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Zinc in PDB 3po3: Arrested Rna Polymerase II Reactivation Intermediate

Enzymatic activity of Arrested Rna Polymerase II Reactivation Intermediate

All present enzymatic activity of Arrested Rna Polymerase II Reactivation Intermediate:
2.7.7.6;

Protein crystallography data

The structure of Arrested Rna Polymerase II Reactivation Intermediate, PDB code: 3po3 was solved by A.C.M.Cheung, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.97 / 3.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.019, 395.067, 280.429, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.9

Other elements in 3po3:

The structure of Arrested Rna Polymerase II Reactivation Intermediate 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 Reactivation Intermediate (pdb code 3po3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Arrested Rna Polymerase II Reactivation Intermediate, PDB code: 3po3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3po3

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Zinc binding site 1 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.1
occ:1.00
 SG A:CYS148 2.2 0.4 1.0
SG A:CYS110 2.3 0.6 1.0
SG A:CYS107 2.3 0.8 1.0
SG A:CYS167 2.4 0.3 1.0
CB A:CYS167 2.7 0.6 1.0
CB A:CYS148 2.9 0.4 1.0
CB A:CYS107 3.2 0.2 1.0
CB A:CYS110 3.3 0.5 1.0
N A:CYS110 3.8 0.1 1.0
CA A:CYS110 4.1 0.2 1.0
CA A:CYS167 4.1 0.1 1.0
O A:GLY166 4.3 0.9 1.0
CA A:CYS148 4.4 0.9 1.0
N A:GLY168 4.5 0.7 1.0
O A:CYS148 4.6 0.5 1.0
C A:CYS167 4.6 0.8 1.0
CA A:CYS107 4.7 0.1 1.0
CB A:HIS109 4.8 0.6 1.0
N A:ASN169 4.8 0.2 1.0
C A:HIS109 4.9 0.7 1.0
N A:CYS167 4.9 0.0 1.0
C A:CYS110 4.9 0.9 1.0
C A:GLY166 5.0 0.6 1.0
C A:CYS148 5.0 0.3 1.0
ND1 A:HIS109 5.0 0.2 1.0

Zinc binding site 2 out of 9 in 3po3

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Zinc binding site 2 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:87.8
occ:1.00
 NE2 A:HIS80 2.0 96.0 1.0
SG A:CYS67 2.2 1.0 1.0
SG A:CYS77 2.4 97.4 1.0
SG A:CYS70 2.5 0.4 1.0
CE1 A:HIS80 2.9 94.5 1.0
CD2 A:HIS80 3.0 96.8 1.0
CB A:CYS67 3.6 0.0 1.0
CB A:CYS77 3.6 94.2 1.0
CB A:CYS70 3.7 0.0 1.0
O A:CYS67 3.9 0.1 1.0
O A:PRO78 4.1 98.0 1.0
ND1 A:HIS80 4.1 94.8 1.0
CG A:HIS80 4.1 94.1 1.0
CA A:CYS77 4.4 91.9 1.0
CD A:PRO78 4.6 87.3 1.0
CA A:CYS67 4.8 1.0 1.0
OE1 A:GLN68 4.8 88.9 1.0
C A:CYS67 4.8 0.3 1.0
NE2 A:GLN68 5.0 65.5 1.0

Zinc binding site 3 out of 9 in 3po3

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Zinc binding site 3 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:94.2
occ:1.00
 SG B:CYS1185 2.2 99.5 1.0
SG B:CYS1166 2.2 97.3 1.0
SG B:CYS1182 2.4 88.1 1.0
SG B:CYS1163 2.4 84.1 1.0
CB B:CYS1185 3.1 97.0 1.0
CB B:CYS1163 3.1 79.4 1.0
N B:CYS1166 3.6 92.7 1.0
CB B:CYS1166 3.7 93.5 1.0
CB B:CYS1182 3.7 85.7 1.0
O B:CYS1166 3.9 0.2 1.0
CA B:CYS1166 4.2 92.8 1.0
CA B:CYS1185 4.5 98.7 1.0
C B:CYS1166 4.5 98.5 1.0
CA B:CYS1163 4.6 78.5 1.0
CB B:ILE1165 4.6 90.8 1.0
C B:ILE1165 4.7 94.5 1.0
O B:GLY1184 4.8 0.1 1.0
CG2 B:THR1170 4.8 97.3 1.0
CB B:THR1170 4.9 91.1 1.0
CA B:ILE1165 4.9 87.0 1.0
N B:ILE1165 5.0 86.0 1.0
CD1 A:ILE30 5.0 0.8 1.0

Zinc binding site 4 out of 9 in 3po3

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Zinc binding site 4 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:94.1
occ:1.00
 SG C:CYS95 2.3 99.7 1.0
SG C:CYS92 2.3 98.6 1.0
SG C:CYS88 2.4 91.0 1.0
SG C:CYS86 2.4 87.3 1.0
CB C:CYS86 3.1 82.5 1.0
N C:CYS92 3.3 95.5 1.0
CB C:CYS92 3.4 95.6 1.0
CB C:CYS95 3.4 96.5 1.0
CB C:CYS88 3.5 88.2 1.0
C C:HIS91 3.8 0.1 1.0
CA C:CYS92 3.9 95.6 1.0
CA C:HIS91 4.1 97.6 1.0
N C:CYS95 4.2 98.5 1.0
N C:CYS88 4.3 87.0 1.0
CA C:CYS95 4.4 97.6 1.0
CA C:CYS86 4.4 83.5 1.0
CA C:CYS88 4.5 87.5 1.0
NZ C:LYS94 4.6 0.7 1.0
O C:HIS91 4.6 0.0 1.0
C C:CYS92 4.7 0.5 1.0
N C:HIS91 4.7 95.8 1.0
C C:CYS86 4.7 89.2 1.0
CB C:LYS94 4.7 99.3 1.0
C C:LYS94 4.8 0.5 1.0
N C:LYS94 4.8 98.7 1.0
N C:ASP93 4.9 0.0 1.0
N C:PHE87 4.9 88.1 1.0

Zinc binding site 5 out of 9 in 3po3

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Zinc binding site 5 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.4
occ:1.00
 SG I:CYS10 2.2 0.6 1.0
SG I:CYS32 2.3 1.0 1.0
SG I:CYS7 2.3 0.7 1.0
SG I:CYS29 2.4 0.2 1.0
CB I:CYS29 3.3 0.9 1.0
CB I:CYS32 3.3 0.7 1.0
CB I:CYS7 3.5 0.0 1.0
CB I:CYS10 3.8 0.3 1.0
N I:CYS32 3.8 0.6 1.0
O I:CYS10 3.9 0.7 1.0
O I:ARG8 3.9 0.9 1.0
N I:CYS10 4.0 0.6 1.0
CA I:CYS32 4.1 0.6 1.0
CA I:CYS10 4.2 0.0 1.0
CB I:TYR34 4.3 0.1 1.0
C I:THR31 4.4 0.8 1.0
C I:CYS10 4.5 0.9 1.0
CB I:THR31 4.7 0.1 1.0
C I:CYS32 4.7 0.8 1.0
CA I:CYS29 4.7 0.2 1.0
CA I:CYS7 4.9 0.2 1.0
CA I:THR31 4.9 0.0 1.0
CB I:ASP9 4.9 0.8 1.0
N I:TYR34 5.0 0.9 1.0

Zinc binding site 6 out of 9 in 3po3

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Zinc binding site 6 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS106 2.3 0.5 1.0
SG I:CYS78 2.3 0.7 1.0
SG I:CYS75 2.3 0.2 1.0
SG I:CYS103 2.4 0.4 1.0
CB I:CYS106 3.1 0.5 1.0
CB I:CYS103 3.2 0.7 1.0
CB I:CYS75 3.3 0.2 1.0
CB I:CYS78 3.3 0.4 1.0
N I:CYS106 3.4 0.1 1.0
CA I:CYS106 3.7 0.5 1.0
N I:CYS78 3.8 0.6 1.0
CA I:CYS78 4.1 0.8 1.0
C I:CYS106 4.4 0.1 1.0
CB I:SER105 4.5 0.1 1.0
C I:SER105 4.6 0.5 1.0
CA I:CYS103 4.6 0.2 1.0
CB I:LYS77 4.7 0.3 1.0
CA I:CYS75 4.7 0.2 1.0
N I:SER107 4.8 0.6 1.0
C I:CYS78 4.9 0.8 1.0
N I:HIS79 4.9 0.5 1.0
C I:LYS77 4.9 0.5 1.0
CA I:SER105 4.9 0.5 1.0
CB I:HIS108 4.9 0.5 1.0
CB I:SER80 5.0 0.6 1.0

Zinc binding site 7 out of 9 in 3po3

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Zinc binding site 7 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:0.9
occ:1.00
 SG J:CYS7 2.2 0.9 1.0
SG J:CYS10 2.3 0.8 1.0
SG J:CYS45 2.4 0.7 1.0
SG J:CYS46 2.4 0.8 1.0
N J:CYS46 3.1 0.2 1.0
CB J:CYS7 3.4 0.4 1.0
CB J:CYS45 3.4 98.7 1.0
CB J:CYS10 3.4 0.3 1.0
C J:CYS45 3.5 0.7 1.0
CA J:CYS46 3.6 0.9 1.0
CB J:CYS46 3.6 0.9 1.0
N J:CYS10 3.8 99.0 1.0
CA J:CYS45 4.0 99.3 1.0
CA J:CYS10 4.1 99.3 1.0
O J:CYS45 4.2 0.1 1.0
NE J:ARG43 4.4 0.9 1.0
N J:GLY11 4.6 97.2 1.0
CB J:SER9 4.7 0.9 1.0
N J:CYS45 4.7 0.1 1.0
CB J:ARG43 4.7 0.7 1.0
CA J:CYS7 4.7 0.9 1.0
C J:CYS10 4.8 0.8 1.0
NH2 J:ARG43 4.8 0.6 1.0
O J:CYS7 4.9 0.5 1.0
C J:SER9 4.9 0.8 1.0
CB J:LYS12 4.9 0.8 1.0
C J:CYS7 4.9 0.6 1.0
N J:LYS12 5.0 0.5 1.0

Zinc binding site 8 out of 9 in 3po3

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Zinc binding site 8 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


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 Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.2
occ:1.00
 SG L:CYS34 2.2 0.7 1.0
SG L:CYS48 2.3 0.1 1.0
SG L:CYS51 2.3 0.1 1.0
SG L:CYS31 2.4 0.7 1.0
CB L:CYS48 3.2 0.9 1.0
CB L:CYS31 3.3 0.7 1.0
OG L:SER36 3.4 0.5 1.0
CB L:CYS51 3.6 0.0 1.0
O L:CYS34 3.7 0.2 1.0
N L:CYS51 3.8 0.4 1.0
O L:CYS51 3.8 0.9 1.0
CB L:CYS34 3.9 0.7 1.0
N L:CYS34 4.1 0.6 1.0
CA L:CYS51 4.2 0.2 1.0
CB L:ASP50 4.4 0.1 1.0
C L:CYS51 4.4 0.6 1.0
CA L:CYS34 4.5 0.1 1.0
C L:CYS34 4.5 0.0 1.0
CA L:CYS48 4.6 0.6 1.0
CB L:GLU33 4.6 0.5 1.0
C L:ASP50 4.8 0.2 1.0
CB L:SER36 4.8 0.1 1.0
CA L:CYS31 4.8 0.2 1.0
OD2 L:ASP50 4.8 0.0 1.0
N L:ASP50 4.9 0.3 1.0
CA L:ASP50 4.9 0.0 1.0

Zinc binding site 9 out of 9 in 3po3

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Zinc binding site 9 out of 9 in the Arrested Rna Polymerase II Reactivation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Arrested Rna Polymerase II Reactivation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn999

b:0.3
occ:1.00
 SG S:CYS274 2.3 0.7 1.0
SG S:CYS302 2.3 1.0 1.0
SG S:CYS271 2.3 0.4 1.0
SG S:CYS299 2.3 0.7 1.0
CB S:CYS271 3.1 0.7 1.0
CB S:CYS302 3.1 0.4 1.0
CB S:CYS299 3.2 0.3 1.0
CB S:CYS274 3.6 0.0 1.0
N S:CYS302 3.7 1.0 1.0
CA S:CYS302 3.9 0.7 1.0
N S:CYS274 4.1 0.8 1.0
CA S:CYS274 4.3 0.4 1.0
N S:GLY303 4.4 0.8 1.0
CB S:ASN304 4.5 0.3 1.0
CA S:CYS271 4.6 0.4 1.0
C S:CYS302 4.6 0.9 1.0
CA S:CYS299 4.6 0.8 1.0
CB S:ALA301 4.7 0.1 1.0
C S:CYS274 4.8 0.3 1.0
C S:ALA301 4.9 0.2 1.0
N S:LYS275 4.9 0.1 1.0
N S:GLU276 5.0 0.9 1.0

Reference:

A.C.Cheung, P.Cramer. Structural Basis of Rna Polymerase II Backtracking, Arrest and Reactivation. Nature V. 471 249 2011.
ISSN: ISSN 0028-0836
PubMed: 21346759
DOI: 10.1038/NATURE09785
Page generated: Sat Oct 26 11:38:16 2024

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