Atomistry » Zinc » PDB 4b3s-4bin » 4bbs
Atomistry »
  Zinc »
    PDB 4b3s-4bin »
      4bbs »

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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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

Go back to Zinc Binding Sites List in 4bbs
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: Wed Dec 16 05:05:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy