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Zinc in PDB 4bbr: Structure of Rna Polymerase II-Tfiib Complex

Enzymatic activity of Structure of Rna Polymerase II-Tfiib Complex

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

Protein crystallography data

The structure of Structure of Rna Polymerase II-Tfiib Complex, PDB code: 4bbr was solved by S.Sainsbury, J.Niesser, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.440, 386.760, 254.350, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.1

Other elements in 4bbr:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:91.2
occ:1.00
 CB A:CYS110 1.9 86.4 1.0
SG A:CYS110 2.3 91.8 1.0
SG A:CYS148 2.4 0.1 1.0
SG A:CYS167 2.5 0.8 1.0
SG A:CYS107 2.5 93.2 1.0
CB A:CYS167 3.1 0.3 1.0
CB A:CYS148 3.2 0.1 1.0
CA A:CYS110 3.4 84.6 1.0
CB A:CYS107 3.4 86.2 1.0
O A:GLY166 3.9 0.7 1.0
O A:CYS167 4.0 0.8 1.0
N A:CYS110 4.0 84.6 1.0
CA A:CYS167 4.3 0.1 1.0
C A:CYS110 4.3 85.1 1.0
C A:CYS167 4.4 0.8 1.0
CA A:CYS148 4.7 0.9 1.0
N A:GLY111 4.7 79.2 1.0
O A:MET108 4.8 90.7 1.0
C A:GLY166 4.8 0.3 1.0
CA A:CYS107 4.8 82.1 1.0
CB A:LYS112 4.9 86.7 1.0
N A:CYS167 4.9 0.7 1.0

Zinc binding site 2 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:51.9
occ:1.00
 NE2 A:HIS80 2.0 47.6 1.0
SG A:CYS67 2.2 78.1 1.0
SG A:CYS70 2.4 90.4 1.0
SG A:CYS77 2.6 67.3 1.0
CD2 A:HIS80 2.9 47.9 1.0
CE1 A:HIS80 3.1 46.7 1.0
CB A:CYS67 3.4 78.2 1.0
CB A:CYS77 3.5 64.2 1.0
CB A:CYS70 3.5 87.9 1.0
O A:CYS67 3.9 84.9 1.0
CG A:HIS80 4.1 46.9 1.0
ND1 A:HIS80 4.2 47.1 1.0
CA A:CYS77 4.3 62.0 1.0
O A:GLN71 4.4 96.2 1.0
OE1 A:GLN68 4.6 47.1 1.0
CA A:CYS67 4.6 81.2 1.0
C A:CYS67 4.6 86.2 1.0
CD A:PRO78 4.7 52.9 1.0
CA A:CYS70 4.8 90.8 1.0
CD A:GLN68 4.8 67.4 1.0
C A:CYS70 4.8 95.3 1.0
N A:GLN71 4.9 92.9 1.0

Zinc binding site 3 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:46.3
occ:1.00
 SG B:CYS1166 2.3 58.6 1.0
SG B:CYS1185 2.3 62.8 1.0
SG B:CYS1163 2.4 47.4 1.0
SG B:CYS1182 2.4 58.2 1.0
CB B:CYS1163 2.9 42.5 1.0
CB B:CYS1185 3.2 60.1 1.0
CB B:CYS1166 3.6 54.9 1.0
CB B:CYS1182 3.8 55.6 1.0
N B:CYS1166 3.9 53.6 1.0
OG1 B:THR1170 4.2 57.9 1.0
CA B:CYS1166 4.3 54.2 1.0
O B:CYS1166 4.3 59.4 1.0
CA B:CYS1163 4.4 41.9 1.0
CA B:CYS1185 4.4 60.9 1.0
N B:CYS1185 4.5 61.9 1.0
CB B:ILE1165 4.6 51.5 1.0
C B:CYS1166 4.7 58.2 1.0
O B:CYS1182 4.9 68.5 1.0
CG2 B:ILE1165 4.9 54.9 1.0
C B:ILE1165 5.0 53.3 1.0
C B:CYS1163 5.0 48.0 1.0

Zinc binding site 4 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:64.9
occ:1.00
 SG C:CYS92 2.3 61.8 1.0
SG C:CYS88 2.3 79.9 1.0
SG C:CYS95 2.3 59.3 1.0
SG C:CYS86 2.4 65.9 1.0
CB C:CYS86 3.2 62.2 1.0
CB C:CYS92 3.3 58.7 1.0
CB C:CYS95 3.3 54.2 1.0
CB C:CYS88 3.4 77.7 1.0
N C:CYS92 3.6 58.6 1.0
CA C:CYS92 4.0 58.0 1.0
N C:CYS88 4.0 78.7 1.0
N C:CYS95 4.1 53.4 1.0
CA C:CYS88 4.3 78.5 1.0
C C:HIS91 4.3 66.1 1.0
CA C:CYS95 4.3 52.9 1.0
CA C:CYS86 4.5 63.7 1.0
CE C:LYS94 4.6 0.5 1.0
C C:CYS92 4.6 60.7 1.0
C C:CYS86 4.6 75.1 1.0
CA C:HIS91 4.6 66.8 1.0
CB C:LYS94 4.7 56.4 1.0
N C:PHE87 4.7 77.5 1.0
NZ C:LYS94 4.8 0.8 1.0
O C:ASP90 4.9 77.4 1.0

Zinc binding site 5 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:78.7
occ:1.00
 SG I:CYS32 2.2 87.6 1.0
SG I:CYS10 2.3 73.5 1.0
SG I:CYS7 2.3 77.0 1.0
SG I:CYS29 2.4 79.6 1.0
CB I:CYS29 3.0 75.0 1.0
CB I:CYS7 3.2 71.6 1.0
CB I:CYS32 3.5 85.6 1.0
CB I:CYS10 3.9 69.8 1.0
N I:CYS10 3.9 68.8 1.0
N I:CYS32 3.9 83.7 1.0
OG1 I:THR31 4.0 87.8 1.0
CB I:TYR34 4.0 82.4 1.0
CA I:CYS32 4.1 85.2 1.0
CA I:CYS10 4.4 68.5 1.0
C I:CYS32 4.5 89.0 1.0
CA I:CYS29 4.5 74.1 1.0
O I:CYS32 4.5 87.0 1.0
CA I:CYS7 4.6 70.2 1.0
N I:TYR34 4.8 84.6 1.0
C I:THR31 4.9 87.3 1.0
CG I:TYR34 4.9 82.8 1.0

Zinc binding site 6 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS106 2.2 0.0 1.0
SG I:CYS78 2.3 0.4 1.0
SG I:CYS75 2.3 0.9 1.0
SG I:CYS103 2.4 0.3 1.0
CB I:CYS103 3.0 0.9 1.0
CB I:CYS75 3.1 0.5 1.0
CB I:CYS106 3.3 0.1 1.0
CB I:CYS78 3.3 0.2 1.0
N I:CYS106 3.6 0.9 1.0
N I:CYS78 3.7 0.4 1.0
CA I:CYS106 3.9 0.6 1.0
CA I:CYS78 4.0 0.8 1.0
C I:CYS106 4.5 0.3 1.0
N I:SER107 4.5 0.8 1.0
CA I:CYS103 4.5 0.7 1.0
CB I:LYS77 4.5 0.7 1.0
CA I:CYS75 4.6 0.8 1.0
CB I:SER105 4.6 0.7 1.0
N I:HIS79 4.7 0.5 1.0
C I:CYS78 4.7 0.2 1.0
N I:HIS108 4.8 0.0 1.0
C I:SER105 4.8 1.0 1.0
CB I:HIS108 4.8 0.2 1.0
C I:LYS77 4.8 0.9 1.0
CB I:SER80 4.9 0.5 1.0
N I:SER80 5.0 1.0 1.0

Zinc binding site 7 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:46.8
occ:1.00
 SG J:CYS45 2.2 41.9 1.0
SG J:CYS10 2.3 45.1 1.0
SG J:CYS7 2.3 56.5 1.0
SG J:CYS46 2.4 49.5 1.0
N J:CYS46 3.1 41.0 1.0
CB J:CYS10 3.2 42.8 1.0
CB J:CYS7 3.2 51.9 1.0
CB J:CYS45 3.3 37.3 1.0
CB J:CYS46 3.6 43.5 1.0
CA J:CYS46 3.6 41.1 1.0
C J:CYS45 3.6 43.5 1.0
N J:CYS10 3.9 43.1 1.0
CA J:CYS45 4.0 37.6 1.0
CA J:CYS10 4.0 42.9 1.0
CG J:ARG43 4.4 60.4 1.0
O J:CYS45 4.4 43.5 1.0
NE J:ARG43 4.4 56.6 1.0
CA J:CYS7 4.6 50.2 1.0
N J:GLY11 4.7 42.5 1.0
N J:CYS45 4.7 39.2 1.0
C J:CYS10 4.7 47.5 1.0
CB J:LYS12 4.9 45.0 1.0
N J:LYS12 4.9 42.0 1.0
CD J:ARG43 4.9 59.0 1.0
CB J:SER9 5.0 46.3 1.0

Zinc binding site 8 out of 9 in 4bbr

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:98.0
occ:1.00
 CB L:CYS51 2.0 0.3 1.0
SG L:CYS48 2.4 90.6 1.0
SG L:CYS51 2.4 0.8 1.0
SG L:CYS31 2.5 85.8 1.0
SG L:CYS34 2.6 86.4 1.0
CB L:CYS48 3.0 86.3 1.0
CB L:CYS31 3.3 79.5 1.0
CA L:CYS51 3.3 0.8 1.0
CB L:CYS34 3.5 85.0 1.0
O L:CYS51 3.8 0.6 1.0
C L:CYS51 3.8 0.2 1.0
N L:CYS34 3.9 83.3 1.0
N L:CYS51 3.9 0.9 1.0
CA L:CYS34 4.2 84.2 1.0
CB L:HIS53 4.3 94.3 1.0
CA L:CYS48 4.5 86.4 1.0
OG L:SER36 4.5 0.4 1.0
CA L:CYS31 4.7 76.5 1.0
N L:GLY52 4.9 0.8 1.0
N L:SER35 4.9 84.0 1.0
C L:CYS48 4.9 94.4 1.0
N L:HIS53 5.0 97.4 1.0
O L:LYS49 5.0 99.6 1.0

Zinc binding site 9 out of 9 in 4bbr

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Zinc binding site 9 out of 9 in the Structure of 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 Structure of Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1216

b:73.5
occ:1.00
 SG M:CYS27 2.3 94.9 1.0
SG M:CYS48 2.3 72.7 1.0
SG M:CYS45 2.4 62.7 1.0
SG M:CYS24 2.4 82.3 1.0
CB M:CYS48 2.9 68.8 1.0
CB M:CYS24 3.3 78.7 1.0
CB M:CYS45 3.4 58.7 1.0
N M:CYS48 3.6 68.5 1.0
CA M:CYS48 3.8 68.1 1.0
CB M:CYS27 4.0 91.6 1.0
N M:CYS27 4.1 91.3 1.0
CB M:GLU26 4.4 90.1 1.0
CA M:CYS27 4.6 92.0 1.0
C M:CYS48 4.7 69.3 1.0
CA M:CYS24 4.8 78.7 1.0
C M:LEU47 4.8 72.0 1.0
CA M:CYS45 4.8 57.9 1.0
N M:GLY49 4.8 63.2 1.0
CB M:LEU47 4.8 66.7 1.0
CB M:LEU50 4.9 57.6 1.0
C M:GLU26 5.0 93.2 1.0

Reference:

S.Sainsbury, J.Niesser, P.Cramer. Structure and Function of the Initially Transcribing Rna Polymerase II-Tfiib Complex Nature V. 493 437 2013.
ISSN: ISSN 0028-0836
PubMed: 23151482
DOI: 10.1038/NATURE11715
Page generated: Sat Oct 26 19:38:20 2024

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