Atomistry » Zinc » PDB 3gjn-3gtp » 3gtl
Atomistry »
  Zinc »
    PDB 3gjn-3gtp »
      3gtl »

Zinc in PDB 3gtl: Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch

Enzymatic activity of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch

All present enzymatic activity of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch:
2.7.7.6;

Protein crystallography data

The structure of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch, PDB code: 3gtl was solved by D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.531, 222.282, 194.813, 90.00, 102.19, 90.00
R / Rfree (%) 27 / 32.2

Other elements in 3gtl:

The structure of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch (pdb code 3gtl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch, PDB code: 3gtl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 1 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.7
occ:1.00
 SG A:CYS148 3.0 0.5 1.0
CB A:CYS110 3.1 0.4 1.0
O A:MET108 3.5 0.3 1.0
O A:CYS167 3.6 0.5 1.0
SG A:CYS110 3.7 0.2 1.0
CB A:CYS107 4.1 0.9 1.0
CB A:CYS148 4.2 0.9 1.0
SG A:CYS167 4.3 0.9 1.0
CA A:CYS110 4.4 0.5 1.0
N A:GLY111 4.5 0.6 1.0
SG A:CYS107 4.5 0.5 1.0
C A:CYS167 4.7 0.5 1.0
C A:MET108 4.7 0.3 1.0
N A:CYS110 4.7 0.3 1.0
C A:CYS107 4.7 0.6 1.0
O A:CYS107 4.8 0.6 1.0
N A:MET108 4.8 0.3 1.0
ND2 A:ASN169 4.9 0.1 1.0
CA A:CYS107 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 2 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.1
occ:1.00
 SG A:CYS77 1.8 1.0 1.0
SG A:CYS70 2.4 0.9 1.0
SG A:CYS67 2.5 0.8 1.0
CB A:CYS67 2.6 0.5 1.0
CE1 A:HIS80 2.7 0.3 1.0
CB A:CYS77 2.8 0.1 1.0
ND1 A:HIS80 3.3 0.4 1.0
CA A:CYS77 3.6 0.8 1.0
NE2 A:HIS80 3.8 0.2 1.0
O A:CYS67 3.9 0.2 1.0
CA A:CYS67 4.0 0.9 1.0
CB A:CYS70 4.1 0.9 1.0
C A:CYS67 4.4 0.2 1.0
C A:CYS77 4.5 0.1 1.0
CG A:HIS80 4.5 0.2 1.0
N A:CYS77 4.6 0.5 1.0
N A:GLY79 4.7 0.1 1.0
CD A:PRO78 4.7 0.3 1.0
CD2 A:HIS80 4.8 0.2 1.0
N A:PRO78 4.8 0.3 1.0
CA A:GLY79 4.9 0.1 1.0
O A:GLN71 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 3 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.0
occ:1.00
 SG B:CYS1185 2.4 0.2 1.0
SG B:CYS1166 2.5 0.3 1.0
SG B:CYS1182 2.6 0.3 1.0
SG B:CYS1163 2.7 0.7 1.0
CB B:CYS1166 2.8 0.8 1.0
CB B:CYS1163 3.1 0.2 1.0
CB B:CYS1185 3.1 0.4 1.0
O B:CYS1166 3.4 0.1 1.0
N B:CYS1166 3.4 0.1 1.0
CA B:CYS1166 3.6 0.6 1.0
C B:CYS1166 3.9 0.1 1.0
CB B:CYS1182 4.1 0.5 1.0
OG1 B:THR1170 4.4 0.9 1.0
C B:ILE1165 4.5 0.7 1.0
CA B:CYS1163 4.5 0.2 1.0
CA B:CYS1185 4.6 0.5 1.0
CB B:THR1170 4.7 0.6 1.0
CB B:ILE1165 4.7 0.6 1.0
N B:CYS1185 4.9 0.6 1.0
CA B:ILE1165 5.0 0.7 1.0

Zinc binding site 4 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 4 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:59.3
occ:1.00
 SG C:CYS92 2.1 75.3 1.0
SG C:CYS86 2.1 72.4 1.0
SG C:CYS88 2.4 74.5 1.0
SG C:CYS95 2.7 67.1 1.0
CB C:CYS86 3.3 72.8 1.0
N C:CYS92 3.3 75.0 1.0
CB C:CYS92 3.3 75.0 1.0
CB C:CYS95 3.4 66.1 1.0
CB C:CYS88 3.4 72.5 1.0
CA C:CYS92 3.8 74.9 1.0
N C:CYS95 3.9 67.8 1.0
C C:HIS91 4.1 75.3 1.0
O C:ASP90 4.1 75.9 1.0
O C:CYS92 4.1 74.8 1.0
N C:CYS88 4.2 71.8 1.0
CA C:CYS88 4.3 72.4 1.0
CA C:CYS95 4.3 66.4 1.0
C C:CYS92 4.4 74.7 1.0
CA C:HIS91 4.5 75.2 1.0
O C:CYS88 4.6 73.2 1.0
CA C:CYS86 4.6 72.8 1.0
C C:CYS86 4.7 72.6 1.0
C C:LYS94 4.7 69.5 1.0
C C:CYS88 4.7 72.9 1.0
CB C:LYS94 4.7 70.2 1.0
O C:CYS86 4.8 72.5 1.0
O C:HIS91 4.9 75.7 1.0

Zinc binding site 5 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 5 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:98.6
occ:1.00
 SG I:CYS10 1.6 0.6 1.0
SG I:CYS29 2.3 0.6 1.0
CB I:CYS10 2.7 0.2 1.0
SG I:CYS32 2.8 0.1 1.0
SG I:CYS7 2.9 0.7 1.0
CB I:CYS29 3.1 0.3 1.0
CB I:THR31 3.4 0.0 1.0
N I:CYS32 3.6 0.2 1.0
CG2 I:THR31 4.0 0.9 1.0
CB I:CYS32 4.0 0.8 1.0
CA I:CYS10 4.1 0.4 1.0
CB I:CYS7 4.1 0.5 1.0
N I:THR31 4.1 0.8 1.0
CA I:THR31 4.1 0.9 1.0
C I:THR31 4.2 0.7 1.0
N I:CYS10 4.3 0.9 1.0
CA I:CYS32 4.4 0.7 1.0
OG1 I:THR31 4.4 0.4 1.0
CA I:CYS29 4.5 0.1 1.0
CB I:TYR34 4.5 0.3 1.0
N I:ASN11 4.6 0.8 1.0
O I:ARG8 4.8 0.7 1.0
C I:CYS29 4.9 0.2 1.0
C I:CYS10 4.9 0.1 1.0
N I:ARG30 4.9 0.2 1.0
N I:TYR34 5.0 0.6 1.0

Zinc binding site 6 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 6 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.4
occ:1.00
 SG I:CYS106 1.8 91.8 1.0
CB I:CYS78 1.9 93.5 1.0
SG I:CYS78 2.0 93.1 1.0
SG I:CYS75 2.2 97.4 1.0
SG I:CYS103 2.7 81.2 1.0
CA I:CYS78 3.2 93.7 1.0
N I:CYS78 3.3 94.6 1.0
CB I:CYS103 3.4 81.9 1.0
CB I:CYS106 3.6 90.4 1.0
CB I:CYS75 3.6 97.1 1.0
N I:CYS106 4.0 89.2 1.0
C I:CYS78 4.2 93.3 1.0
N I:HIS79 4.2 92.7 1.0
CA I:CYS106 4.4 90.2 1.0
OG I:SER80 4.5 89.6 1.0
C I:LYS77 4.6 95.3 1.0
CB I:HIS108 4.6 91.8 1.0
CB I:SER105 4.7 87.5 1.0
CA I:CYS75 4.7 97.0 1.0
C I:SER105 4.8 88.4 1.0
CD2 I:HIS108 4.8 90.7 1.0
O I:CYS75 4.8 96.9 1.0
CA I:CYS103 4.9 82.0 1.0
N I:SER80 4.9 90.6 1.0
O I:SER80 5.0 88.4 1.0
CB I:LYS77 5.0 95.6 1.0
N I:SER105 5.0 86.8 1.0

Zinc binding site 7 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 7 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:66.7
occ:1.00
 SG J:CYS46 1.9 44.4 1.0
SG J:CYS45 2.1 49.2 1.0
N J:CYS46 2.3 49.6 1.0
CB J:CYS46 2.3 48.2 1.0
SG J:CYS10 2.4 35.9 1.0
CA J:CYS46 2.6 48.8 1.0
CB J:CYS10 2.7 37.7 1.0
C J:CYS45 3.2 50.3 1.0
CB J:CYS45 3.4 50.8 1.0
SG J:CYS7 3.4 19.9 1.0
CA J:CYS10 3.7 37.3 1.0
N J:CYS10 3.7 34.5 1.0
CA J:CYS45 3.8 50.7 1.0
O J:ARG43 3.9 61.3 1.0
CB J:CYS7 4.0 29.4 1.0
O J:CYS45 4.0 50.4 1.0
CB J:ARG43 4.1 62.8 1.0
C J:CYS46 4.2 49.0 1.0
CG J:ARG43 4.2 63.5 1.0
OG J:SER9 4.2 30.5 1.0
N J:CYS45 4.3 52.2 1.0
CD J:ARG43 4.6 64.8 1.0
C J:ARG43 4.6 61.3 1.0
N J:ARG47 4.7 48.6 1.0
C J:CYS10 4.7 38.8 1.0
C J:SER9 4.8 33.0 1.0
N J:GLY11 4.9 40.9 1.0
CB J:SER9 4.9 31.9 1.0

Zinc binding site 8 out of 8 in 3gtl

Go back to Zinc Binding Sites List in 3gtl
Zinc binding site 8 out of 8 in the Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Backtracked Rna Polymerase II Complex with 13MER with G<>U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.2
occ:1.00
 SG L:CYS51 1.8 0.2 1.0
CB L:CYS51 2.3 0.5 1.0
SG L:CYS34 2.7 0.6 1.0
SG L:CYS31 3.0 0.7 1.0
SG L:CYS48 3.4 0.8 1.0
CA L:CYS51 3.8 0.1 1.0
CB L:CYS34 3.9 0.6 1.0
C L:CYS51 4.3 1.0 1.0
N L:CYS34 4.3 0.3 1.0
CB L:CYS31 4.4 0.3 1.0
O L:CYS51 4.6 0.9 1.0
CB L:CYS48 4.7 0.8 1.0
CA L:CYS34 4.7 0.6 1.0
N L:CYS51 4.8 0.1 1.0
N L:GLY52 4.9 0.6 1.0

Reference:

D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, R.D.Kornberg. Structural Basis of Transcription: Backtracked Rna Polymerase II at 3.4 Angstrom Resolution. Science V. 324 1203 2009.
ISSN: ISSN 0036-8075
PubMed: 19478184
DOI: 10.1126/SCIENCE.1168729
Page generated: Thu Oct 24 13:55:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy