.0
CB C:CYS92 3.1 0.8 1.0
N C:CYS92 3.1 0.4 1.0
CB C:CYS88 3.4 0.7 1.0
CA C:CYS92 3.6 0.7 1.0
CB C:CYS86 3.6 0.8 1.0
CB C:CYS95 3.6 0.4 1.0
C C:HIS91 3.7 0.5 1.0
O C:ASP90 4.1 0.3 1.0
N C:CYS95 4.2 0.3 1.0
CA C:HIS91 4.2 0.0 1.0
C C:CYS92 4.2 0.2 1.0
O C:HIS91 4.2 0.8 1.0
CA C:CYS95 4.5 0.5 1.0
N C:CYS88 4.5 0.9 1.0
CA C:CYS88 4.6 0.0 1.0
O C:CYS92 4.6 1.0 1.0
CB C:LYS94 4.7 0.6 1.0
N C:ASP93 4.9 0.1 1.0
N C:LYS94 4.9 0.0 1.0
CA C:CYS86 5.0 0.6 1.0

Zinc binding site 5 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:82.0
occ:0.93
 SG I:CYS10 2.0 0.7 1.0
SG I:CYS29 2.2 0.4 1.0
CB I:CYS10 2.2 0.1 1.0
N I:CYS32 2.6 0.2 1.0
SG I:CYS32 2.7 0.7 1.0
CB I:THR31 3.1 0.8 1.0
CB I:CYS32 3.2 0.2 1.0
C I:THR31 3.4 0.0 1.0
CA I:CYS32 3.4 0.4 1.0
CA I:THR31 3.5 0.9 1.0
N I:THR31 3.7 0.1 1.0
CA I:CYS10 3.7 0.9 1.0
CG2 I:THR31 3.8 0.1 1.0
CB I:CYS29 3.8 0.2 1.0
OG1 I:THR31 4.1 0.8 1.0
SG I:CYS7 4.2 0.3 1.0
C I:CYS32 4.2 0.2 1.0
N I:CYS10 4.2 0.3 1.0
O I:THR31 4.4 0.4 1.0
O I:CYS29 4.5 0.5 1.0
C I:CYS29 4.5 0.8 1.0
O I:CYS32 4.6 0.0 1.0
C I:CYS10 4.8 0.8 1.0
CA I:CYS29 4.8 0.8 1.0
N I:SER33 4.9 0.6 1.0
CB I:CYS7 4.9 0.4 1.0
C I:ARG30 4.9 0.8 1.0
N I:ARG30 5.0 0.8 1.0

Zinc binding site 6 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:81.4
occ:0.87
 SG I:CYS106 1.8 0.7 1.0
SG I:CYS75 2.1 0.3 1.0
SG I:CYS78 2.2 0.7 1.0
CB I:CYS78 2.4 0.1 1.0
SG I:CYS103 2.6 0.1 1.0
N I:CYS78 3.1 0.4 1.0
CA I:CYS78 3.3 0.8 1.0
CB I:CYS103 3.4 1.0 1.0
CB I:CYS106 3.6 0.2 1.0
CB I:CYS75 3.6 0.6 1.0
N I:CYS106 3.9 0.3 1.0
CA I:CYS106 4.3 0.3 1.0
C I:LYS77 4.3 0.9 1.0
C I:CYS78 4.3 0.9 1.0
CB I:LYS77 4.4 0.2 1.0
N I:HIS79 4.5 0.4 1.0
CB I:HIS108 4.6 0.4 1.0
O I:CYS75 4.6 0.8 1.0
OG I:SER80 4.7 0.3 1.0
CA I:CYS75 4.8 0.4 1.0
CA I:LYS77 4.8 0.9 1.0
CA I:CYS103 4.8 0.6 1.0
CD2 I:HIS108 4.8 0.2 1.0
CB I:SER105 4.9 0.5 1.0
C I:CYS75 4.9 0.2 1.0
C I:SER105 4.9 0.7 1.0
N I:LYS77 4.9 0.2 1.0
C I:CYS106 5.0 0.6 1.0
N I:SER80 5.0 0.8 1.0
O I:SER80 5.0 0.5 1.0

Zinc binding site 7 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:87.7
occ:0.88
 SG J:CYS45 2.0 79.6 1.0
SG J:CYS46 2.1 78.9 1.0
N J:CYS46 2.4 75.3 1.0
SG J:CYS10 2.5 77.7 1.0
CB J:CYS46 2.6 77.1 1.0
CA J:CYS46 2.6 76.1 1.0
CB J:CYS10 2.7 74.3 1.0
C J:CYS45 3.1 73.8 1.0
CG J:ARG43 3.2 79.2 1.0
SG J:CYS7 3.2 67.8 1.0
CB J:CYS45 3.5 73.7 1.0
CD J:ARG43 3.5 77.7 1.0
O J:CYS45 3.7 72.5 1.0
CA J:CYS45 3.8 73.5 1.0
CA J:CYS10 3.8 73.0 1.0
N J:CYS10 3.9 71.0 1.0
CB J:CYS7 4.0 71.0 1.0
C J:CYS46 4.1 76.2 1.0
N J:CYS45 4.2 73.4 1.0
CB J:ARG43 4.4 80.5 1.0
CD1 B:ILE1006 4.5 64.4 1.0
OG J:SER9 4.7 67.5 1.0
C J:CYS10 4.7 73.7 1.0
N J:ARG47 4.7 74.7 1.0
O J:ARG43 4.9 80.0 1.0
N J:GLY11 4.9 73.5 1.0
NE J:ARG43 4.9 78.2 1.0
O J:CYS46 5.0 77.8 1.0

Zinc binding site 8 out of 8 in 3m4o

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


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.8
occ:0.67
 SG L:CYS51 2.0 0.3 1.0
SG L:CYS34 2.5 0.4 1.0
SG L:CYS48 2.7 0.3 1.0
CB L:CYS51 3.2 0.8 1.0
CB L:CYS31 3.2 0.8 1.0
SG L:CYS31 3.6 0.5 1.0
CB L:CYS34 3.7 0.8 1.0
CB L:SER36 3.9 0.8 1.0
CB L:CYS48 3.9 0.5 1.0
N L:CYS34 3.9 0.1 1.0
CA L:CYS34 4.3 0.3 1.0
N L:SER36 4.4 0.7 1.0
N L:SER35 4.4 0.7 1.0
CA L:CYS31 4.6 0.7 1.0
CA L:CYS51 4.6 0.7 1.0
C L:CYS34 4.6 0.2 1.0
CA L:SER36 4.8 0.5 1.0
OG L:SER36 4.9 0.2 1.0
C L:CYS31 4.9 0.1 1.0
C L:CYS51 5.0 0.7 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: Sat Oct 26 09:06:46 2024

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