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Zinc in PDB 3k1f: Crystal Structure of Rna Polymerase II in Complex with Tfiib

Enzymatic activity of Crystal Structure of Rna Polymerase II in Complex with Tfiib

All present enzymatic activity of Crystal Structure of Rna Polymerase II in Complex with Tfiib:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Rna Polymerase II in Complex with Tfiib, PDB code: 3k1f was solved by D.Kostrewa, M.E.Zeller, K.-J.Armache, M.Seizl, K.Leike, M.Thomm, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.69 / 4.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.970, 408.270, 275.240, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rna Polymerase II in Complex with Tfiib (pdb code 3k1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Rna Polymerase II in Complex with Tfiib, PDB code: 3k1f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:0.8
occ:1.00
 SG A:CYS167 2.3 0.6 1.0
SG A:CYS110 2.4 0.7 1.0
SG A:CYS107 2.4 0.1 1.0
SG A:CYS148 2.5 0.3 1.0
CB A:CYS107 3.0 0.9 1.0
CB A:CYS148 3.1 1.0 1.0
CB A:CYS110 3.5 1.0 1.0
O A:GLY166 3.7 0.3 1.0
O A:CYS167 3.8 0.6 1.0
CB A:CYS167 4.1 0.4 1.0
CA A:CYS107 4.4 0.2 1.0
C A:GLY166 4.6 0.8 1.0
O A:MET108 4.6 0.1 1.0
CA A:CYS148 4.6 0.3 1.0
C A:CYS167 4.6 0.2 1.0
CA A:CYS167 4.7 0.5 1.0
CA A:CYS110 4.7 0.9 1.0
C A:CYS107 4.8 0.1 1.0
N A:CYS110 4.9 0.9 1.0
ND1 A:HIS109 4.9 0.1 1.0
N A:CYS167 5.0 0.2 1.0

Zinc binding site 2 out of 9 in 3k1f

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


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:65.8
occ:1.00
 NE2 A:HIS80 2.1 95.1 1.0
CB A:CYS67 2.3 0.5 1.0
SG A:CYS67 2.4 0.7 1.0
SG A:CYS77 2.4 0.3 1.0
SG A:CYS70 2.5 0.9 1.0
CD2 A:HIS80 2.8 95.5 1.0
CE1 A:HIS80 3.3 95.1 1.0
CA A:CYS67 3.5 0.8 1.0
OE1 A:GLN68 3.5 0.2 1.0
C A:CYS67 3.8 0.4 1.0
O A:CYS67 3.8 0.1 1.0
O A:PRO78 4.0 98.3 1.0
CG A:HIS80 4.1 95.7 1.0
CB A:CYS77 4.1 0.3 1.0
CB A:CYS70 4.2 0.5 1.0
ND1 A:HIS80 4.3 95.5 1.0
N A:GLN71 4.3 0.6 1.0
O A:GLN71 4.4 0.7 1.0
N A:CYS67 4.6 0.3 1.0
CD A:GLN68 4.7 0.9 1.0
N A:GLN68 4.8 0.9 1.0
CA A:GLN71 4.8 0.4 1.0
O A:LEU58 5.0 0.9 1.0

Zinc binding site 3 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:78.0
occ:1.00
 SG B:CYS1185 2.3 0.8 1.0
SG B:CYS1166 2.4 86.1 1.0
SG B:CYS1163 2.4 87.5 1.0
SG B:CYS1182 2.4 0.2 1.0
CB B:CYS1163 3.1 86.2 1.0
CB B:CYS1185 3.4 0.7 1.0
CB B:CYS1182 3.7 0.4 1.0
N B:CYS1166 3.7 85.6 1.0
CB B:CYS1166 4.0 85.7 1.0
O B:CYS1166 4.1 83.9 1.0
CB B:ILE1165 4.2 86.5 1.0
CA B:CYS1166 4.3 85.0 1.0
CG2 B:ILE1165 4.5 87.1 1.0
CA B:CYS1163 4.6 85.7 1.0
C B:ILE1165 4.7 84.8 1.0
C B:CYS1166 4.7 84.0 1.0
CA B:ILE1165 4.7 85.4 1.0
CA B:CYS1185 4.8 0.0 1.0
N B:ILE1165 4.8 84.7 1.0

Zinc binding site 4 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:62.1
occ:1.00
 SG C:CYS92 2.3 0.7 1.0
SG C:CYS88 2.4 0.6 1.0
SG C:CYS95 2.4 0.7 1.0
SG C:CYS86 2.4 0.6 1.0
CB C:CYS86 3.1 0.6 1.0
CB C:CYS92 3.3 0.6 1.0
N C:CYS92 3.5 1.0 1.0
CB C:CYS95 3.6 0.9 1.0
CB C:CYS88 3.6 0.9 1.0
CA C:CYS92 3.9 0.0 1.0
N C:CYS95 4.1 0.5 1.0
C C:HIS91 4.2 0.4 1.0
CA C:CYS95 4.5 0.6 1.0
CA C:HIS91 4.5 0.4 1.0
CB C:LYS94 4.5 0.6 1.0
CA C:CYS86 4.5 0.9 1.0
C C:CYS92 4.5 0.3 1.0
O C:ASP90 4.6 0.2 1.0
N C:CYS88 4.7 0.7 1.0
CA C:CYS88 4.7 0.8 1.0
N C:LYS94 4.8 0.0 1.0
C C:LYS94 4.9 0.0 1.0
C C:CYS86 4.9 0.9 1.0
O C:HIS91 5.0 0.8 1.0
O C:CYS92 5.0 0.6 1.0

Zinc binding site 5 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:0.4
occ:1.00
 SG I:CYS29 2.3 1.0 1.0
SG I:CYS10 2.3 1.0 1.0
SG I:CYS7 2.4 0.8 1.0
SG I:CYS32 2.4 0.8 1.0
CB I:CYS29 2.8 0.1 1.0
CB I:CYS7 3.3 0.8 1.0
CB I:CYS32 3.8 0.8 1.0
N I:CYS10 3.8 0.1 1.0
CB I:CYS10 3.9 0.1 1.0
N I:CYS32 4.2 0.2 1.0
CA I:CYS10 4.2 0.3 1.0
CA I:CYS29 4.3 0.8 1.0
CB I:THR31 4.5 0.1 1.0
CB I:TYR34 4.6 0.9 1.0
CA I:CYS32 4.6 0.4 1.0
OD1 I:ASN12 4.6 0.9 1.0
C I:CYS10 4.6 0.9 1.0
C I:CYS29 4.7 0.7 1.0
CB I:ASP9 4.7 0.1 1.0
CA I:CYS7 4.8 0.9 1.0
C I:THR31 4.8 0.4 1.0
N I:ASN11 4.8 0.6 1.0
O I:CYS29 4.8 0.3 1.0
OG1 I:THR31 4.9 0.8 1.0
N I:THR31 4.9 0.6 1.0
C I:ASP9 4.9 0.6 1.0
CB I:ASN12 4.9 0.2 1.0
CD2 I:TYR34 5.0 0.1 1.0
CA I:THR31 5.0 0.3 1.0

Zinc binding site 6 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:0.5
occ:1.00
 SG I:CYS106 2.4 0.9 1.0
SG I:CYS78 2.4 0.3 1.0
SG I:CYS103 2.4 0.2 1.0
SG I:CYS75 2.4 1.0 1.0
CB I:CYS75 2.9 0.3 1.0
CB I:CYS103 2.9 0.8 1.0
CB I:CYS106 3.7 0.2 1.0
CB I:CYS78 3.9 0.1 1.0
N I:CYS106 4.1 0.1 1.0
N I:CYS78 4.2 0.1 1.0
N I:SER107 4.3 0.2 1.0
CB I:HIS108 4.4 0.2 1.0
CA I:CYS75 4.4 0.6 1.0
CA I:CYS106 4.4 0.4 1.0
CA I:CYS103 4.4 0.0 1.0
CA I:CYS78 4.5 0.1 1.0
N I:HIS108 4.7 0.7 1.0
OG I:SER80 4.7 0.2 1.0
N I:HIS79 4.8 0.3 1.0
C I:CYS106 4.8 0.5 1.0
CB I:SER105 4.8 0.8 1.0
CB I:SER80 4.8 0.6 1.0
N I:SER80 4.9 0.1 1.0

Zinc binding site 7 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:1.0
occ:1.00
 SG J:CYS45 2.4 0.6 1.0
SG J:CYS10 2.4 0.9 1.0
SG J:CYS7 2.4 0.0 1.0
SG J:CYS46 2.5 0.5 1.0
N J:CYS46 3.2 0.3 1.0
CB J:CYS10 3.2 0.3 1.0
CB J:CYS7 3.3 1.0 1.0
C J:CYS45 3.4 0.5 1.0
CB J:CYS45 3.5 0.9 1.0
CA J:CYS46 3.6 0.3 1.0
CB J:CYS46 3.6 0.1 1.0
N J:CYS10 3.7 98.1 1.0
O J:CYS45 3.9 0.5 1.0
CA J:CYS10 4.0 99.5 1.0
CA J:CYS45 4.0 0.7 1.0
NE J:ARG43 4.2 0.1 1.0
CG J:ARG43 4.3 0.0 1.0
N J:GLY11 4.3 98.7 1.0
C J:CYS10 4.6 99.9 1.0
CA J:CYS7 4.8 0.7 1.0
N J:CYS45 4.8 0.2 1.0
N J:LYS12 4.8 0.8 1.0
CD J:ARG43 4.8 0.2 1.0
CB J:SER9 4.8 95.0 1.0
C J:SER9 4.8 95.6 1.0
NH2 J:ARG43 4.9 0.7 1.0
CZ J:ARG43 4.9 0.8 1.0

Zinc binding site 8 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:0.7
occ:1.00
 SG L:CYS34 2.3 0.3 1.0
SG L:CYS51 2.3 0.3 1.0
SG L:CYS48 2.4 0.8 1.0
SG L:CYS31 2.5 0.8 1.0
CB L:CYS34 3.2 0.7 1.0
CB L:CYS31 3.2 0.4 1.0
CB L:CYS51 3.3 0.3 1.0
CB L:CYS48 3.5 0.1 1.0
N L:CYS34 3.8 0.9 1.0
N L:CYS51 4.0 0.8 1.0
CA L:CYS34 4.1 0.6 1.0
CA L:CYS51 4.3 0.9 1.0
CB L:ASP50 4.5 0.1 1.0
CA L:CYS31 4.7 0.3 1.0
C L:ASP50 4.8 0.4 1.0
OG L:SER36 4.8 0.9 1.0
C L:CYS34 4.9 1.0 1.0
CA L:CYS48 4.9 0.1 1.0
N L:SER35 5.0 0.1 1.0
C L:GLU33 5.0 0.3 1.0

Zinc binding site 9 out of 9 in 3k1f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Rna Polymerase II in Complex with Tfiib within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn3009

b:71.1
occ:1.00
 SG M:CYS48 2.4 96.2 1.0
SG M:CYS27 2.4 0.0 1.0
SG M:CYS45 2.4 94.9 1.0
SG M:CYS24 2.4 0.2 1.0
CB M:CYS48 3.1 97.1 1.0
CB M:CYS27 3.4 0.7 1.0
N M:CYS48 3.6 97.4 1.0
CB M:CYS24 3.6 0.8 1.0
CB M:CYS45 3.7 93.6 1.0
N M:CYS27 3.8 0.7 1.0
CA M:CYS48 3.8 96.9 1.0
CA M:CYS27 4.2 0.9 1.0
CB M:GLU26 4.4 0.8 1.0
CB M:LEU47 4.4 98.2 1.0
C M:CYS48 4.5 95.7 1.0
CB M:LEU50 4.6 98.6 1.0
N M:GLY49 4.6 97.3 1.0
C M:LEU47 4.7 97.0 1.0
N M:LEU50 4.7 98.7 1.0
C M:GLU26 4.8 1.0 1.0
CD2 M:LEU47 4.9 99.3 1.0
CA M:LEU47 5.0 97.6 1.0
CA M:CYS24 5.0 0.7 1.0

Reference:

D.Kostrewa, M.E.Zeller, K.J.Armache, M.Seizl, K.Leike, M.Thomm, P.Cramer. Rna Polymerase II-Tfiib Structure and Mechanism of Transcription Initiation. Nature V. 462 323 2009.
ISSN: ISSN 0028-0836
PubMed: 19820686
DOI: 10.1038/NATURE08548
Page generated: Sat Oct 26 07:37:09 2024

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