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Zinc in PDB 4bbs: Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex

Enzymatic activity of Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex

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

Protein crystallography data

The structure of Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex, PDB code: 4bbs 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) 49.273 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.170, 386.010, 254.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.47 / 22.5

Other elements in 4bbs:

The structure of Structure of An Initially Transcribing 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 An Initially Transcribing Rna Polymerase II- Tfiib Complex (pdb code 4bbs). 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 An Initially Transcribing Rna Polymerase II- Tfiib Complex, PDB code: 4bbs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4bbs

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Zinc binding site 1 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:1.0
occ:1.00
 CB A:CYS110 2.1 0.8 1.0
SG A:CYS110 2.3 90.3 1.0
SG A:CYS148 2.3 0.6 1.0
SG A:CYS167 2.3 0.3 1.0
SG A:CYS107 2.3 0.5 1.0
CB A:CYS167 2.9 0.6 1.0
CB A:CYS148 3.1 0.5 1.0
CB A:CYS107 3.4 0.2 1.0
CA A:CYS110 3.6 0.2 1.0
O A:CYS167 4.0 0.9 1.0
O A:GLY166 4.1 1.0 1.0
CA A:CYS167 4.1 0.0 1.0
C A:CYS167 4.2 0.3 1.0
N A:CYS110 4.2 0.2 1.0
C A:CYS110 4.6 99.4 1.0
CA A:CYS148 4.6 0.9 1.0
CA A:CYS107 4.8 0.6 1.0
N A:GLY111 4.8 0.6 1.0
O A:MET108 4.8 0.5 1.0
C A:GLY166 4.9 0.5 1.0
N A:CYS167 4.9 0.8 1.0
CB A:LYS112 4.9 0.7 1.0
N A:GLY168 4.9 0.8 1.0

Zinc binding site 2 out of 9 in 4bbs

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Zinc binding site 2 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:94.0
occ:1.00
 NE2 A:HIS80 2.1 73.8 1.0
SG A:CYS77 2.3 95.2 1.0
SG A:CYS70 2.3 0.5 1.0
SG A:CYS67 2.3 69.7 1.0
CE1 A:HIS80 2.6 78.1 1.0
CB A:CYS77 3.4 74.2 1.0
CB A:CYS70 3.4 0.3 1.0
CD2 A:HIS80 3.4 74.9 1.0
CB A:CYS67 3.7 0.6 1.0
ND1 A:HIS80 3.8 76.4 1.0
O A:CYS67 3.9 0.2 1.0
CA A:CYS77 4.2 72.3 1.0
CG A:HIS80 4.3 72.9 1.0
O A:GLN71 4.4 0.5 1.0
NE2 A:GLN68 4.6 84.0 1.0
CD A:PRO78 4.7 69.6 1.0
CA A:CYS70 4.7 0.5 1.0
C A:CYS67 4.7 0.0 1.0
CA A:CYS67 4.8 0.7 1.0
CD A:GLN68 4.8 0.6 1.0
OE1 A:GLN68 4.8 1.0 1.0
C A:CYS70 4.9 0.8 1.0
N A:GLY79 4.9 59.6 1.0
N A:GLN71 5.0 0.5 1.0
C A:CYS77 5.0 73.8 1.0

Zinc binding site 3 out of 9 in 4bbs

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Zinc binding site 3 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:71.9
occ:1.00
 SG B:CYS1166 2.3 80.9 1.0
SG B:CYS1163 2.3 85.9 1.0
SG B:CYS1182 2.3 97.5 1.0
SG B:CYS1185 2.3 76.1 1.0
CB B:CYS1163 3.0 67.4 1.0
CB B:CYS1185 3.2 89.7 1.0
CB B:CYS1182 3.6 0.6 1.0
CB B:CYS1166 3.9 78.8 1.0
N B:CYS1166 4.0 80.8 1.0
O B:CYS1166 4.2 0.4 1.0
OG1 B:THR1170 4.3 88.4 1.0
CA B:CYS1185 4.4 89.6 1.0
CA B:CYS1166 4.5 81.2 1.0
CA B:CYS1163 4.5 65.0 1.0
N B:CYS1185 4.5 90.3 1.0
O B:CYS1182 4.5 0.4 1.0
CB B:ILE1165 4.6 70.7 1.0
C B:CYS1166 4.8 88.0 1.0
CA B:CYS1182 4.9 99.7 1.0

Zinc binding site 4 out of 9 in 4bbs

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Zinc binding site 4 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:86.8
occ:1.00
 SG C:CYS92 2.3 62.3 1.0
SG C:CYS88 2.3 78.4 1.0
SG C:CYS95 2.3 89.4 1.0
SG C:CYS86 2.3 0.7 1.0
CB C:CYS86 3.0 0.7 1.0
CB C:CYS95 3.2 86.2 1.0
CB C:CYS92 3.5 98.7 1.0
N C:CYS92 3.7 84.4 1.0
CB C:CYS88 3.8 0.2 1.0
CA C:CYS92 4.1 89.5 1.0
N C:CYS95 4.2 83.0 1.0
C C:HIS91 4.3 82.3 1.0
O C:ASP90 4.3 0.7 1.0
CA C:CYS95 4.3 83.0 1.0
CA C:CYS86 4.4 97.8 1.0
N C:CYS88 4.4 0.5 1.0
CA C:HIS91 4.6 88.3 1.0
C C:CYS86 4.6 98.8 1.0
CA C:CYS88 4.6 0.1 1.0
C C:CYS92 4.7 82.0 1.0
CB C:LYS94 4.8 84.1 1.0
N C:PHE87 4.8 0.8 1.0
CE C:LYS94 4.9 0.7 1.0
C C:LYS94 5.0 81.2 1.0
O C:CYS86 5.0 95.3 1.0

Zinc binding site 5 out of 9 in 4bbs

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Zinc binding site 5 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.7
occ:1.00
 SG I:CYS10 2.3 75.2 1.0
SG I:CYS32 2.3 0.6 1.0
SG I:CYS29 2.3 0.7 1.0
SG I:CYS7 2.3 93.7 1.0
CB I:CYS29 2.8 0.2 1.0
CB I:CYS7 3.2 93.0 1.0
CB I:CYS32 3.6 0.3 1.0
CB I:TYR34 3.8 96.1 1.0
OG1 I:THR31 3.9 0.3 1.0
N I:CYS32 3.9 0.8 1.0
CB I:CYS10 4.1 0.3 1.0
CA I:CYS32 4.2 0.3 1.0
CA I:CYS29 4.3 1.0 1.0
N I:CYS10 4.3 0.4 1.0
N I:TYR34 4.4 1.0 1.0
C I:CYS32 4.5 0.3 1.0
CA I:CYS7 4.6 94.9 1.0
CA I:TYR34 4.7 0.1 1.0
C I:THR31 4.8 0.2 1.0
CA I:CYS10 4.8 0.9 1.0
N I:SER33 4.8 0.4 1.0
C I:CYS29 4.9 0.3 1.0
CG I:TYR34 4.9 93.2 1.0
O I:CYS32 4.9 0.7 1.0
N I:THR31 5.0 0.3 1.0

Zinc binding site 6 out of 9 in 4bbs

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Zinc binding site 6 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.9
occ:1.00
 SG I:CYS78 2.3 0.8 1.0
SG I:CYS103 2.3 0.8 1.0
SG I:CYS106 2.3 0.6 1.0
SG I:CYS75 2.3 0.9 1.0
CB I:CYS75 2.7 0.3 1.0
CB I:CYS103 3.1 0.2 1.0
CB I:CYS106 3.6 0.2 1.0
CB I:CYS78 3.6 1.0 1.0
N I:CYS106 3.8 0.7 1.0
N I:CYS78 4.0 0.1 1.0
CA I:CYS75 4.2 0.9 1.0
CA I:CYS106 4.2 0.4 1.0
CA I:CYS78 4.3 0.6 1.0
CB I:SER105 4.4 0.4 1.0
CA I:CYS103 4.6 0.5 1.0
N I:SER80 4.6 0.5 1.0
CB I:SER80 4.6 0.1 1.0
N I:HIS79 4.6 0.2 1.0
C I:CYS78 4.6 0.8 1.0
OG I:SER105 4.7 0.0 1.0
CB I:LYS77 4.8 0.7 1.0
CB I:HIS108 4.9 0.5 1.0
N I:SER107 4.9 0.7 1.0
C I:CYS106 4.9 0.6 1.0
C I:SER105 4.9 0.8 1.0
C I:CYS75 4.9 0.6 1.0
N I:CYS75 5.0 0.3 1.0

Zinc binding site 7 out of 9 in 4bbs

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Zinc binding site 7 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:69.1
occ:1.00
 SG J:CYS45 2.3 76.0 1.0
SG J:CYS10 2.3 47.1 1.0
SG J:CYS46 2.3 86.3 1.0
SG J:CYS7 2.3 88.9 1.0
N J:CYS46 3.0 56.9 1.0
CB J:CYS45 3.2 64.3 1.0
CB J:CYS10 3.3 70.4 1.0
CB J:CYS7 3.3 74.0 1.0
C J:CYS45 3.3 62.9 1.0
CA J:CYS46 3.4 56.3 1.0
CB J:CYS46 3.4 46.1 1.0
CA J:CYS45 3.8 63.7 1.0
O J:CYS45 3.9 67.2 1.0
N J:CYS10 3.9 68.7 1.0
CA J:CYS10 4.1 68.8 1.0
N J:GLY11 4.5 72.4 1.0
NE J:ARG43 4.5 83.4 1.0
N J:CYS45 4.6 66.6 1.0
CG J:ARG43 4.6 78.5 1.0
C J:CYS10 4.7 67.4 1.0
CA J:CYS7 4.7 74.6 1.0
C J:CYS46 4.9 63.0 1.0
CB J:SER9 4.9 66.4 1.0
N J:LYS12 5.0 58.3 1.0

Zinc binding site 8 out of 9 in 4bbs

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Zinc binding site 8 out of 9 in the Structure of An Initially Transcribing 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 Structure of An Initially Transcribing Rna Polymerase II- Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.6
occ:1.00
 SG L:CYS34 2.3 0.9 1.0
SG L:CYS51 2.3 0.5 1.0
CB L:CYS51 2.3 0.8 1.0
SG L:CYS48 2.3 0.3 1.0
SG L:CYS31 2.3 0.2 1.0
CB L:CYS31 3.2 0.9 1.0
CB L:CYS48 3.3 0.3 1.0
CB L:CYS34 3.5 0.8 1.0
CA L:CYS51 3.7 0.2 1.0
N L:CYS34 3.7 0.3 1.0
O L:CYS51 3.9 0.5 1.0
C L:CYS51 4.0 0.8 1.0
CB L:HIS53 4.1 0.9 1.0
CA L:CYS34 4.2 0.2 1.0
N L:CYS51 4.2 0.1 1.0
CB L:GLU33 4.5 0.1 1.0
OG L:SER36 4.6 0.8 1.0
CA L:CYS31 4.7 0.3 1.0
O L:LYS49 4.7 0.6 1.0
CA L:CYS48 4.7 0.4 1.0
C L:GLU33 4.8 0.8 1.0
N L:GLU33 4.8 0.6 1.0
ND1 L:HIS53 4.8 0.2 1.0
N L:SER35 4.9 0.4 1.0
C L:CYS34 4.9 0.5 1.0
CA L:GLU33 4.9 0.1 1.0
CG L:HIS53 5.0 1.0 1.0
N L:GLY52 5.0 0.7 1.0
N L:HIS53 5.0 0.6 1.0

Zinc binding site 9 out of 9 in 4bbs

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

b:0.9
occ:1.00
 SG M:CYS48 2.3 92.6 1.0
SG M:CYS27 2.3 0.0 1.0
SG M:CYS24 2.3 0.5 1.0
SG M:CYS45 2.3 0.0 1.0
CB M:CYS24 3.0 0.9 1.0
CB M:CYS48 3.2 0.6 1.0
CB M:CYS45 3.2 85.0 1.0
CB M:CYS27 3.5 0.3 1.0
N M:CYS48 3.6 0.8 1.0
CA M:CYS48 3.9 97.4 1.0
N M:CYS27 4.2 1.0 1.0
CA M:CYS24 4.5 0.8 1.0
CA M:CYS27 4.5 0.4 1.0
CB M:LEU47 4.5 100.0 1.0
CA M:CYS45 4.6 82.5 1.0
N M:GLY49 4.7 78.8 1.0
C M:CYS48 4.7 85.8 1.0
C M:LEU47 4.7 99.0 1.0
CB M:LEU50 4.8 80.7 1.0
CB M:GLU26 4.9 0.0 1.0
C M:CYS45 5.0 87.8 1.0
O M:CYS45 5.0 89.1 1.0
CA M:LEU47 5.0 97.7 1.0
N M:LEU50 5.0 84.9 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 19:38:45 2024

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