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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

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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

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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

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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

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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

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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

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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

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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

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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

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