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Zinc in PDB 3k7a: Crystal Structure of An Rna Polymerase II-Tfiib Complex

Enzymatic activity of Crystal Structure of An Rna Polymerase II-Tfiib Complex

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

Protein crystallography data

The structure of Crystal Structure of An Rna Polymerase II-Tfiib Complex, PDB code: 3k7a was solved by X.Liu, D.A.Bushnell, D.Wang, G.Calero, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 204.150, 216.210, 420.980, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 31.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Rna Polymerase II-Tfiib Complex (pdb code 3k7a). 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 An Rna Polymerase II-Tfiib Complex, PDB code: 3k7a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3k7a

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Zinc binding site 1 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.4
occ:1.00
 SG A:CYS167 2.3 0.7 1.0
SG A:CYS110 2.8 0.3 1.0
SG A:CYS107 3.2 0.2 1.0
SG A:CYS148 3.5 0.7 1.0
O A:MET108 3.6 0.1 1.0
CB A:CYS110 3.6 0.2 1.0
O A:CYS167 3.8 0.7 1.0
CB A:CYS167 3.8 0.1 1.0
N A:CYS110 3.8 0.4 1.0
CB A:CYS107 4.0 0.6 1.0
CB A:CYS148 4.1 0.2 1.0
CA A:CYS110 4.2 0.4 1.0
C A:MET108 4.6 0.4 1.0
CB A:HIS109 4.6 0.2 1.0
N A:GLY111 4.6 0.3 1.0
C A:CYS167 4.6 0.7 1.0
O A:CYS107 4.7 0.9 1.0
CA A:CYS167 4.7 0.9 1.0
C A:CYS107 4.8 0.3 1.0
C A:CYS110 4.8 0.7 1.0
ND2 A:ASN169 4.9 0.8 1.0
C A:HIS109 4.9 0.4 1.0

Zinc binding site 2 out of 9 in 3k7a

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Zinc binding site 2 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:1.0
occ:1.00
 SG A:CYS70 2.3 0.3 1.0
SG A:CYS77 2.5 0.4 1.0
NE2 A:HIS80 2.5 0.8 1.0
SG A:CYS67 2.5 0.4 1.0
CB A:CYS77 3.3 0.3 1.0
CE1 A:HIS80 3.3 0.3 1.0
CA A:CYS77 3.5 0.1 1.0
CD2 A:HIS80 3.5 0.5 1.0
CB A:CYS67 4.0 0.6 1.0
CB A:CYS70 4.0 0.6 1.0
C A:CYS77 4.0 0.2 1.0
CD A:PRO78 4.1 0.8 1.0
O A:PRO78 4.1 0.1 1.0
N A:PRO78 4.2 0.5 1.0
O A:CYS67 4.3 0.9 1.0
ND1 A:HIS80 4.5 0.3 1.0
CG A:HIS80 4.6 0.1 1.0
N A:CYS77 4.8 0.9 1.0
O A:GLN71 4.8 0.2 1.0
C A:PRO78 4.8 0.8 1.0
O A:CYS77 4.8 0.1 1.0
O A:GLU76 4.9 0.7 1.0
CG A:PRO78 4.9 0.1 1.0
C A:CYS67 5.0 0.1 1.0

Zinc binding site 3 out of 9 in 3k7a

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Zinc binding site 3 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.8
occ:1.00
 SG B:CYS1182 2.2 0.2 1.0
SG B:CYS1185 2.2 0.5 1.0
SG B:CYS1163 2.3 0.0 1.0
SG B:CYS1166 2.3 0.3 1.0
CB B:CYS1185 2.5 0.2 1.0
CB B:CYS1163 3.1 0.4 1.0
CB B:CYS1182 3.7 0.4 1.0
CB B:CYS1166 3.9 0.7 1.0
CA B:CYS1185 3.9 0.7 1.0
N B:CYS1166 4.2 0.0 1.0
O B:CYS1166 4.3 0.2 1.0
ND2 B:ASN1187 4.4 0.2 1.0
N B:CYS1185 4.5 0.7 1.0
CA B:CYS1166 4.5 94.8 1.0
CA B:CYS1163 4.6 0.2 1.0
O B:CYS1182 4.9 0.4 1.0
C B:CYS1166 4.9 0.4 1.0
C B:CYS1185 5.0 0.7 1.0
CA B:CYS1182 5.0 0.8 1.0

Zinc binding site 4 out of 9 in 3k7a

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Zinc binding site 4 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.3
occ:1.00
 SG C:CYS86 2.2 0.6 1.0
SG C:CYS92 2.3 0.5 1.0
SG C:CYS88 2.3 0.9 1.0
SG C:CYS95 2.3 0.2 1.0
CB C:CYS86 2.9 0.0 1.0
CB C:CYS95 3.3 0.1 1.0
CB C:CYS88 3.3 0.5 1.0
CB C:CYS92 3.5 0.1 1.0
N C:CYS92 3.6 0.2 1.0
N C:CYS95 4.0 0.5 1.0
C C:HIS91 4.1 0.9 1.0
CA C:CYS92 4.1 0.0 1.0
CA C:HIS91 4.1 0.2 1.0
CA C:CYS95 4.3 0.6 1.0
CA C:CYS86 4.3 0.1 1.0
N C:CYS88 4.3 0.3 1.0
CA C:CYS88 4.4 0.2 1.0
CB C:LYS94 4.5 0.0 1.0
C C:LYS94 4.5 1.0 1.0
C C:CYS86 4.6 0.2 1.0
O C:ASP90 4.7 0.4 1.0
C C:CYS92 4.8 0.3 1.0
N C:LYS94 4.8 0.7 1.0
O C:CYS86 4.8 0.7 1.0
CA C:LYS94 4.8 0.7 1.0
O C:HIS91 5.0 0.5 1.0
N C:HIS91 5.0 0.5 1.0

Zinc binding site 5 out of 9 in 3k7a

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Zinc binding site 5 out of 9 in the Crystal Structure of An 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 Crystal Structure of An 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:CYS10 2.2 0.2 1.0
SG I:CYS29 2.4 0.4 1.0
SG I:CYS32 2.5 0.3 1.0
CB I:CYS32 2.8 0.5 1.0
CB I:CYS10 2.9 0.3 1.0
CG2 I:THR31 2.9 0.7 1.0
N I:CYS32 3.7 0.2 1.0
SG I:CYS7 3.8 0.0 1.0
CA I:CYS32 3.8 0.2 1.0
CB I:CYS29 3.9 0.5 1.0
C I:THR31 4.0 0.3 1.0
CB I:THR31 4.3 0.0 1.0
CA I:CYS10 4.3 0.2 1.0
O I:THR31 4.5 0.8 1.0
N I:CYS10 4.5 0.2 1.0
CA I:THR31 4.6 0.4 1.0
CB I:CYS7 4.8 0.8 1.0
N I:THR31 4.9 0.7 1.0
OG1 I:THR31 5.0 0.5 1.0

Zinc binding site 6 out of 9 in 3k7a

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Zinc binding site 6 out of 9 in the Crystal Structure of An 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 Crystal Structure of An 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:CYS103 2.3 0.6 1.0
CB I:CYS78 2.3 0.8 1.0
SG I:CYS75 2.3 0.3 1.0
SG I:CYS106 2.3 0.1 1.0
CB I:CYS75 2.5 0.0 1.0
CB I:CYS103 3.0 0.1 1.0
N I:CYS78 3.2 1.0 1.0
CA I:CYS78 3.2 0.2 1.0
CB I:CYS106 3.2 0.9 1.0
SG I:CYS78 3.6 0.2 1.0
CA I:CYS75 3.9 0.6 1.0
C I:CYS78 4.1 0.4 1.0
O I:CYS75 4.3 0.3 1.0
CB I:HIS108 4.3 0.2 1.0
C I:CYS75 4.3 0.6 1.0
N I:HIS79 4.4 0.3 1.0
CA I:CYS106 4.4 0.7 1.0
OG I:SER80 4.4 0.9 1.0
C I:LYS77 4.5 0.5 1.0
CA I:CYS103 4.5 0.5 1.0
N I:CYS106 4.5 0.0 1.0
N I:CYS75 4.6 0.7 1.0
CB I:SER80 4.7 0.3 1.0
N I:SER80 4.8 0.3 1.0
N I:LYS77 4.9 0.7 1.0
CB I:LYS77 4.9 0.4 1.0
CA I:LYS77 5.0 0.2 1.0

Zinc binding site 7 out of 9 in 3k7a

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Zinc binding site 7 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.3
occ:1.00
 N J:CYS46 2.0 0.4 1.0
SG J:CYS45 2.3 0.0 1.0
SG J:CYS10 2.4 0.8 1.0
C J:CYS45 2.4 0.7 1.0
SG J:CYS7 2.5 0.5 1.0
CA J:CYS46 2.5 0.6 1.0
SG J:CYS46 2.6 0.3 1.0
CB J:CYS46 2.9 0.9 1.0
CB J:CYS45 2.9 0.5 1.0
O J:CYS45 3.0 0.9 1.0
CA J:CYS45 3.2 0.3 1.0
CB J:CYS10 3.2 0.2 1.0
N J:CYS10 3.5 0.5 1.0
CB J:CYS7 3.5 0.2 1.0
CA J:CYS10 3.9 0.2 1.0
C J:CYS46 4.0 1.0 1.0
N J:CYS45 4.1 0.1 1.0
CB J:SER9 4.4 1.0 1.0
C J:SER9 4.6 0.0 1.0
N J:ARG47 4.6 0.1 1.0
O J:ARG43 4.7 0.8 1.0
CA J:SER9 4.8 0.0 1.0
N J:SER9 4.8 0.9 1.0
NE J:ARG43 4.9 0.5 1.0
O J:CYS46 4.9 0.0 1.0
N J:GLY11 5.0 0.8 1.0
CA J:CYS7 5.0 1.0 1.0
C J:TYR44 5.0 0.5 1.0

Zinc binding site 8 out of 9 in 3k7a

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Zinc binding site 8 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.8
occ:1.00
 CB L:CYS31 2.3 0.0 1.0
SG L:CYS51 2.3 0.5 1.0
SG L:CYS48 2.3 0.9 1.0
SG L:CYS31 2.4 0.7 1.0
SG L:CYS34 2.5 0.9 1.0
CB L:CYS48 3.0 0.6 1.0
CA L:CYS31 3.8 0.8 1.0
O L:CYS51 3.9 0.2 1.0
CB L:CYS34 3.9 0.5 1.0
N L:SER35 4.0 0.8 1.0
CB L:CYS51 4.1 0.2 1.0
N L:CYS34 4.2 0.6 1.0
C L:CYS34 4.2 0.7 1.0
CA L:CYS34 4.3 0.6 1.0
N L:CYS31 4.5 0.3 1.0
OG L:SER36 4.5 0.6 1.0
CA L:CYS48 4.5 0.9 1.0
N L:SER36 4.5 0.9 1.0
C L:CYS31 4.6 0.1 1.0
CA L:SER35 4.7 0.6 1.0
N L:LYS49 4.8 0.6 1.0
C L:CYS51 4.8 0.3 1.0
O L:CYS34 4.9 0.2 1.0
CA L:CYS51 5.0 0.6 1.0

Zinc binding site 9 out of 9 in 3k7a

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Zinc binding site 9 out of 9 in the Crystal Structure of An 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 Crystal Structure of An Rna Polymerase II-Tfiib Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn346

b:0.2
occ:1.00
 N M:CYS48 2.4 0.2 1.0
CA M:CYS48 2.8 1.0 1.0
C M:LEU47 3.5 0.1 1.0
C M:CYS48 3.9 0.2 1.0
N M:GLY49 4.0 0.7 1.0
CA M:LEU47 4.1 0.0 1.0
CA M:CYS24 4.1 0.4 1.0
N M:CYS27 4.2 0.0 1.0
O M:LEU47 4.4 0.8 1.0
O M:CYS27 4.4 0.1 1.0
N M:LEU47 4.5 0.1 1.0
CA M:CYS27 4.7 0.8 1.0
C M:CYS24 4.8 0.4 1.0
C M:CYS27 4.8 0.9 1.0
CA M:CYS45 4.8 0.9 1.0
O M:CYS48 4.9 0.2 1.0

Reference:

X.Liu, D.A.Bushnell, D.Wang, G.Calero, R.D.Kornberg. Structure of An Rna Polymerase II-Tfiib Complex and the Transcription Initiation Mechanism. Science V. 327 206 2010.
ISSN: ISSN 0036-8075
PubMed: 19965383
DOI: 10.1126/SCIENCE.1182015
Page generated: Sat Oct 26 07:42:21 2024

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