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Zinc in PDB 1r5u: Rna Polymerase II Tfiib Complex

Enzymatic activity of Rna Polymerase II Tfiib Complex

All present enzymatic activity of Rna Polymerase II Tfiib Complex:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Tfiib Complex, PDB code: 1r5u was solved by D.A.Bushnell, K.D.Westover, R.Davis, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 212.438, 217.182, 422.876, 90.00, 90.00, 90.00
R / Rfree (%) 34.5 / 37.3

Other elements in 1r5u:

The structure of Rna Polymerase II Tfiib Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Tfiib Complex (pdb code 1r5u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II Tfiib Complex, PDB code: 1r5u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1r5u

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Zinc binding site 1 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.2
occ:1.00
 SG A:CYS167 2.3 0.4 1.0
SG A:CYS110 2.8 0.2 1.0
SG A:CYS148 3.2 0.9 1.0
SG A:CYS107 3.8 0.2 1.0
CB A:CYS107 3.9 0.2 1.0
O A:MET108 3.9 0.3 1.0
CB A:CYS110 3.9 0.2 1.0
CB A:CYS148 4.0 0.9 1.0
N A:CYS110 4.0 0.5 1.0
O A:CYS167 4.1 0.2 1.0
CB A:CYS167 4.1 0.4 1.0
CA A:CYS110 4.4 0.5 1.0
O A:CYS107 4.6 0.1 1.0
C A:CYS110 4.7 0.5 1.0
N A:GLY111 4.8 0.9 1.0
C A:CYS107 4.8 0.1 1.0
C A:MET108 4.9 0.3 1.0
C A:CYS167 4.9 0.2 1.0
ND2 A:ASN169 5.0 0.9 1.0
CA A:CYS107 5.0 0.1 1.0

Zinc binding site 2 out of 9 in 1r5u

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Zinc binding site 2 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.2
occ:1.00
 SG A:CYS67 2.0 0.9 1.0
NE2 A:HIS80 2.1 0.4 1.0
SG A:CYS70 2.3 0.2 1.0
CD2 A:HIS80 3.0 0.4 1.0
CB A:CYS67 3.0 0.9 1.0
CE1 A:HIS80 3.2 0.4 1.0
O A:CYS67 3.2 0.8 1.0
SG A:CYS77 3.5 0.4 1.0
CB A:CYS70 3.6 0.2 1.0
C A:CYS67 3.7 0.8 1.0
CA A:CYS67 4.0 0.8 1.0
CG A:HIS80 4.2 0.4 1.0
ND1 A:HIS80 4.2 0.4 1.0
CB A:CYS77 4.4 0.4 1.0
CA A:CYS77 4.5 1.0 1.0
N A:GLN68 4.5 0.6 1.0
O A:GLN71 4.6 0.7 1.0
CB A:GLN68 4.6 0.6 1.0
CA A:CYS70 4.7 0.0 1.0
C A:CYS70 4.8 0.0 1.0
C A:CYS77 4.9 1.0 1.0
O A:PRO78 4.9 0.5 1.0

Zinc binding site 3 out of 9 in 1r5u

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Zinc binding site 3 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.2
occ:1.00
 SG B:CYS1166 1.7 0.8 1.0
SG B:CYS1182 2.5 0.3 1.0
SG B:CYS1163 2.8 88.3 1.0
SG B:CYS1185 3.0 0.7 1.0
CB B:CYS1163 3.2 88.3 1.0
CB B:CYS1185 3.3 0.7 1.0
CB B:CYS1166 3.5 0.8 1.0
O B:CYS1166 3.9 0.1 1.0
N B:CYS1166 4.2 0.1 1.0
CB B:CYS1182 4.2 0.3 1.0
CA B:CYS1166 4.3 0.1 1.0
CA B:CYS1185 4.6 0.6 1.0
C B:CYS1166 4.6 0.1 1.0
O B:CYS1182 4.6 0.8 1.0
CA B:CYS1163 4.8 0.5 1.0
CB B:THR1170 4.9 1.0 1.0
N B:CYS1185 4.9 0.6 1.0

Zinc binding site 4 out of 9 in 1r5u

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Zinc binding site 4 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.2
occ:1.00
 SG C:CYS86 1.9 0.0 1.0
SG C:CYS92 2.2 0.1 1.0
SG C:CYS95 2.2 0.0 1.0
SG C:CYS88 2.3 0.9 1.0
CB C:CYS86 2.8 0.0 1.0
CB C:CYS88 3.3 0.9 1.0
CB C:CYS95 3.4 0.0 1.0
CB C:CYS92 3.5 0.1 1.0
N C:CYS92 3.6 0.7 1.0
C C:HIS91 3.9 0.4 1.0
CA C:CYS92 4.1 0.7 1.0
N C:CYS95 4.1 0.6 1.0
CA C:CYS86 4.2 0.8 1.0
N C:CYS88 4.2 0.1 1.0
CA C:HIS91 4.2 0.4 1.0
CA C:CYS88 4.3 0.1 1.0
O C:ASP90 4.4 0.0 1.0
CA C:CYS95 4.4 0.6 1.0
CB C:LYS94 4.5 0.0 1.0
C C:CYS86 4.5 0.8 1.0
O C:HIS91 4.6 0.4 1.0
C C:CYS92 4.7 0.7 1.0
C C:LYS94 4.8 0.2 1.0
O C:CYS86 4.8 0.8 1.0
O C:CYS92 4.8 0.7 1.0
N C:LYS94 4.9 0.2 1.0
N C:PHE87 5.0 0.6 1.0

Zinc binding site 5 out of 9 in 1r5u

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Zinc binding site 5 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.2
occ:1.00
 SG I:CYS7 1.1 0.0 1.0
CB I:CYS7 1.8 0.0 1.0
CD2 I:TYR34 2.3 0.9 1.0
CA I:CYS7 2.6 0.0 1.0
CG I:TYR34 2.9 0.9 1.0
C I:CYS7 3.1 0.0 1.0
CE2 I:TYR34 3.1 0.9 1.0
CB I:TYR34 3.2 0.9 1.0
N I:ARG8 3.3 0.0 1.0
CB I:CYS29 3.5 0.0 1.0
O I:ARG8 3.6 0.0 1.0
CD1 I:TYR34 3.9 0.9 1.0
N I:CYS7 3.9 0.0 1.0
CD2 I:LEU14 4.0 0.9 1.0
O I:CYS7 4.0 0.0 1.0
SG I:CYS10 4.1 0.3 1.0
CZ I:TYR34 4.1 0.9 1.0
SG I:CYS29 4.1 0.0 1.0
C I:ARG8 4.2 0.0 1.0
SG I:CYS32 4.4 0.7 1.0
CE1 I:TYR34 4.4 0.9 1.0
CA I:ARG8 4.5 0.0 1.0
CA I:TYR34 4.6 0.8 1.0
CG I:ARG8 4.7 0.0 1.0
CG I:LEU14 4.9 0.9 1.0
CA I:CYS29 4.9 0.0 1.0
CD1 I:LEU14 4.9 0.9 1.0
C I:TYR34 5.0 0.8 1.0
OD2 I:ASP9 5.0 0.7 1.0

Zinc binding site 6 out of 9 in 1r5u

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Zinc binding site 6 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.2
occ:1.00
 SG I:CYS106 1.5 0.2 1.0
SG I:CYS103 1.8 0.0 1.0
SG I:CYS75 2.3 0.0 1.0
CB I:CYS103 2.5 0.0 1.0
SG I:CYS78 2.5 0.9 1.0
CB I:CYS106 3.0 0.2 1.0
CB I:CYS75 3.1 0.0 1.0
N I:CYS106 3.3 0.5 1.0
CA I:CYS106 3.7 0.5 1.0
CB I:HIS108 3.8 0.1 1.0
CA I:CYS103 3.9 0.9 1.0
CB I:CYS78 4.1 0.9 1.0
N I:HIS108 4.2 0.1 1.0
C I:CYS106 4.3 0.5 1.0
N I:SER107 4.3 0.1 1.0
C I:SER105 4.3 0.2 1.0
N I:CYS78 4.3 0.5 1.0
C I:CYS103 4.4 0.9 1.0
N I:SER105 4.6 0.2 1.0
O I:CYS103 4.6 0.9 1.0
CA I:CYS75 4.6 0.1 1.0
CB I:SER105 4.6 0.5 1.0
OG I:SER80 4.6 0.9 1.0
CA I:HIS108 4.7 0.1 1.0
CA I:SER105 4.7 0.2 1.0
CA I:CYS78 4.7 0.5 1.0
N I:CYS103 4.8 0.9 1.0
CG I:HIS108 4.8 0.1 1.0
CB I:LYS77 4.9 0.5 1.0
CB I:SER80 5.0 0.9 1.0

Zinc binding site 7 out of 9 in 1r5u

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Zinc binding site 7 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.2
occ:1.00
 SG J:CYS46 1.8 0.9 1.0
SG J:CYS45 1.9 93.5 1.0
SG J:CYS10 2.1 0.1 1.0
SG J:CYS7 2.5 0.8 1.0
N J:CYS46 3.0 0.1 1.0
CB J:CYS46 3.1 0.9 1.0
CB J:CYS45 3.3 93.5 1.0
CA J:CYS46 3.3 0.1 1.0
C J:CYS45 3.3 0.3 1.0
CB J:CYS10 3.5 0.1 1.0
CB J:CYS7 3.5 0.8 1.0
N J:CYS10 3.7 0.3 1.0
O J:CYS45 3.8 0.3 1.0
CA J:CYS45 3.9 0.3 1.0
CA J:CYS10 4.1 0.3 1.0
CB J:SER9 4.3 0.1 1.0
NE J:ARG43 4.3 0.1 1.0
CG J:ARG43 4.4 0.1 1.0
N J:CYS45 4.6 0.3 1.0
CD J:ARG43 4.6 0.1 1.0
N J:GLY11 4.8 0.5 1.0
C J:CYS46 4.8 0.1 1.0
C J:CYS10 4.8 0.3 1.0
C J:SER9 4.8 89.0 1.0
CB J:LYS12 4.9 0.7 1.0
CA J:CYS7 5.0 0.7 1.0

Zinc binding site 8 out of 9 in 1r5u

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Zinc binding site 8 out of 9 in the Rna Polymerase II Tfiib Complex


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 Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.7
occ:1.00
 SG L:CYS34 1.7 0.8 1.0
SG L:CYS51 1.8 0.2 1.0
SG L:CYS31 2.5 0.6 1.0
SG L:CYS48 2.5 0.9 1.0
CB L:CYS48 3.4 0.9 1.0
CB L:CYS31 3.4 0.6 1.0
CB L:CYS34 3.5 0.8 1.0
CB L:CYS51 3.6 0.2 1.0
O L:CYS51 4.0 0.0 1.0
N L:CYS34 4.0 0.6 1.0
CA L:CYS34 4.3 0.6 1.0
CA L:CYS51 4.5 0.0 1.0
CD2 L:HIS53 4.5 0.9 1.0
N L:CYS51 4.7 0.0 1.0
C L:CYS51 4.7 0.0 1.0
O L:LYS49 4.8 0.6 1.0
N L:LYS49 4.8 0.6 1.0
CA L:CYS48 4.8 0.8 1.0
CA L:CYS31 4.9 0.4 1.0
C L:CYS34 5.0 0.6 1.0

Zinc binding site 9 out of 9 in 1r5u

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Zinc binding site 9 out of 9 in the Rna Polymerase II Tfiib Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn209

b:0.0
occ:1.00
 N M:UNK48 3.5 0.0 1.0
CA M:UNK48 4.0 0.0 1.0
N M:UNK27 4.4 0.0 1.0
CA M:UNK27 4.5 0.0 1.0
C M:UNK47 4.6 0.0 1.0
C M:UNK26 4.7 0.0 1.0
CA M:UNK47 4.7 0.0 1.0
CA M:UNK45 4.7 0.0 1.0
CA M:UNK24 4.8 0.0 1.0
N M:UNK47 4.8 0.0 1.0
C M:UNK48 4.9 0.0 1.0
N M:UNK49 4.9 0.0 1.0
O M:UNK26 4.9 0.0 1.0

Reference:

D.A.Bushnell, K.D.Westover, R.E.Davis, R.D.Kornberg. Structural Basis of Transcription: An Rna Polymerase II-Tfiib Cocrystal at 4.5 Angstroms. Science V. 303 983 2004.
ISSN: ISSN 0036-8075
PubMed: 14963322
DOI: 10.1126/SCIENCE.1090838
Page generated: Wed Oct 16 18:25:38 2024

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