Atomistry » Zinc » PDB 3k14-3kek » 3k7a
Atomistry »
  Zinc »
    PDB 3k14-3kek »
      3k7a »

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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 3 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 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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 4 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 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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 5 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 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

Go back to Zinc Binding Sites List in 3k7a
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

Go back to Zinc Binding Sites List in 3k7a
Zinc binding site 7 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 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

Go back to Zinc Binding Sites List in 3k7a
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

Go back to Zinc Binding Sites List in 3k7a
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

Last articles

As in 2IM2
As in 2IA5
As in 2IM1
As in 2IM0
As in 2ILZ
As in 2ILY
As in 2H79
As in 2I0K
As in 2HZE
As in 2H77
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy