Atomistry » Zinc » PDB 4brr-4bxx » 4bxx
Atomistry »
  Zinc »
    PDB 4brr-4bxx »
      4bxx »

Zinc in PDB 4bxx: Arrested Rna Polymerase II-BYE1 Complex

Enzymatic activity of Arrested Rna Polymerase II-BYE1 Complex

All present enzymatic activity of Arrested Rna Polymerase II-BYE1 Complex:
2.7.7.6;

Protein crystallography data

The structure of Arrested Rna Polymerase II-BYE1 Complex, PDB code: 4bxx was solved by K.Kinkelin, G.G.Wozniak, S.B.Rothbart, M.Lidschreiber, B.D.Strahl, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 3.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.920, 392.670, 281.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.98 / 20.77

Other elements in 4bxx:

The structure of Arrested Rna Polymerase II-BYE1 Complex also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Arrested Rna Polymerase II-BYE1 Complex (pdb code 4bxx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Arrested Rna Polymerase II-BYE1 Complex, PDB code: 4bxx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 1 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.2
occ:1.00
 SG A:CYS107 2.3 0.9 1.0
SG A:CYS110 2.3 0.4 1.0
SG A:CYS148 2.3 0.9 1.0
SG A:CYS167 2.4 0.6 1.0
CB A:CYS167 2.7 0.8 1.0
CB A:CYS148 3.1 0.4 1.0
CB A:CYS107 3.2 0.8 1.0
CB A:CYS110 3.3 0.1 1.0
N A:CYS110 3.8 1.0 1.0
CA A:CYS167 4.1 0.8 1.0
CA A:CYS110 4.1 0.0 1.0
O A:CYS167 4.2 0.7 1.0
O A:GLY166 4.3 0.4 1.0
C A:CYS167 4.4 1.0 1.0
CA A:CYS148 4.6 0.4 1.0
CA A:CYS107 4.7 0.4 1.0
CB A:LYS112 4.8 0.1 1.0
CB A:HIS109 4.9 0.8 1.0
C A:CYS110 4.9 0.2 1.0
N A:CYS167 4.9 0.3 1.0
C A:HIS109 4.9 0.9 1.0
N A:GLY111 4.9 0.3 1.0
C A:GLY166 5.0 0.5 1.0
ND1 A:HIS109 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 2 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:79.5
occ:1.00
 NE2 A:HIS80 2.1 82.5 1.0
SG A:CYS67 2.3 0.7 1.0
SG A:CYS77 2.3 83.7 1.0
SG A:CYS70 2.5 0.0 1.0
CD2 A:HIS80 3.1 83.2 1.0
CE1 A:HIS80 3.1 82.7 1.0
CB A:CYS77 3.3 79.0 1.0
CB A:CYS70 3.5 1.0 1.0
CB A:CYS67 3.6 0.9 1.0
CG A:HIS80 4.2 82.2 1.0
ND1 A:HIS80 4.3 83.8 1.0
OE1 A:GLN68 4.3 91.0 1.0
CA A:CYS77 4.3 78.2 1.0
O A:PRO78 4.4 87.8 1.0
O A:CYS67 4.4 0.5 1.0
CD A:GLN68 4.6 0.2 1.0
O A:GLN71 4.7 0.9 1.0
O A:LEU58 4.7 98.9 1.0
CA A:CYS67 4.8 0.4 1.0
CG A:GLN68 4.8 0.1 1.0
CA A:CYS70 4.9 0.8 1.0
C A:CYS67 4.9 1.0 1.0
C A:CYS77 5.0 81.2 1.0

Zinc binding site 3 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 3 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:83.0
occ:1.00
 SG B:CYS1166 2.3 89.4 1.0
SG B:CYS1182 2.3 78.7 1.0
SG B:CYS1163 2.3 78.4 1.0
SG B:CYS1185 2.3 81.6 1.0
CB B:CYS1163 3.1 72.8 1.0
CB B:CYS1185 3.1 80.1 1.0
CB B:CYS1182 3.7 75.5 1.0
CB B:CYS1166 3.7 85.7 1.0
N B:CYS1166 3.9 86.0 1.0
O B:CYS1166 4.0 91.5 1.0
CA B:CYS1166 4.3 85.3 1.0
CA B:CYS1185 4.4 83.5 1.0
N B:CYS1185 4.5 85.5 1.0
CA B:CYS1163 4.6 71.8 1.0
C B:CYS1166 4.6 90.1 1.0
CB B:ILE1165 4.7 81.7 1.0
O B:CYS1182 4.7 87.8 1.0
CB B:THR1170 4.9 90.7 1.0
N B:ILE1165 4.9 78.3 1.0
C B:ILE1165 5.0 87.0 1.0
CA B:CYS1182 5.0 76.7 1.0

Zinc binding site 4 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 4 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:81.8
occ:1.00
 SG C:CYS95 2.3 81.1 1.0
SG C:CYS86 2.3 80.4 1.0
SG C:CYS88 2.3 83.8 1.0
SG C:CYS92 2.4 82.3 1.0
CB C:CYS86 3.1 75.3 1.0
CB C:CYS95 3.3 78.0 1.0
N C:CYS92 3.4 79.3 1.0
CB C:CYS92 3.4 79.3 1.0
CB C:CYS88 3.4 81.4 1.0
C C:HIS91 3.9 84.3 1.0
CA C:CYS92 3.9 79.5 1.0
N C:CYS95 4.0 80.1 1.0
CA C:HIS91 4.1 83.0 1.0
CA C:CYS95 4.3 79.0 1.0
N C:CYS88 4.3 79.9 1.0
C C:CYS92 4.4 84.4 1.0
CA C:CYS88 4.5 81.1 1.0
CA C:CYS86 4.5 75.4 1.0
O C:HIS91 4.6 83.7 1.0
CB C:LYS94 4.7 80.4 1.0
O C:ASP90 4.7 89.6 1.0
O C:CYS92 4.7 82.2 1.0
C C:CYS86 4.8 79.0 1.0
C C:LYS94 4.9 83.9 1.0
N C:LYS94 4.9 81.5 1.0
N C:HIS91 4.9 83.6 1.0

Zinc binding site 5 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 5 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.6
occ:1.00
 SG I:CYS10 2.2 0.5 1.0
SG I:CYS32 2.3 0.8 1.0
SG I:CYS7 2.3 0.6 1.0
SG I:CYS29 2.3 0.8 1.0
CB I:CYS29 3.1 0.4 1.0
CB I:CYS32 3.2 0.1 1.0
CB I:CYS7 3.4 0.9 1.0
CB I:CYS10 3.9 0.1 1.0
N I:CYS32 3.9 0.1 1.0
CA I:CYS32 4.1 0.5 1.0
OG1 I:THR31 4.1 0.3 1.0
N I:CYS10 4.1 0.7 1.0
CB I:TYR34 4.2 0.2 1.0
CA I:CYS10 4.5 0.9 1.0
CB I:ASP9 4.5 0.3 1.0
C I:THR31 4.6 0.8 1.0
CA I:CYS29 4.6 0.8 1.0
C I:CYS32 4.7 0.0 1.0
CA I:CYS7 4.8 0.8 1.0
C I:ASP9 4.8 0.9 1.0
O I:ARG8 4.9 0.5 1.0
N I:TYR34 4.9 0.5 1.0

Zinc binding site 6 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 6 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.4
occ:1.00
 SG I:CYS78 2.3 0.4 1.0
SG I:CYS106 2.3 0.0 1.0
SG I:CYS103 2.3 0.5 1.0
SG I:CYS75 2.3 0.1 1.0
CB I:CYS103 2.9 0.4 1.0
CB I:CYS106 3.0 0.0 1.0
CB I:CYS75 3.1 0.7 1.0
CB I:CYS78 3.3 0.7 1.0
N I:CYS78 3.8 0.2 1.0
N I:CYS106 4.0 0.2 1.0
CA I:CYS106 4.0 0.1 1.0
CA I:CYS78 4.1 0.4 1.0
CA I:CYS103 4.4 0.0 1.0
C I:SER105 4.5 0.8 1.0
CA I:CYS75 4.6 0.6 1.0
N I:HIS79 4.6 0.3 1.0
CD2 I:HIS108 4.7 0.5 1.0
OG I:SER80 4.7 0.8 1.0
CB I:SER80 4.7 0.1 1.0
C I:CYS78 4.7 0.2 1.0
C I:CYS106 4.7 0.5 1.0
N I:SER107 4.9 0.9 1.0
O I:SER105 4.9 0.5 1.0
N I:SER80 5.0 0.1 1.0
C I:LYS77 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 7 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:90.2
occ:1.00
 SG J:CYS46 2.2 0.4 1.0
SG J:CYS45 2.3 94.1 1.0
SG J:CYS7 2.3 92.6 1.0
SG J:CYS10 2.4 85.5 1.0
N J:CYS46 3.0 95.8 1.0
CB J:CYS7 3.2 89.3 1.0
CA J:CYS46 3.4 96.5 1.0
CB J:CYS46 3.4 98.1 1.0
C J:CYS45 3.4 97.5 1.0
CB J:CYS10 3.5 80.6 1.0
CB J:CYS45 3.5 90.6 1.0
N J:CYS10 3.9 79.6 1.0
O J:CYS45 4.0 96.7 1.0
CA J:CYS45 4.0 92.0 1.0
CA J:CYS10 4.2 79.1 1.0
NE J:ARG43 4.2 0.4 1.0
CB J:SER9 4.6 86.4 1.0
NH2 J:ARG43 4.6 0.5 1.0
CB J:ARG43 4.6 96.7 1.0
N J:CYS45 4.7 94.2 1.0
CA J:CYS7 4.7 88.5 1.0
N J:GLY11 4.7 80.9 1.0
O J:ARG43 4.8 0.4 1.0
C J:CYS46 4.9 99.7 1.0
CZ J:ARG43 4.9 0.8 1.0
CB J:LYS12 5.0 91.7 1.0
C J:SER9 5.0 83.0 1.0

Zinc binding site 8 out of 8 in 4bxx

Go back to Zinc Binding Sites List in 4bxx
Zinc binding site 8 out of 8 in the Arrested Rna Polymerase II-BYE1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Arrested Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.4
occ:1.00
 SG L:CYS48 2.3 0.0 1.0
SG L:CYS34 2.4 0.6 1.0
SG L:CYS51 2.4 0.9 1.0
SG L:CYS31 2.5 0.1 1.0
CB L:CYS48 3.0 0.6 1.0
CB L:CYS34 3.6 0.7 1.0
CB L:CYS31 3.7 0.1 1.0
N L:CYS34 4.1 0.9 1.0
CB L:CYS51 4.2 0.2 1.0
CA L:CYS34 4.4 0.8 1.0
CA L:CYS48 4.5 0.1 1.0
OG L:SER36 4.5 0.8 1.0
O L:CYS51 4.8 0.0 1.0
O L:HIS53 4.8 0.5 1.0
O L:GLY52 4.9 0.7 1.0

Reference:

K.Kinkelin, G.G.Wozniak, S.B.Rothbart, M.Lidschreiber, B.D.Strahl, P.Cramer. Structures of Rna Polymerase II Complexes with BYE1, A Chromatin-Binding PHF3/DIDO1 Homologue Proc.Natl.Acad.Sci.Usa V. 110 15277 2013.
ISSN: ISSN 0027-8424
PubMed: 24003114
DOI: 10.1073/PNAS.1311010110
Page generated: Wed Aug 20 16:24:16 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy