Atomistry » Zinc » PDB 3m1k-3m6o » 3m3y
Atomistry »
  Zinc »
    PDB 3m1k-3m6o »
      3m3y »

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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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

Go back to Zinc Binding Sites List in 3m3y
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: Sat Oct 26 09:05:16 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy