Atomistry » Zinc » PDB 4bue-4c1c » 4by1
Atomistry »
  Zinc »
    PDB 4bue-4c1c »
      4by1 »

Zinc in PDB 4by1: Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp

Enzymatic activity of Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp

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

Protein crystallography data

The structure of Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp, PDB code: 4by1 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) 48.95 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.240, 391.580, 281.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.49 / 20.62

Other elements in 4by1:

The structure of Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp 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 Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp (pdb code 4by1). 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 Soaked with Ampcpp, PDB code: 4by1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 1 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.5
occ:1.00
 SG A:CYS107 2.3 0.6 1.0
SG A:CYS167 2.3 0.4 1.0
SG A:CYS110 2.3 0.5 1.0
SG A:CYS148 2.4 1.0 1.0
CB A:CYS148 3.1 0.9 1.0
CB A:CYS107 3.4 0.8 1.0
CB A:CYS110 3.4 0.6 1.0
N A:CYS110 3.7 0.1 1.0
ND2 A:ASN169 4.0 0.6 1.0
O A:GLY166 4.0 0.6 1.0
CA A:CYS110 4.1 0.1 1.0
CB A:CYS167 4.1 1.0 1.0
O A:CYS167 4.5 0.3 1.0
CB A:HIS109 4.6 0.2 1.0
O A:GLY168 4.6 0.7 1.0
CA A:CYS148 4.6 0.2 1.0
C A:HIS109 4.7 0.5 1.0
C A:CYS167 4.8 0.2 1.0
CA A:CYS107 4.8 0.4 1.0
ND1 A:HIS109 4.8 0.3 1.0
CA A:CYS167 4.9 0.9 1.0
C A:CYS110 5.0 0.4 1.0
CA A:HIS109 5.0 0.7 1.0
C A:GLY166 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 2 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:77.2
occ:1.00
 NE2 A:HIS80 2.2 94.7 1.0
SG A:CYS77 2.3 0.9 1.0
SG A:CYS67 2.4 0.9 1.0
SG A:CYS70 2.4 0.3 1.0
CD2 A:HIS80 2.6 94.9 1.0
CB A:CYS77 3.3 98.8 1.0
CE1 A:HIS80 3.5 93.6 1.0
CB A:CYS70 3.6 0.2 1.0
CG A:HIS80 3.9 93.1 1.0
CB A:CYS67 3.9 0.1 1.0
O A:CYS67 4.3 0.4 1.0
ND1 A:HIS80 4.3 93.5 1.0
O A:PRO78 4.4 96.2 1.0
CD A:GLN68 4.5 0.5 1.0
CA A:CYS77 4.5 97.8 1.0
O A:LEU58 4.5 99.9 1.0
NE2 A:GLN68 4.5 95.2 1.0
O A:GLN71 4.6 0.9 1.0
OE1 A:GLN68 4.6 91.5 1.0
CG A:GLN68 4.8 0.0 1.0
CA A:CYS70 4.8 0.8 1.0
C A:CYS67 5.0 0.6 1.0
C A:CYS77 5.0 98.9 1.0

Zinc binding site 3 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 3 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:92.9
occ:1.00
 SG B:CYS1166 2.3 91.0 1.0
SG B:CYS1185 2.3 97.8 1.0
SG B:CYS1182 2.3 96.5 1.0
SG B:CYS1163 2.4 87.8 1.0
CB B:CYS1185 2.9 95.2 1.0
CB B:CYS1163 3.0 82.0 1.0
CB B:CYS1182 3.6 93.5 1.0
O B:CYS1166 3.7 88.4 1.0
CB B:CYS1166 3.7 86.6 1.0
N B:CYS1166 3.8 84.4 1.0
CA B:CYS1166 4.2 84.6 1.0
CA B:CYS1185 4.2 97.1 1.0
C B:CYS1166 4.4 87.7 1.0
N B:CYS1185 4.4 97.9 1.0
CA B:CYS1163 4.5 79.9 1.0
CB B:ILE1165 4.8 84.3 1.0
O B:CYS1182 4.8 0.1 1.0
OG1 B:THR1170 4.8 93.9 1.0
C B:ILE1165 4.9 86.4 1.0
CA B:CYS1182 5.0 95.0 1.0
N B:ILE1165 5.0 79.7 1.0

Zinc binding site 4 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 4 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:92.7
occ:1.00
 SG C:CYS88 2.2 89.3 1.0
SG C:CYS92 2.3 0.9 1.0
SG C:CYS86 2.4 91.9 1.0
SG C:CYS95 2.4 0.5 1.0
CB C:CYS86 3.2 86.1 1.0
CB C:CYS95 3.4 97.6 1.0
CB C:CYS92 3.5 99.3 1.0
CB C:CYS88 3.5 87.1 1.0
N C:CYS92 3.6 96.8 1.0
C C:HIS91 3.9 0.1 1.0
N C:CYS95 4.0 98.8 1.0
CA C:CYS92 4.1 97.9 1.0
CA C:HIS91 4.2 97.0 1.0
CA C:CYS95 4.3 97.7 1.0
N C:CYS88 4.3 84.8 1.0
CA C:CYS86 4.5 85.9 1.0
CB C:LYS94 4.6 0.5 1.0
O C:HIS91 4.6 0.8 1.0
C C:CYS92 4.6 0.1 1.0
CA C:CYS88 4.6 86.5 1.0
O C:CYS92 4.7 99.0 1.0
C C:LYS94 4.7 0.1 1.0
N C:PHE87 4.8 82.3 1.0
C C:CYS86 4.9 87.3 1.0
N C:LYS94 4.9 98.8 1.0
CA C:LYS94 5.0 98.4 1.0

Zinc binding site 5 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 5 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.4
occ:1.00
 SG I:CYS10 2.2 0.8 1.0
SG I:CYS7 2.3 0.1 1.0
SG I:CYS32 2.3 0.4 1.0
SG I:CYS29 2.3 0.9 1.0
CB I:CYS7 3.5 0.1 1.0
CB I:CYS32 3.5 0.1 1.0
CB I:CYS29 3.6 0.2 1.0
C I:THR31 3.8 0.4 1.0
N I:CYS32 3.9 0.8 1.0
O I:THR31 3.9 0.6 1.0
CB I:CYS10 3.9 0.9 1.0
CB I:THR31 4.1 0.8 1.0
CA I:CYS32 4.2 0.2 1.0
O I:ARG8 4.3 0.4 1.0
CA I:THR31 4.4 0.5 1.0
CB I:TYR34 4.5 0.2 1.0
N I:THR31 4.6 0.2 1.0
N I:CYS10 4.7 0.5 1.0
CA I:CYS10 4.8 0.7 1.0
CA I:CYS7 4.8 0.3 1.0
C I:CYS32 4.8 0.4 1.0
CB I:ASN12 4.9 0.2 1.0
OG1 I:THR31 4.9 0.5 1.0
O I:CYS7 4.9 0.4 1.0
CA I:CYS29 5.0 0.8 1.0
C I:CYS7 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 6 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.5
occ:1.00
 SG I:CYS78 2.3 0.0 1.0
SG I:CYS75 2.3 0.7 1.0
SG I:CYS106 2.3 0.2 1.0
SG I:CYS103 2.5 0.9 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS106 3.1 0.6 1.0
CB I:CYS75 3.1 0.2 1.0
CB I:CYS78 3.4 0.3 1.0
N I:CYS106 3.5 0.5 1.0
CA I:CYS106 3.8 0.1 1.0
N I:CYS78 4.0 0.9 1.0
CA I:CYS78 4.2 0.2 1.0
CA I:CYS103 4.5 0.3 1.0
CB I:SER105 4.5 0.3 1.0
CA I:CYS75 4.6 0.4 1.0
C I:SER105 4.6 0.6 1.0
N I:HIS79 4.6 0.0 1.0
C I:CYS106 4.7 0.8 1.0
N I:SER107 4.7 0.2 1.0
CB I:SER80 4.8 0.1 1.0
C I:CYS78 4.8 0.1 1.0
OG I:SER80 4.8 0.2 1.0
N I:SER80 4.8 0.3 1.0
CD2 I:HIS108 4.8 0.1 1.0
CA I:SER105 4.9 0.7 1.0
N I:SER105 4.9 0.2 1.0

Zinc binding site 7 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 7 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:85.5
occ:1.00
 SG J:CYS7 2.3 0.3 1.0
SG J:CYS10 2.4 98.2 1.0
SG J:CYS46 2.4 96.2 1.0
SG J:CYS45 2.5 90.8 1.0
CB J:CYS7 3.0 96.6 1.0
N J:CYS46 3.2 88.6 1.0
CA J:CYS46 3.5 89.5 1.0
CB J:CYS46 3.5 91.8 1.0
CB J:CYS10 3.6 93.5 1.0
CB J:CYS45 3.6 86.0 1.0
N J:CYS10 3.6 92.1 1.0
C J:CYS45 3.7 89.8 1.0
CA J:CYS10 4.0 92.1 1.0
CA J:CYS45 4.2 86.1 1.0
O J:CYS45 4.2 88.4 1.0
N J:GLY11 4.3 93.1 1.0
C J:CYS10 4.5 96.8 1.0
CA J:CYS7 4.5 94.7 1.0
N J:LYS12 4.5 92.2 1.0
CB J:SER9 4.6 95.5 1.0
CG J:ARG43 4.6 0.4 1.0
CB J:LYS12 4.7 96.3 1.0
C J:SER9 4.7 95.3 1.0
C J:CYS7 4.9 98.1 1.0
NE J:ARG43 4.9 0.4 1.0
O J:CYS7 5.0 98.7 1.0
N J:CYS45 5.0 88.1 1.0
C J:CYS46 5.0 94.5 1.0

Zinc binding site 8 out of 8 in 4by1

Go back to Zinc Binding Sites List in 4by1
Zinc binding site 8 out of 8 in the Elongating Rna Polymerase II-BYE1 Tld Complex Soaked with Ampcpp


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 Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.8
occ:1.00
 SG L:CYS48 2.3 0.2 1.0
SG L:CYS34 2.4 0.1 1.0
SG L:CYS51 2.4 0.2 1.0
SG L:CYS31 2.5 0.7 1.0
CB L:CYS48 3.1 0.8 1.0
CB L:CYS51 3.8 0.3 1.0
CB L:CYS31 3.8 0.1 1.0
CB L:CYS34 3.8 0.3 1.0
N L:CYS34 4.1 0.4 1.0
O L:CYS51 4.2 0.1 1.0
N L:CYS51 4.3 0.8 1.0
OG L:SER36 4.4 0.3 1.0
CA L:CYS51 4.5 0.8 1.0
CA L:CYS34 4.5 0.7 1.0
CA L:CYS48 4.6 0.5 1.0
C L:CYS51 4.6 0.8 1.0
CB L:GLU33 4.9 0.6 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 20:09:12 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy