Atomistry » Zinc » PDB 4bua-4c09 » 4by7
Atomistry »
  Zinc »
    PDB 4bua-4c09 »
      4by7 »

Zinc in PDB 4by7: Elongating Rna Polymerase II-BYE1 Tld Complex

Enzymatic activity of Elongating Rna Polymerase II-BYE1 Tld Complex

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

Protein crystallography data

The structure of Elongating Rna Polymerase II-BYE1 Tld Complex, PDB code: 4by7 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) 48.84 / 3.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.500, 390.680, 281.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.94 / 21.19

Other elements in 4by7:

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

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Elongating Rna Polymerase II-BYE1 Tld Complex (pdb code 4by7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Elongating Rna Polymerase II-BYE1 Tld Complex, PDB code: 4by7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 1 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 SG A:CYS167 2.2 0.7 1.0
SG A:CYS107 2.3 0.5 1.0
SG A:CYS110 2.3 0.4 1.0
SG A:CYS148 2.4 0.2 1.0
CB A:CYS148 3.0 0.6 1.0
CB A:CYS107 3.1 0.9 1.0
CB A:CYS110 3.4 0.0 1.0
CB A:CYS167 3.6 0.1 1.0
N A:CYS167 3.7 0.6 1.0
N A:CYS110 3.9 0.9 1.0
CA A:CYS167 4.1 0.6 1.0
CA A:CYS110 4.2 0.2 1.0
O A:CYS167 4.3 0.1 1.0
C A:CYS167 4.3 0.9 1.0
CA A:CYS148 4.5 0.6 1.0
CA A:CYS107 4.6 0.9 1.0
C A:GLY166 4.8 0.5 1.0
CB A:HIS109 4.9 0.2 1.0
C A:HIS109 4.9 0.8 1.0
C A:CYS110 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 2 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:80.8
occ:1.00
 NE2 A:HIS80 2.1 83.7 1.0
SG A:CYS67 2.2 0.7 1.0
SG A:CYS77 2.4 83.2 1.0
SG A:CYS70 2.6 0.1 1.0
CD2 A:HIS80 2.8 84.4 1.0
CE1 A:HIS80 3.3 83.7 1.0
CB A:CYS67 3.6 0.9 1.0
CB A:CYS77 3.6 79.0 1.0
CB A:CYS70 4.0 0.8 1.0
CG A:HIS80 4.1 83.3 1.0
O A:PRO78 4.3 84.3 1.0
ND1 A:HIS80 4.3 84.8 1.0
CA A:CYS77 4.4 79.1 1.0
O A:CYS67 4.5 0.1 1.0
OE1 A:GLN68 4.6 64.8 1.0
O A:GLN71 4.6 0.7 1.0
CD A:GLN68 4.7 88.0 1.0
CA A:CYS67 4.8 0.5 1.0
CD A:PRO78 4.9 79.0 1.0
NE2 A:GLN68 4.9 77.0 1.0
C A:CYS67 4.9 0.0 1.0
CG A:GLN68 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 3 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:87.9
occ:1.00
 SG B:CYS1166 2.2 91.8 1.0
SG B:CYS1185 2.4 88.8 1.0
SG B:CYS1182 2.4 83.6 1.0
SG B:CYS1163 2.4 88.3 1.0
CB B:CYS1163 3.1 82.1 1.0
CB B:CYS1185 3.4 86.4 1.0
CB B:CYS1166 3.8 88.0 1.0
O B:CYS1166 3.8 92.7 1.0
CB B:CYS1182 3.9 80.0 1.0
N B:CYS1166 3.9 88.1 1.0
CA B:CYS1166 4.3 87.5 1.0
O B:GLY1184 4.4 95.2 1.0
C B:CYS1166 4.5 91.2 1.0
CA B:CYS1163 4.6 80.2 1.0
CB B:THR1170 4.7 97.7 1.0
CG2 B:THR1170 4.7 0.9 1.0
CB B:ILE1165 4.7 85.1 1.0
CA B:CYS1185 4.8 88.2 1.0
O B:CYS1182 4.9 91.2 1.0
C B:ILE1165 5.0 89.9 1.0
OG1 B:THR1170 5.0 96.2 1.0
N B:ILE1165 5.0 81.3 1.0

Zinc binding site 4 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 4 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:88.7
occ:1.00
 SG C:CYS86 2.3 84.4 1.0
SG C:CYS95 2.3 84.5 1.0
SG C:CYS88 2.3 87.1 1.0
SG C:CYS92 2.4 80.4 1.0
CB C:CYS86 3.3 78.8 1.0
CB C:CYS95 3.4 81.0 1.0
CB C:CYS88 3.4 83.9 1.0
CB C:CYS92 3.4 76.9 1.0
N C:CYS92 3.5 77.7 1.0
CA C:CYS92 4.0 77.1 1.0
C C:HIS91 4.0 84.7 1.0
N C:CYS95 4.0 82.1 1.0
CA C:CYS95 4.3 81.3 1.0
CA C:HIS91 4.3 81.9 1.0
N C:CYS88 4.3 82.0 1.0
C C:CYS92 4.4 82.1 1.0
CA C:CYS88 4.5 83.0 1.0
CB C:LYS94 4.5 83.5 1.0
CA C:CYS86 4.6 78.2 1.0
O C:HIS91 4.6 85.8 1.0
O C:CYS92 4.6 78.9 1.0
O C:ASP90 4.6 91.2 1.0
C C:LYS94 4.7 86.1 1.0
C C:CYS86 4.8 80.8 1.0
N C:LYS94 4.8 82.2 1.0
CA C:LYS94 4.9 81.7 1.0

Zinc binding site 5 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 5 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:0.9
occ:1.00
 SG I:CYS10 2.2 0.1 1.0
SG I:CYS32 2.2 0.5 1.0
SG I:CYS7 2.3 0.1 1.0
SG I:CYS29 2.4 0.7 1.0
CB I:CYS32 3.2 0.2 1.0
CB I:CYS29 3.3 0.9 1.0
CB I:CYS7 3.5 0.6 1.0
CB I:CYS10 3.6 0.0 1.0
N I:CYS32 3.8 0.9 1.0
CA I:CYS32 4.0 0.3 1.0
N I:CYS10 4.1 0.6 1.0
CB I:TYR34 4.2 0.7 1.0
CA I:CYS10 4.3 0.7 1.0
C I:THR31 4.5 0.2 1.0
CB I:THR31 4.6 0.1 1.0
C I:CYS32 4.6 0.4 1.0
O I:ARG8 4.7 0.5 1.0
CA I:CYS29 4.8 1.0 1.0
N I:TYR34 4.9 0.4 1.0
CB I:ASP9 4.9 0.5 1.0
CA I:CYS7 4.9 0.5 1.0
CA I:THR31 4.9 0.5 1.0
C I:CYS10 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 6 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:0.5
occ:1.00
 SG I:CYS106 2.3 0.8 1.0
SG I:CYS78 2.3 0.0 1.0
SG I:CYS75 2.4 0.8 1.0
SG I:CYS103 2.4 0.5 1.0
CB I:CYS75 3.0 0.5 1.0
CB I:CYS103 3.1 0.8 1.0
CB I:CYS78 3.2 0.5 1.0
CB I:CYS106 3.5 0.9 1.0
N I:CYS78 3.7 0.7 1.0
N I:CYS106 3.9 0.5 1.0
CA I:CYS78 4.0 0.1 1.0
CA I:CYS106 4.2 0.4 1.0
CA I:CYS75 4.5 0.1 1.0
CA I:CYS103 4.6 0.9 1.0
C I:CYS78 4.6 0.3 1.0
N I:HIS79 4.7 0.7 1.0
CB I:SER105 4.7 0.6 1.0
CB I:HIS108 4.7 0.9 1.0
N I:SER107 4.8 0.3 1.0
CB I:SER80 4.8 0.5 1.0
N I:SER80 4.8 0.1 1.0
C I:CYS106 4.8 0.7 1.0
C I:LYS77 4.9 0.5 1.0
N I:HIS108 4.9 1.0 1.0

Zinc binding site 7 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 7 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:84.5
occ:1.00
 SG J:CYS10 2.3 91.2 1.0
SG J:CYS45 2.3 82.6 1.0
SG J:CYS46 2.3 92.0 1.0
SG J:CYS7 2.4 95.3 1.0
N J:CYS46 3.0 86.1 1.0
CB J:CYS7 3.2 91.1 1.0
CA J:CYS46 3.3 86.8 1.0
CB J:CYS46 3.4 88.5 1.0
CB J:CYS10 3.4 86.0 1.0
C J:CYS45 3.5 87.0 1.0
CB J:CYS45 3.6 78.7 1.0
N J:CYS10 3.9 83.7 1.0
CA J:CYS45 4.1 80.7 1.0
O J:CYS45 4.1 86.3 1.0
CA J:CYS10 4.2 83.8 1.0
CG J:ARG43 4.3 92.8 1.0
NE J:ARG43 4.7 0.1 1.0
CA J:CYS7 4.7 88.5 1.0
CB J:SER9 4.7 85.9 1.0
N J:CYS45 4.8 83.7 1.0
C J:CYS10 4.8 87.6 1.0
CZ J:ARG43 4.8 0.6 1.0
C J:CYS46 4.9 91.2 1.0
O J:ARG43 4.9 92.9 1.0
CB J:LYS12 4.9 87.8 1.0
NH2 J:ARG43 4.9 0.6 1.0
C J:SER9 5.0 86.1 1.0
N J:GLY11 5.0 82.7 1.0

Zinc binding site 8 out of 8 in 4by7

Go back to Zinc Binding Sites List in 4by7
Zinc binding site 8 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex


Mono view


Stereo pair view

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

b:0.8
occ:1.00
 SG L:CYS48 2.4 0.0 1.0
SG L:CYS34 2.4 0.4 1.0
SG L:CYS51 2.4 0.7 1.0
SG L:CYS31 2.5 0.9 1.0
CB L:CYS48 3.1 0.3 1.0
CB L:CYS31 3.5 0.2 1.0
CB L:CYS51 4.0 0.6 1.0
CB L:CYS34 4.0 0.5 1.0
N L:CYS51 4.1 0.3 1.0
CB L:ASP50 4.3 0.2 1.0
O L:CYS51 4.4 0.2 1.0
N L:CYS34 4.4 0.9 1.0
CA L:CYS51 4.6 0.0 1.0
CA L:CYS48 4.6 0.6 1.0
CA L:CYS34 4.8 1.0 1.0
CB L:HIS53 4.8 0.2 1.0
C L:CYS51 4.8 0.1 1.0
OG L:SER36 4.9 0.3 1.0
CA L:CYS31 4.9 0.9 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: Sat Oct 26 20:10:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy