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Zinc in PDB 3po2: Arrested Rna Polymerase II Elongation Complex

Enzymatic activity of Arrested Rna Polymerase II Elongation Complex

All present enzymatic activity of Arrested Rna Polymerase II Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Arrested Rna Polymerase II Elongation Complex, PDB code: 3po2 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) 48.98 / 3.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 224.570, 394.550, 282.140, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.8

Other elements in 3po2:

The structure of Arrested Rna Polymerase II Elongation 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 Elongation Complex (pdb code 3po2). 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 Elongation Complex, PDB code: 3po2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3po2

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

b:0.2
occ:1.00
 SG A:CYS167 2.3 0.6 1.0
SG A:CYS107 2.3 0.1 1.0
SG A:CYS110 2.3 0.4 1.0
SG A:CYS148 2.4 0.7 1.0
CB A:CYS107 3.0 0.8 1.0
CB A:CYS148 3.2 0.0 1.0
CB A:CYS110 3.3 0.6 1.0
N A:CYS167 3.6 0.9 1.0
N A:CYS110 3.7 0.4 1.0
CB A:CYS167 3.7 0.8 1.0
CA A:CYS110 4.0 0.3 1.0
CA A:CYS167 4.1 0.3 1.0
C A:CYS167 4.4 0.1 1.0
O A:CYS167 4.5 0.7 1.0
CA A:CYS107 4.5 0.9 1.0
C A:GLY166 4.6 0.1 1.0
CA A:GLY166 4.7 0.8 1.0
CA A:CYS148 4.7 0.1 1.0
C A:CYS110 4.8 0.8 1.0
C A:HIS109 4.9 0.8 1.0
ND1 A:HIS109 4.9 0.5 1.0
N A:GLY111 5.0 0.3 1.0
CB A:LYS112 5.0 0.9 1.0
CB A:HIS109 5.0 0.8 1.0

Zinc binding site 2 out of 8 in 3po2

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

b:94.3
occ:1.00
 NE2 A:HIS80 2.0 93.6 1.0
SG A:CYS67 2.2 98.4 1.0
SG A:CYS77 2.2 94.8 1.0
SG A:CYS70 2.3 79.5 1.0
CE1 A:HIS80 2.8 92.2 1.0
CD2 A:HIS80 3.1 94.3 1.0
CB A:CYS67 3.3 98.1 1.0
CB A:CYS77 3.4 91.1 1.0
CB A:CYS70 3.5 77.8 1.0
N A:CYS70 3.8 81.7 1.0
ND1 A:HIS80 4.0 92.5 1.0
CG A:HIS80 4.1 92.2 1.0
CA A:CYS77 4.2 89.7 1.0
CA A:CYS70 4.2 80.8 1.0
CD A:PRO78 4.5 85.7 1.0
CB A:THR69 4.6 87.3 1.0
CA A:CYS67 4.7 0.1 1.0
N A:GLY79 4.8 86.4 1.0
C A:THR69 4.9 89.2 1.0
C A:CYS77 4.9 90.2 1.0
N A:PRO78 4.9 84.6 1.0
O A:CYS67 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 3po2

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

b:99.8
occ:1.00
 SG B:CYS1166 2.2 94.3 1.0
SG B:CYS1185 2.3 0.7 1.0
SG B:CYS1182 2.4 87.0 1.0
SG B:CYS1163 2.4 92.7 1.0
CB B:CYS1185 3.1 100.0 1.0
CB B:CYS1163 3.1 87.0 1.0
CB B:CYS1166 3.3 91.0 1.0
CB B:CYS1182 3.6 84.3 1.0
N B:CYS1166 3.6 90.8 1.0
CA B:CYS1166 4.0 90.2 1.0
O B:GLY1184 4.6 0.2 1.0
CA B:CYS1185 4.6 0.9 1.0
CA B:CYS1163 4.6 84.7 1.0
CB B:ILE1165 4.7 88.0 1.0
C B:ILE1165 4.8 92.9 1.0
C B:CYS1166 4.8 93.0 1.0
CA B:CYS1182 4.9 86.8 1.0
ND2 B:ASN1187 5.0 0.9 1.0
N B:GLY1167 5.0 88.7 1.0
N B:ILE1165 5.0 85.8 1.0

Zinc binding site 4 out of 8 in 3po2

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

b:93.6
occ:1.00
 SG C:CYS95 2.2 87.1 1.0
SG C:CYS86 2.3 83.0 1.0
SG C:CYS88 2.3 88.2 1.0
SG C:CYS92 2.3 95.0 1.0
N C:CYS92 3.2 90.4 1.0
CB C:CYS92 3.2 91.2 1.0
CB C:CYS86 3.3 78.6 1.0
CB C:CYS95 3.4 84.0 1.0
CA C:CYS92 3.7 90.7 1.0
CB C:CYS88 3.7 85.8 1.0
C C:HIS91 3.8 95.3 1.0
N C:CYS95 4.0 85.9 1.0
CA C:HIS91 4.1 93.2 1.0
C C:CYS92 4.2 94.7 1.0
CA C:CYS95 4.3 85.0 1.0
N C:CYS88 4.4 84.9 1.0
N C:HIS91 4.5 93.4 1.0
O C:CYS92 4.5 92.9 1.0
CA C:CYS86 4.6 79.5 1.0
O C:HIS91 4.7 94.9 1.0
CA C:CYS88 4.7 85.5 1.0
CB C:LYS94 4.8 86.7 1.0
N C:LYS94 4.8 86.1 1.0
C C:LYS94 4.8 90.5 1.0
C C:CYS86 4.8 82.6 1.0
OG C:SER83 4.9 0.8 1.0

Zinc binding site 5 out of 8 in 3po2

Go back to Zinc Binding Sites List in 3po2
Zinc binding site 5 out of 8 in the Arrested Rna Polymerase II Elongation 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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.5
occ:1.00
 SG I:CYS32 2.2 0.0 1.0
SG I:CYS7 2.3 0.6 1.0
SG I:CYS29 2.3 0.6 1.0
SG I:CYS10 2.4 0.1 1.0
CB I:CYS10 2.6 0.2 1.0
CB I:CYS29 3.2 0.2 1.0
CB I:CYS32 3.3 0.0 1.0
CB I:CYS7 3.3 0.7 1.0
N I:CYS32 3.8 0.4 1.0
CA I:CYS10 4.0 0.7 1.0
CA I:CYS32 4.1 0.0 1.0
O I:ASP9 4.1 0.9 1.0
CB I:TYR34 4.3 0.9 1.0
N I:CYS10 4.5 0.7 1.0
C I:ASP9 4.5 0.1 1.0
CB I:THR31 4.6 0.9 1.0
C I:THR31 4.6 0.9 1.0
CA I:CYS29 4.7 0.2 1.0
C I:CYS32 4.7 0.1 1.0
O I:ARG8 4.7 0.6 1.0
CA I:CYS7 4.7 1.0 1.0
OD2 I:ASP9 4.9 0.8 1.0
OD1 I:ASN12 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 3po2

Go back to Zinc Binding Sites List in 3po2
Zinc binding site 6 out of 8 in the Arrested Rna Polymerase II Elongation 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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS78 2.3 0.9 1.0
SG I:CYS106 2.3 0.2 1.0
SG I:CYS75 2.3 0.6 1.0
SG I:CYS103 2.5 0.6 1.0
CB I:CYS106 2.5 0.4 1.0
CB I:CYS103 3.1 0.5 1.0
N I:CYS106 3.2 0.1 1.0
CB I:CYS75 3.3 0.9 1.0
CB I:CYS78 3.3 0.8 1.0
CA I:CYS106 3.4 0.5 1.0
N I:CYS78 3.7 0.0 1.0
CA I:CYS78 4.0 0.9 1.0
C I:CYS106 4.2 0.3 1.0
C I:SER105 4.5 0.1 1.0
N I:SER107 4.5 0.2 1.0
CB I:SER105 4.5 1.0 1.0
CA I:CYS103 4.6 0.1 1.0
CB I:LYS77 4.6 0.2 1.0
CA I:CYS75 4.8 0.4 1.0
C I:CYS78 4.8 0.7 1.0
C I:LYS77 4.8 0.3 1.0
N I:HIS79 4.9 0.0 1.0
CA I:SER105 4.9 0.8 1.0
CB I:SER80 5.0 0.8 1.0

Zinc binding site 7 out of 8 in 3po2

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

b:0.8
occ:1.00
 SG J:CYS45 2.2 97.1 1.0
SG J:CYS46 2.2 0.7 1.0
SG J:CYS7 2.3 0.5 1.0
SG J:CYS10 2.4 97.0 1.0
N J:CYS46 3.1 97.8 1.0
CB J:CYS7 3.2 98.6 1.0
CB J:CYS45 3.4 92.3 1.0
CB J:CYS46 3.5 0.8 1.0
CB J:CYS10 3.5 92.3 1.0
CA J:CYS46 3.5 98.9 1.0
C J:CYS45 3.6 98.9 1.0
N J:CYS10 3.8 89.2 1.0
CA J:CYS45 4.1 93.1 1.0
CA J:CYS10 4.1 90.4 1.0
O J:CYS45 4.4 98.3 1.0
CG J:ARG43 4.4 0.8 1.0
CA J:CYS7 4.6 96.8 1.0
CB J:LYS12 4.7 97.2 1.0
CB J:SER9 4.7 90.8 1.0
NE J:ARG43 4.8 0.3 1.0
N J:CYS45 4.8 95.4 1.0
C J:CYS10 4.8 95.3 1.0
C J:SER9 4.9 91.4 1.0
N J:GLY11 4.9 91.4 1.0

Zinc binding site 8 out of 8 in 3po2

Go back to Zinc Binding Sites List in 3po2
Zinc binding site 8 out of 8 in the Arrested Rna Polymerase II Elongation 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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.5
occ:1.00
 SG L:CYS48 2.4 0.8 1.0
SG L:CYS34 2.4 1.0 1.0
SG L:CYS51 2.4 0.2 1.0
SG L:CYS31 2.4 0.5 1.0
CB L:CYS48 3.1 0.1 1.0
CB L:CYS31 3.5 0.5 1.0
CB L:CYS34 3.7 0.0 1.0
CB L:CYS51 4.1 0.4 1.0
N L:CYS34 4.1 0.5 1.0
N L:CYS51 4.4 1.0 1.0
CA L:CYS34 4.4 1.0 1.0
CB L:HIS53 4.5 0.1 1.0
CA L:CYS48 4.6 0.2 1.0
OG L:SER36 4.7 0.3 1.0
CA L:CYS51 4.8 0.4 1.0
CA L:CYS31 4.9 0.8 1.0
O L:CYS51 4.9 0.9 1.0
CB L:ASP50 4.9 0.8 1.0
N L:SER35 5.0 0.2 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: Wed Dec 16 04:43:37 2020

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