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Zinc in PDB 3gtp: Backtracked Rna Polymerase II Complex with 24MER Rna

Enzymatic activity of Backtracked Rna Polymerase II Complex with 24MER Rna

All present enzymatic activity of Backtracked Rna Polymerase II Complex with 24MER Rna:
2.7.7.6;

Protein crystallography data

The structure of Backtracked Rna Polymerase II Complex with 24MER Rna, PDB code: 3gtp 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 / 3.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.778, 222.113, 194.854, 90.00, 102.06, 90.00
R / Rfree (%) 26.6 / 29.9

Other elements in 3gtp:

The structure of Backtracked Rna Polymerase II Complex with 24MER Rna 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 24MER Rna (pdb code 3gtp). 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 24MER Rna, PDB code: 3gtp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3gtp

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Zinc binding site 1 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.7
occ:1.00
 SG A:CYS110 2.6 0.1 1.0
SG A:CYS148 3.0 0.3 1.0
SG A:CYS107 3.1 0.3 1.0
CB A:CYS110 3.1 0.2 1.0
SG A:CYS167 3.8 1.0 1.0
O A:MET108 3.8 0.4 1.0
N A:GLY111 4.2 0.0 1.0
CA A:CYS110 4.3 0.2 1.0
N A:CYS167 4.3 0.1 1.0
CB A:CYS107 4.3 0.3 1.0
O A:CYS167 4.3 0.5 1.0
N A:CYS110 4.4 0.7 1.0
CB A:CYS148 4.5 0.5 1.0
C A:CYS110 4.7 0.6 1.0
CA A:GLY166 4.7 0.7 1.0
C A:CYS167 4.9 0.6 1.0
C A:GLY166 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 3gtp

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Zinc binding site 2 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.8
occ:1.00
 SG A:CYS77 1.9 0.3 1.0
SG A:CYS70 2.3 0.2 1.0
CE1 A:HIS80 2.5 0.6 1.0
CB A:CYS67 2.6 0.9 1.0
SG A:CYS67 2.8 0.8 1.0
CB A:CYS77 3.1 0.3 1.0
ND1 A:HIS80 3.3 0.6 1.0
NE2 A:HIS80 3.6 0.4 1.0
CA A:CYS77 3.8 0.9 1.0
O A:CYS67 3.8 0.0 1.0
CB A:CYS70 3.9 0.9 1.0
CA A:CYS67 4.0 0.6 1.0
C A:CYS67 4.4 0.1 1.0
CG A:HIS80 4.5 0.4 1.0
O A:GLN71 4.7 0.8 1.0
CD2 A:HIS80 4.7 0.5 1.0
C A:CYS77 4.7 0.3 1.0
CD A:PRO78 4.8 0.8 1.0
N A:CYS77 4.8 0.3 1.0

Zinc binding site 3 out of 8 in 3gtp

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Zinc binding site 3 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.1
occ:1.00
 SG B:CYS1166 1.8 0.6 1.0
SG B:CYS1182 2.4 0.5 1.0
SG B:CYS1163 2.5 0.2 1.0
CB B:CYS1163 3.0 0.9 1.0
SG B:CYS1185 3.0 0.3 1.0
CB B:CYS1166 3.1 0.1 1.0
CB B:CYS1185 3.2 0.0 1.0
O B:CYS1166 3.3 0.1 1.0
CB B:CYS1182 3.8 0.2 1.0
N B:CYS1166 3.8 0.8 1.0
CA B:CYS1166 3.9 0.9 1.0
C B:CYS1166 4.0 0.3 1.0
CA B:CYS1163 4.5 0.8 1.0
CA B:CYS1185 4.6 0.1 1.0
O B:CYS1182 4.7 0.5 1.0
C B:ILE1165 4.8 0.7 1.0
CB B:THR1170 4.9 0.6 1.0
OG1 B:THR1170 4.9 0.8 1.0
CB B:ILE1165 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 3gtp

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Zinc binding site 4 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.2
occ:1.00
 SG C:CYS86 2.1 0.4 1.0
SG C:CYS88 2.1 0.7 1.0
SG C:CYS92 2.3 0.1 1.0
SG C:CYS95 2.4 0.8 1.0
CB C:CYS92 3.2 0.5 1.0
CB C:CYS95 3.4 0.5 1.0
CB C:CYS88 3.4 0.6 1.0
CB C:CYS86 3.4 0.6 1.0
N C:CYS92 3.4 0.6 1.0
CA C:CYS92 3.8 0.5 1.0
C C:HIS91 3.9 0.6 1.0
N C:CYS95 4.2 0.0 1.0
O C:ASP90 4.2 0.5 1.0
N C:CYS88 4.2 0.1 1.0
CA C:HIS91 4.3 0.1 1.0
CA C:CYS88 4.3 0.7 1.0
CA C:CYS95 4.4 0.3 1.0
C C:CYS92 4.5 0.8 1.0
O C:CYS92 4.5 0.9 1.0
O C:CYS86 4.5 0.4 1.0
O C:HIS91 4.5 0.8 1.0
C C:CYS86 4.6 0.2 1.0
O C:CYS88 4.6 0.2 1.0
CA C:CYS86 4.6 0.6 1.0
C C:LYS94 4.8 1.0 1.0
CB C:LYS94 4.8 0.4 1.0
C C:CYS88 4.8 0.1 1.0

Zinc binding site 5 out of 8 in 3gtp

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Zinc binding site 5 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.6
occ:1.00
 SG I:CYS10 1.8 0.8 1.0
CB I:CYS10 1.9 0.1 1.0
SG I:CYS29 1.9 0.6 1.0
SG I:CYS32 2.7 0.9 1.0
CB I:THR31 2.9 0.3 1.0
N I:CYS32 3.0 0.4 1.0
CG2 I:THR31 3.3 0.1 1.0
CA I:CYS10 3.4 0.3 1.0
CB I:CYS29 3.4 0.8 1.0
CA I:THR31 3.6 0.3 1.0
CB I:CYS32 3.6 0.6 1.0
N I:THR31 3.7 0.3 1.0
SG I:CYS7 3.7 0.2 1.0
C I:THR31 3.7 0.5 1.0
CA I:CYS32 3.9 0.4 1.0
OG1 I:THR31 4.0 0.3 1.0
N I:CYS10 4.0 0.8 1.0
C I:CYS10 4.4 0.4 1.0
CA I:CYS29 4.7 0.6 1.0
C I:CYS32 4.7 0.1 1.0
CB I:CYS7 4.8 0.6 1.0
N I:ARG30 4.8 1.0 1.0
O I:CYS10 4.8 0.3 1.0
C I:ASP9 4.9 0.3 1.0
O I:THR31 4.9 0.6 1.0
C I:CYS29 4.9 0.3 1.0
C I:ARG30 5.0 0.3 1.0
CB I:TYR34 5.0 0.7 1.0

Zinc binding site 6 out of 8 in 3gtp

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Zinc binding site 6 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.3
occ:1.00
 SG I:CYS106 1.9 0.7 1.0
CB I:CYS78 2.1 1.0 1.0
SG I:CYS78 2.3 0.5 1.0
SG I:CYS103 2.5 0.4 1.0
SG I:CYS75 2.8 0.5 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS75 3.1 0.6 1.0
CA I:CYS78 3.5 1.0 1.0
CB I:CYS106 3.7 0.7 1.0
CD2 I:HIS108 3.7 0.2 1.0
N I:CYS78 3.8 0.7 1.0
CB I:HIS108 3.9 0.8 1.0
CG I:HIS108 4.2 0.2 1.0
N I:CYS106 4.4 0.8 1.0
C I:CYS78 4.5 0.5 1.0
CA I:CYS106 4.5 0.2 1.0
CA I:CYS103 4.5 0.2 1.0
CA I:CYS75 4.6 0.4 1.0
O I:CYS106 4.7 0.0 1.0
N I:HIS79 4.7 0.9 1.0
C I:CYS106 4.8 0.1 1.0
CB I:LYS77 4.9 0.0 1.0
C I:LYS77 4.9 0.4 1.0
NE2 I:HIS108 5.0 0.5 1.0

Zinc binding site 7 out of 8 in 3gtp

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Zinc binding site 7 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.7
occ:1.00
 SG J:CYS45 1.8 98.5 1.0
SG J:CYS46 1.8 97.3 1.0
SG J:CYS10 2.2 95.6 1.0
CB J:CYS10 2.5 93.2 1.0
CB J:CYS46 2.6 98.5 1.0
N J:CYS46 2.6 98.8 1.0
CA J:CYS46 3.0 98.5 1.0
SG J:CYS7 3.4 89.0 1.0
CB J:CYS45 3.5 98.8 1.0
C J:CYS45 3.5 99.0 1.0
CA J:CYS10 3.6 92.8 1.0
N J:CYS10 3.6 91.8 1.0
CD J:ARG43 3.7 0.3 1.0
CG J:ARG43 3.8 0.1 1.0
CA J:CYS45 4.0 99.2 1.0
N J:CYS45 4.3 0.3 1.0
CB J:ARG43 4.3 0.8 1.0
CB J:CYS7 4.4 91.3 1.0
C J:CYS46 4.4 98.5 1.0
O J:CYS45 4.5 99.4 1.0
OG J:SER9 4.5 91.2 1.0
CD1 B:ILE1006 4.6 88.6 1.0
O J:ARG43 4.6 0.8 1.0
C J:SER9 4.6 91.4 1.0
C J:CYS10 4.8 92.7 1.0
C J:ARG43 4.8 0.4 1.0
N J:ARG47 4.9 98.3 1.0

Zinc binding site 8 out of 8 in 3gtp

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Zinc binding site 8 out of 8 in the Backtracked Rna Polymerase II Complex with 24MER Rna


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 24MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.2
occ:1.00
 SG L:CYS51 1.9 0.5 1.0
SG L:CYS48 2.3 0.8 1.0
SG L:CYS31 2.6 0.4 1.0
SG L:CYS34 2.6 0.9 1.0
CB L:CYS51 2.7 0.5 1.0
CB L:CYS31 3.5 0.1 1.0
CB L:CYS48 3.8 0.0 1.0
CA L:CYS51 4.1 0.2 1.0
CB L:SER36 4.4 0.6 1.0
CB L:CYS34 4.5 0.8 1.0
C L:CYS51 4.6 0.1 1.0
N L:CYS34 4.7 0.6 1.0
N L:CYS51 4.8 0.3 1.0
O L:CYS51 4.9 0.2 1.0
CA L:CYS31 5.0 0.0 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 13:58:16 2024

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