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Zinc in PDB 4bxz: Rna Polymerase II-BYE1 Complex

Enzymatic activity of Rna Polymerase II-BYE1 Complex

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

Protein crystallography data

The structure of Rna Polymerase II-BYE1 Complex, PDB code: 4bxz 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) 49.63 / 4.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.550, 392.090, 279.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.06 / 25.27

Other elements in 4bxz:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 4bxz

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Zinc binding site 1 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:1.0
occ:1.00
 SG A:CYS107 2.2 0.9 1.0
SG A:CYS110 2.3 0.2 1.0
SG A:CYS167 2.7 0.1 1.0
CB A:CYS167 2.9 0.9 1.0
CB A:CYS107 3.0 0.9 1.0
CB A:CYS110 3.7 0.9 1.0
O A:GLY166 3.8 0.5 1.0
N A:CYS110 3.9 0.3 1.0
CB A:HIS109 3.9 1.0 1.0
O A:CYS167 4.0 0.1 1.0
CB A:CYS148 4.0 0.9 1.0
SG A:CYS148 4.0 0.6 1.0
CA A:CYS167 4.1 0.4 1.0
C A:CYS167 4.3 0.3 1.0
CA A:CYS107 4.4 0.1 1.0
CA A:CYS110 4.4 0.7 1.0
C A:GLY166 4.6 1.0 1.0
N A:CYS167 4.7 0.5 1.0
C A:HIS109 4.8 0.0 1.0
C A:CYS107 4.8 0.5 1.0
CA A:HIS109 4.8 0.2 1.0
O A:CYS107 4.9 0.2 1.0
CG A:HIS109 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 4bxz

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Zinc binding site 2 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:0.4
occ:1.00
 SG A:CYS67 2.2 0.6 1.0
CB A:CYS67 2.9 0.5 1.0
CB A:CYS70 3.0 0.6 1.0
SG A:CYS70 3.2 0.0 1.0
SG A:CYS77 3.2 0.6 1.0
CD2 A:HIS80 3.5 0.4 1.0
O A:CYS67 3.7 0.3 1.0
C A:CYS70 3.9 0.2 1.0
N A:GLN71 3.9 0.1 1.0
CA A:CYS70 4.0 1.0 1.0
NE2 A:HIS80 4.0 0.7 1.0
O A:PRO78 4.1 0.4 1.0
O A:GLN71 4.1 0.8 1.0
CA A:CYS67 4.2 0.2 1.0
C A:CYS67 4.3 0.9 1.0
CB A:CYS77 4.3 0.8 1.0
OE1 A:GLN68 4.4 0.1 1.0
O A:CYS70 4.4 0.0 1.0
CG A:HIS80 4.4 0.3 1.0
C A:GLN71 4.5 0.2 1.0
CA A:GLN71 4.6 0.8 1.0
CA A:CYS77 4.6 0.1 1.0
NE2 A:GLN68 4.7 0.7 1.0
N A:CYS70 4.7 0.9 1.0
CD A:GLN68 4.9 0.8 1.0
CD A:PRO78 5.0 0.3 1.0

Zinc binding site 3 out of 8 in 4bxz

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Zinc binding site 3 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:96.2
occ:1.00
 SG B:CYS1163 2.5 0.8 1.0
CB B:CYS1185 2.6 0.9 1.0
SG B:CYS1166 2.6 0.1 1.0
SG B:CYS1185 2.7 0.1 1.0
CB B:CYS1163 3.0 0.7 1.0
SG B:CYS1182 3.2 0.8 1.0
O B:CYS1166 3.6 0.5 1.0
N B:CYS1166 3.7 1.0 1.0
CB B:CYS1166 3.9 0.6 1.0
CA B:CYS1185 4.0 0.6 1.0
CA B:CYS1166 4.2 0.0 1.0
OG1 B:THR1170 4.3 0.1 1.0
N B:CYS1185 4.4 0.5 1.0
C B:CYS1166 4.4 0.1 1.0
CD1 B:ILE1165 4.4 0.4 1.0
CA B:CYS1163 4.5 0.9 1.0
CB B:ILE1165 4.5 0.2 1.0
CG2 B:THR1170 4.7 0.5 1.0
C B:ILE1165 4.7 0.2 1.0
CB B:THR1170 4.7 0.9 1.0
CB B:CYS1182 4.7 0.5 1.0
N B:ILE1165 4.9 0.9 1.0
O B:LYS1183 4.9 0.3 1.0
CA B:ILE1165 4.9 0.2 1.0
C B:CYS1163 5.0 0.1 1.0
C B:CYS1185 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 4bxz

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Zinc binding site 4 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:0.5
occ:1.00
 SG C:CYS95 2.3 0.1 1.0
SG C:CYS92 2.4 0.6 1.0
SG C:CYS86 2.4 0.1 1.0
SG C:CYS88 2.4 0.4 1.0
CB C:CYS86 3.2 0.8 1.0
CB C:CYS88 3.4 0.1 1.0
CB C:CYS92 3.4 0.3 1.0
N C:CYS92 3.6 0.2 1.0
CB C:CYS95 3.7 0.8 1.0
O C:CYS92 3.8 0.2 1.0
CA C:CYS92 3.8 0.1 1.0
CB C:LYS94 3.9 0.4 1.0
N C:CYS95 4.0 0.5 1.0
C C:CYS92 4.0 0.0 1.0
N C:CYS88 4.3 0.8 1.0
C C:HIS91 4.4 0.6 1.0
CA C:CYS88 4.5 0.4 1.0
CA C:CYS95 4.5 0.7 1.0
CG C:LYS94 4.5 0.5 1.0
N C:LYS94 4.5 0.8 1.0
CA C:LYS94 4.6 0.8 1.0
C C:LYS94 4.6 0.1 1.0
CA C:CYS86 4.7 0.7 1.0
O C:ASP90 4.7 0.4 1.0
CE C:LYS94 4.8 0.9 1.0
CD C:LYS94 4.8 0.7 1.0
CA C:HIS91 4.8 0.2 1.0
O C:SER83 4.9 0.7 1.0
N C:PHE87 4.9 0.1 1.0
N C:ASP93 5.0 0.6 1.0

Zinc binding site 5 out of 8 in 4bxz

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Zinc binding site 5 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.1
occ:1.00
 SG I:CYS32 2.2 0.2 1.0
SG I:CYS10 2.2 0.7 1.0
CB I:CYS32 2.7 0.8 1.0
SG I:CYS29 2.8 1.0 1.0
SG I:CYS7 3.0 0.7 1.0
CB I:CYS10 3.5 0.3 1.0
N I:CYS32 3.5 0.5 1.0
CB I:CYS7 3.6 0.5 1.0
CA I:CYS32 3.7 0.9 1.0
CB I:CYS29 3.7 0.3 1.0
C I:THR31 3.9 0.9 1.0
O I:THR31 4.2 0.2 1.0
N I:CYS10 4.2 0.8 1.0
CB I:THR31 4.4 0.4 1.0
CA I:CYS10 4.4 0.1 1.0
CA I:THR31 4.6 0.2 1.0
C I:CYS32 4.7 0.1 1.0
CB I:ASP9 4.9 0.0 1.0
N I:SER33 5.0 0.7 1.0
O I:CYS29 5.0 0.3 1.0
CB I:TYR34 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 4bxz

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Zinc binding site 6 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS106 2.2 0.2 1.0
SG I:CYS78 2.5 0.9 1.0
SG I:CYS75 2.6 0.4 1.0
CB I:CYS78 3.1 0.5 1.0
CB I:CYS75 3.5 0.6 1.0
CB I:HIS108 3.6 0.9 1.0
N I:CYS78 3.6 0.3 1.0
SG I:CYS103 3.7 0.7 1.0
CB I:CYS106 3.8 0.2 1.0
CA I:CYS78 3.9 0.5 1.0
CB I:CYS103 3.9 0.1 1.0
CG I:HIS108 4.3 0.0 1.0
N I:HIS108 4.5 0.1 1.0
CD2 I:HIS108 4.5 0.0 1.0
C I:CYS78 4.5 0.6 1.0
CA I:HIS108 4.6 0.2 1.0
C I:LYS77 4.6 0.9 1.0
O I:HIS108 4.6 0.1 1.0
N I:HIS79 4.7 0.1 1.0
CA I:CYS106 4.8 1.0 1.0
N I:LYS77 4.9 0.1 1.0
N I:CYS106 4.9 0.5 1.0
CA I:CYS75 4.9 0.1 1.0

Zinc binding site 7 out of 8 in 4bxz

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Zinc binding site 7 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:0.8
occ:1.00
 SG J:CYS10 2.2 0.5 1.0
SG J:CYS45 2.2 0.4 1.0
SG J:CYS7 2.2 0.4 1.0
N J:CYS46 3.2 0.0 1.0
CB J:CYS10 3.2 0.8 1.0
CB J:CYS45 3.2 0.1 1.0
CB J:CYS7 3.2 0.9 1.0
SG J:CYS46 3.3 0.3 1.0
N J:CYS10 3.3 0.3 1.0
C J:CYS45 3.4 0.1 1.0
CA J:CYS46 3.6 0.8 1.0
CB J:CYS46 3.7 0.3 1.0
CA J:CYS10 3.8 0.8 1.0
CA J:CYS45 3.9 0.7 1.0
O J:CYS45 4.0 0.4 1.0
C J:SER9 4.4 0.4 1.0
N J:SER9 4.5 0.4 1.0
CB J:SER9 4.5 0.1 1.0
N J:GLY11 4.5 0.7 1.0
CA J:CYS7 4.6 0.8 1.0
CA J:SER9 4.7 0.3 1.0
C J:CYS10 4.7 0.6 1.0
NH2 J:ARG43 4.7 0.6 1.0
NE J:ARG43 4.8 0.1 1.0
N J:CYS45 4.8 0.0 1.0
C J:CYS7 4.8 0.2 1.0
CZ J:ARG43 4.8 0.4 1.0
N J:PHE8 4.9 0.1 1.0
CG J:ARG43 5.0 0.7 1.0

Zinc binding site 8 out of 8 in 4bxz

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Zinc binding site 8 out of 8 in the 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 Rna Polymerase II-BYE1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.9
occ:1.00
 SG L:CYS48 2.2 0.4 1.0
SG L:CYS51 2.2 0.8 1.0
SG L:CYS31 2.5 0.0 1.0
SG L:CYS34 2.5 0.4 1.0
CB L:CYS48 3.1 0.6 1.0
CB L:CYS31 3.5 0.5 1.0
CB L:CYS34 3.7 0.1 1.0
CB L:CYS51 3.8 0.1 1.0
OG L:SER36 3.9 0.4 1.0
N L:CYS51 4.1 0.0 1.0
OE1 L:GLU33 4.1 0.6 1.0
O L:CYS51 4.3 1.0 1.0
N L:CYS34 4.4 0.3 1.0
CA L:CYS51 4.4 0.1 1.0
CA L:CYS48 4.5 0.2 1.0
CA L:CYS34 4.6 1.0 1.0
CB L:ASP50 4.8 0.6 1.0
C L:CYS51 4.8 0.8 1.0
N L:SER35 4.9 0.4 1.0
CA L:CYS31 4.9 0.4 1.0
C L:CYS48 5.0 0.5 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 20:08:03 2024

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