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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

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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

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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

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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

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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

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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

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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

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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

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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: Sat Oct 26 20:08:05 2024

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