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Zinc in PDB 3gtm: Co-Complex of Backtracked Rna Polymerase II with Tfiis

Enzymatic activity of Co-Complex of Backtracked Rna Polymerase II with Tfiis

All present enzymatic activity of Co-Complex of Backtracked Rna Polymerase II with Tfiis:
2.7.7.6;

Protein crystallography data

The structure of Co-Complex of Backtracked Rna Polymerase II with Tfiis, PDB code: 3gtm 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) 40.00 / 3.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.329, 218.530, 193.913, 90.00, 100.32, 90.00
R / Rfree (%) 23.4 / 28.9

Other elements in 3gtm:

The structure of Co-Complex of Backtracked Rna Polymerase II with Tfiis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Complex of Backtracked Rna Polymerase II with Tfiis (pdb code 3gtm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Co-Complex of Backtracked Rna Polymerase II with Tfiis, PDB code: 3gtm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3gtm

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Zinc binding site 1 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.7
occ:1.00
 O A:MET108 2.7 0.6 1.0
SG A:CYS148 2.8 0.1 1.0
SG A:CYS107 3.0 0.6 1.0
SG A:CYS110 3.0 0.2 1.0
O A:CYS167 3.4 0.2 1.0
CB A:CYS148 3.5 0.3 1.0
CB A:CYS107 3.8 0.8 1.0
N A:CYS110 4.0 0.7 1.0
C A:MET108 4.0 0.0 1.0
CB A:CYS110 4.1 0.9 1.0
CB A:HIS109 4.3 0.1 1.0
C A:CYS107 4.5 0.3 1.0
N A:MET108 4.5 0.7 1.0
CA A:CYS110 4.6 1.0 1.0
C A:CYS167 4.6 0.8 1.0
CD2 A:HIS109 4.7 0.5 1.0
O A:CYS107 4.7 1.0 1.0
CA A:CYS107 4.8 0.4 1.0
C A:HIS109 4.8 0.1 1.0
CA A:HIS109 4.8 0.7 1.0
N A:HIS109 4.9 0.5 1.0
CG A:HIS109 4.9 0.1 1.0
CA A:CYS148 4.9 0.9 1.0
CA A:MET108 4.9 1.0 1.0
SG A:CYS167 5.0 0.9 1.0
N A:GLY111 5.0 0.2 1.0

Zinc binding site 2 out of 9 in 3gtm

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Zinc binding site 2 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1736

b:73.0
occ:1.00
 NE2 A:HIS80 2.2 92.8 1.0
SG A:CYS67 2.5 0.9 1.0
SG A:CYS77 2.7 87.1 1.0
CD2 A:HIS80 2.8 93.0 1.0
SG A:CYS70 3.1 0.3 1.0
CB A:CYS67 3.2 0.4 1.0
CE1 A:HIS80 3.4 92.5 1.0
O A:CYS67 3.4 0.7 1.0
CB A:CYS70 3.4 0.8 1.0
CB A:CYS77 3.8 86.6 1.0
OE1 A:GLN68 4.0 0.1 1.0
CG A:HIS80 4.1 93.2 1.0
C A:CYS67 4.2 0.2 1.0
CA A:CYS67 4.3 0.2 1.0
ND1 A:HIS80 4.3 92.2 1.0
CD A:GLN68 4.4 0.8 1.0
O A:LEU58 4.4 79.1 1.0
NE2 A:GLN68 4.4 0.8 1.0
CA A:CYS70 4.8 0.3 1.0
O A:GLN71 5.0 0.7 1.0

Zinc binding site 3 out of 9 in 3gtm

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Zinc binding site 3 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:82.2
occ:1.00
 SG B:CYS1166 2.4 86.5 1.0
SG B:CYS1163 2.6 84.9 1.0
SG B:CYS1185 2.7 0.8 1.0
SG B:CYS1182 2.7 0.9 1.0
CB B:CYS1185 2.8 0.6 1.0
CB B:CYS1163 2.9 84.0 1.0
CB B:CYS1166 3.7 84.8 1.0
O B:CYS1166 3.8 82.4 1.0
N B:CYS1166 3.9 83.8 1.0
CB B:CYS1182 4.1 0.2 1.0
CA B:CYS1185 4.1 0.5 1.0
CA B:CYS1166 4.1 83.6 1.0
C B:CYS1166 4.3 82.3 1.0
O B:CYS1185 4.4 0.5 1.0
CA B:CYS1163 4.4 83.1 1.0
N B:CYS1185 4.4 0.5 1.0
C B:CYS1185 4.6 0.0 1.0
O B:CYS1163 4.8 82.3 1.0
C B:CYS1163 4.9 83.2 1.0

Zinc binding site 4 out of 9 in 3gtm

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Zinc binding site 4 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:58.8
occ:1.00
 SG C:CYS86 2.3 75.0 1.0
SG C:CYS92 2.4 53.8 1.0
SG C:CYS95 2.5 53.0 1.0
N C:CYS92 2.6 52.8 1.0
SG C:CYS88 2.7 66.3 1.0
CB C:CYS86 2.7 74.4 1.0
CB C:CYS92 2.9 53.3 1.0
CA C:CYS92 3.3 53.1 1.0
C C:HIS91 3.3 70.0 1.0
CA C:HIS91 3.6 69.7 1.0
CB C:CYS95 3.8 53.1 1.0
N C:HIS91 3.9 69.8 1.0
CB C:CYS88 3.9 66.2 1.0
O C:CYS86 4.0 74.2 1.0
CA C:CYS86 4.0 74.7 1.0
C C:CYS86 4.2 74.7 1.0
C C:CYS92 4.3 53.2 1.0
O C:HIS91 4.3 70.2 1.0
N C:CYS88 4.6 65.5 1.0
C C:ASP90 4.7 90.9 1.0
O C:CYS92 4.7 52.9 1.0
N C:CYS95 4.7 55.0 1.0
N C:CYS86 4.8 74.5 1.0
CA C:CYS95 4.8 53.5 1.0
CA C:CYS88 4.8 66.0 1.0
O C:SER83 4.9 37.9 1.0

Zinc binding site 5 out of 9 in 3gtm

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Zinc binding site 5 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:73.1
occ:1.00
 SG I:CYS32 2.3 96.4 1.0
SG I:CYS10 2.5 87.6 1.0
SG I:CYS7 2.6 94.7 1.0
OD2 I:ASP9 3.1 0.6 1.0
CB I:CYS32 3.1 95.7 1.0
SG I:CYS29 3.4 67.8 1.0
CB I:CYS10 3.4 87.8 1.0
CB I:CYS29 3.6 67.1 1.0
CB I:TYR34 3.7 68.0 1.0
CB I:CYS7 3.7 94.8 1.0
N I:CYS10 4.0 86.8 1.0
CA I:CYS10 4.1 87.0 1.0
O I:ARG8 4.2 0.7 1.0
CG I:ASP9 4.3 0.6 1.0
CG I:TYR34 4.5 66.2 1.0
C I:CYS10 4.5 86.2 1.0
CA I:CYS32 4.5 96.7 1.0
N I:ASN11 4.6 76.8 1.0
N I:TYR34 4.7 71.0 1.0
CD1 I:TYR34 4.7 64.9 1.0
CA I:TYR34 4.8 69.4 1.0
N I:CYS32 4.9 97.5 1.0
N I:SER33 5.0 82.2 1.0

Zinc binding site 6 out of 9 in 3gtm

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Zinc binding site 6 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:37.8
occ:1.00
 SG I:CYS78 2.5 62.7 1.0
SG I:CYS106 2.5 71.2 1.0
SG I:CYS103 2.5 57.8 1.0
SG I:CYS75 2.6 85.2 1.0
CB I:CYS78 2.9 63.8 1.0
CB I:CYS103 3.4 57.6 1.0
CB I:CYS106 3.5 72.4 1.0
N I:CYS106 3.7 71.6 1.0
N I:CYS78 3.7 63.5 1.0
CB I:CYS75 3.8 84.0 1.0
CA I:CYS78 3.8 63.9 1.0
CA I:CYS106 4.1 72.2 1.0
CB I:SER105 4.1 65.3 1.0
C I:SER105 4.5 65.9 1.0
CB I:HIS108 4.5 65.0 1.0
C I:CYS78 4.5 63.8 1.0
N I:HIS79 4.7 64.7 1.0
CA I:SER105 4.7 65.1 1.0
N I:SER105 4.8 63.7 1.0
CA I:CYS103 4.8 57.1 1.0
C I:CYS106 4.8 72.0 1.0
N I:SER107 4.9 75.5 1.0
OG I:SER105 5.0 64.8 1.0
N I:HIS108 5.0 65.2 1.0
C I:LYS77 5.0 79.3 1.0

Zinc binding site 7 out of 9 in 3gtm

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Zinc binding site 7 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:35.3
occ:1.00
 SG J:CYS46 2.3 56.1 1.0
SG J:CYS45 2.5 54.2 1.0
SG J:CYS7 2.5 34.0 1.0
SG J:CYS10 2.7 46.6 1.0
N J:CYS46 2.9 55.1 1.0
CB J:CYS10 3.0 47.5 1.0
CB J:CYS7 3.1 35.0 1.0
CB J:CYS46 3.3 55.1 1.0
CA J:CYS46 3.3 54.6 1.0
C J:CYS45 3.5 52.9 1.0
CB J:CYS45 3.6 53.7 1.0
N J:CYS10 3.7 46.9 1.0
CA J:CYS10 3.9 47.7 1.0
O J:CYS45 4.1 52.9 1.0
CA J:CYS45 4.1 53.2 1.0
N J:GLY11 4.2 43.3 1.0
OG J:SER9 4.2 39.4 1.0
CG J:ARG43 4.4 56.6 1.0
CA J:CYS7 4.6 35.1 1.0
C J:CYS10 4.6 48.4 1.0
NE J:ARG43 4.6 58.0 1.0
CD J:ARG43 4.8 57.5 1.0
C J:CYS46 4.8 54.0 1.0
N J:LYS12 4.9 49.5 1.0
N J:CYS45 4.9 53.8 1.0
C J:SER9 4.9 40.8 1.0
CE J:MET49 5.0 33.0 1.0

Zinc binding site 8 out of 9 in 3gtm

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Zinc binding site 8 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.5
occ:1.00
 SG L:CYS34 2.3 88.1 1.0
SG L:CYS51 2.4 0.7 1.0
SG L:CYS31 2.6 0.5 1.0
CB L:CYS48 2.8 97.4 1.0
SG L:CYS48 2.8 96.3 1.0
CB L:CYS31 3.0 0.8 1.0
CB L:CYS51 3.0 0.4 1.0
O L:CYS51 3.5 0.8 1.0
CA L:CYS51 3.9 0.3 1.0
C L:CYS51 4.0 0.0 1.0
CB L:CYS34 4.1 87.9 1.0
N L:CYS51 4.2 0.7 1.0
CA L:CYS48 4.3 98.7 1.0
CA L:CYS31 4.3 0.6 1.0
O L:HIS53 4.5 0.0 1.0
N L:LYS49 4.7 87.8 1.0
C L:CYS48 4.8 99.5 1.0
OG L:SER36 5.0 74.9 1.0
N L:CYS34 5.0 86.7 1.0

Zinc binding site 9 out of 9 in 3gtm

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Zinc binding site 9 out of 9 in the Co-Complex of Backtracked Rna Polymerase II with Tfiis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Co-Complex of Backtracked Rna Polymerase II with Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn310

b:1.0
occ:1.00
 CA S:CYS299 4.0 0.9 1.0
N S:CYS274 4.3 0.4 1.0
CA S:CYS302 4.4 0.8 1.0
N S:LYS273 4.4 0.2 1.0
N S:CYS302 4.6 0.9 1.0
CA S:LYS273 4.6 0.5 1.0
CA S:CYS271 4.7 0.3 1.0
N S:GLY303 4.7 0.0 1.0
C S:CYS299 4.8 0.7 1.0
N S:CYS299 4.8 0.6 1.0
N S:ASN304 4.8 0.2 1.0
N S:GLY272 4.9 0.1 1.0
C S:CYS302 4.9 0.0 1.0
O S:CYS299 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: Wed Aug 20 09:44:12 2025

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