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Zinc in PDB 4a3d: Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid

Enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid

All present enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid, PDB code: 4a3d was solved by A.C.M.Cheung, S.Sainsbury, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.96 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.910, 391.360, 283.920, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 4a3d:

The structure of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid (pdb code 4a3d). 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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid, PDB code: 4a3d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4a3d

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.6
occ:1.00
 SG A:CYS148 2.3 0.1 1.0
SG A:CYS110 2.3 0.3 1.0
SG A:CYS167 2.4 1.0 1.0
SG A:CYS107 2.4 0.3 1.0
CB A:CYS167 2.6 0.9 1.0
CB A:CYS110 3.1 0.1 1.0
CB A:CYS148 3.1 0.7 1.0
CB A:CYS107 3.3 0.8 1.0
N A:CYS110 3.7 0.9 1.0
CA A:CYS110 4.0 0.5 1.0
CA A:CYS167 4.0 0.2 1.0
O A:CYS167 4.2 0.9 1.0
O A:GLY166 4.2 0.6 1.0
C A:CYS167 4.3 1.0 1.0
CA A:CYS148 4.6 0.8 1.0
CA A:CYS107 4.7 0.9 1.0
N A:CYS167 4.8 0.9 1.0
C A:HIS109 4.8 0.8 1.0
C A:CYS110 4.8 0.3 1.0
C A:GLY166 4.9 0.5 1.0
CB A:HIS109 4.9 0.9 1.0
NE2 A:GLN171 4.9 0.5 1.0
CD2 A:HIS109 4.9 0.6 1.0
N A:GLY111 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 4a3d

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:67.6
occ:1.00
 NE2 A:HIS80 2.1 83.5 1.0
SG A:CYS67 2.4 86.8 1.0
SG A:CYS77 2.4 80.9 1.0
SG A:CYS70 2.5 82.4 1.0
CD2 A:HIS80 2.5 84.0 1.0
CE1 A:HIS80 3.2 83.4 1.0
CB A:CYS67 3.3 82.8 1.0
CB A:CYS70 3.3 80.1 1.0
CB A:CYS77 3.7 76.8 1.0
N A:CYS70 3.7 82.3 1.0
CG A:HIS80 3.8 82.8 1.0
CA A:CYS70 4.1 81.5 1.0
ND1 A:HIS80 4.1 84.2 1.0
O A:PRO78 4.1 90.8 1.0
OG1 A:THR69 4.5 85.3 1.0
CA A:CYS77 4.6 76.9 1.0
C A:CYS70 4.7 88.3 1.0
O A:LEU58 4.7 98.7 1.0
CA A:CYS67 4.7 83.6 1.0
C A:THR69 4.9 86.5 1.0
N A:THR69 5.0 80.6 1.0

Zinc binding site 3 out of 8 in 4a3d

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:77.4
occ:1.00
 SG B:CYS1166 2.2 81.5 1.0
SG B:CYS1182 2.4 78.4 1.0
SG B:CYS1163 2.4 85.5 1.0
SG B:CYS1185 2.4 75.6 1.0
CB B:CYS1163 2.9 79.3 1.0
CB B:CYS1185 3.4 74.6 1.0
O B:CYS1166 3.5 78.8 1.0
CB B:CYS1166 3.7 76.8 1.0
N B:CYS1166 3.7 75.4 1.0
CB B:CYS1182 3.8 76.0 1.0
CA B:CYS1166 4.1 75.3 1.0
C B:CYS1166 4.2 78.5 1.0
CA B:CYS1163 4.4 77.4 1.0
OG1 B:THR1170 4.5 83.4 1.0
CA B:CYS1185 4.7 78.3 1.0
CB B:THR1170 4.7 85.6 1.0
CG2 B:THR1170 4.8 88.3 1.0
CB B:ILE1165 4.8 75.4 1.0
C B:ILE1165 4.8 77.0 1.0
O B:CYS1182 4.9 86.7 1.0
N B:ILE1165 4.9 74.2 1.0
CD1 B:ILE1165 4.9 68.3 1.0
C B:CYS1163 5.0 80.0 1.0
N B:CYS1185 5.0 81.8 1.0

Zinc binding site 4 out of 8 in 4a3d

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:88.5
occ:1.00
 SG C:CYS95 2.2 74.6 1.0
SG C:CYS92 2.2 80.7 1.0
SG C:CYS86 2.3 79.0 1.0
SG C:CYS88 2.3 74.0 1.0
CB C:CYS92 3.2 77.7 1.0
CB C:CYS86 3.3 73.5 1.0
CB C:CYS95 3.3 71.8 1.0
N C:CYS92 3.5 79.2 1.0
CB C:CYS88 3.7 71.6 1.0
CA C:CYS92 3.9 78.4 1.0
C C:HIS91 4.0 85.5 1.0
N C:CYS95 4.0 76.1 1.0
CA C:CYS95 4.3 73.8 1.0
CA C:HIS91 4.3 83.0 1.0
N C:CYS88 4.3 71.2 1.0
C C:CYS92 4.4 84.2 1.0
O C:ASP90 4.5 90.1 1.0
CA C:CYS86 4.6 72.8 1.0
O C:HIS91 4.6 86.1 1.0
CA C:CYS88 4.6 72.0 1.0
CB C:LYS94 4.7 78.4 1.0
C C:LYS94 4.7 82.5 1.0
O C:CYS92 4.8 82.2 1.0
N C:PHE87 4.8 69.7 1.0
C C:CYS86 4.9 73.4 1.0
N C:LYS94 4.9 79.4 1.0

Zinc binding site 5 out of 8 in 4a3d

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.1
occ:1.00
 SG I:CYS7 2.2 0.9 1.0
SG I:CYS29 2.3 0.6 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS32 2.3 0.5 1.0
CB I:CYS10 2.6 0.0 1.0
CB I:CYS29 3.2 0.6 1.0
CB I:CYS7 3.3 0.5 1.0
CB I:CYS32 3.4 0.0 1.0
N I:CYS10 3.7 0.7 1.0
CA I:CYS10 3.7 0.2 1.0
N I:CYS32 3.8 0.9 1.0
CA I:CYS32 4.1 0.0 1.0
CB I:TYR34 4.3 0.1 1.0
OG1 I:THR31 4.3 0.1 1.0
C I:THR31 4.7 0.2 1.0
CA I:CYS29 4.7 0.4 1.0
CA I:CYS7 4.7 0.6 1.0
C I:CYS32 4.7 0.3 1.0
O I:ARG8 4.8 0.5 1.0
C I:ASP9 4.8 0.2 1.0
CB I:ASP9 4.8 0.9 1.0
C I:CYS10 4.9 0.2 1.0
CB I:THR31 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 4a3d

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Zinc binding site 6 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.5
occ:1.00
 SG I:CYS106 2.3 0.5 1.0
SG I:CYS78 2.3 0.6 1.0
SG I:CYS75 2.4 0.8 1.0
SG I:CYS103 2.4 0.2 1.0
CB I:CYS106 3.1 1.0 1.0
CB I:CYS103 3.2 0.2 1.0
CB I:CYS75 3.2 0.1 1.0
CB I:CYS78 3.5 0.7 1.0
N I:CYS78 3.6 0.8 1.0
N I:CYS106 3.7 0.9 1.0
CA I:CYS106 3.9 0.4 1.0
CA I:CYS78 4.0 0.4 1.0
OG I:SER105 4.1 0.9 1.0
CB I:SER80 4.6 0.6 1.0
C I:CYS78 4.6 0.0 1.0
C I:CYS106 4.6 0.1 1.0
CB I:LYS77 4.6 0.9 1.0
N I:HIS79 4.6 0.5 1.0
CA I:CYS103 4.6 0.4 1.0
CA I:CYS75 4.7 0.8 1.0
N I:SER80 4.7 0.2 1.0
C I:LYS77 4.7 0.0 1.0
N I:SER107 4.7 0.6 1.0
CB I:HIS108 5.0 0.1 1.0
CA I:LYS77 5.0 0.1 1.0
N I:LYS77 5.0 0.6 1.0
C I:SER105 5.0 0.4 1.0

Zinc binding site 7 out of 8 in 4a3d

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:91.4
occ:1.00
 SG J:CYS7 2.2 87.4 1.0
SG J:CYS46 2.3 89.7 1.0
SG J:CYS45 2.4 88.5 1.0
SG J:CYS10 2.5 91.7 1.0
CB J:CYS7 3.2 83.7 1.0
N J:CYS46 3.3 85.2 1.0
CB J:CYS45 3.5 83.8 1.0
CB J:CYS10 3.5 86.3 1.0
CB J:CYS46 3.6 86.0 1.0
N J:CYS10 3.6 80.4 1.0
CA J:CYS46 3.6 85.1 1.0
C J:CYS45 3.7 88.2 1.0
CA J:CYS10 4.0 82.9 1.0
CA J:CYS45 4.2 84.3 1.0
O J:CYS45 4.2 87.6 1.0
NE J:ARG43 4.3 0.6 1.0
NH2 J:ARG43 4.5 0.5 1.0
C J:SER9 4.6 79.9 1.0
N J:GLY11 4.6 79.2 1.0
CA J:CYS7 4.6 81.8 1.0
CB J:SER9 4.6 76.9 1.0
C J:CYS10 4.7 83.7 1.0
CA J:SER9 4.9 73.3 1.0
C J:CYS7 4.9 81.2 1.0
N J:LYS12 4.9 87.5 1.0
N J:CYS45 4.9 86.6 1.0
N J:SER9 4.9 72.7 1.0
CZ J:ARG43 4.9 1.0 1.0
CB J:LYS12 5.0 92.9 1.0
CB J:ARG43 5.0 93.8 1.0

Zinc binding site 8 out of 8 in 4a3d

Go back to Zinc Binding Sites List in 4a3d
Zinc binding site 8 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid


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 Initial Transcribing Complex with A 6NT Dna-Rna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.5
occ:1.00
 SG L:CYS48 2.3 0.1 1.0
SG L:CYS34 2.3 0.5 1.0
SG L:CYS51 2.4 0.6 1.0
SG L:CYS31 2.5 0.1 1.0
CB L:CYS48 3.1 0.9 1.0
CB L:CYS51 3.4 0.4 1.0
CB L:CYS31 3.6 0.4 1.0
CB L:CYS34 3.6 0.9 1.0
OG L:SER36 4.0 0.3 1.0
N L:CYS51 4.3 0.9 1.0
CA L:CYS51 4.3 0.7 1.0
N L:CYS34 4.5 0.2 1.0
CA L:CYS48 4.5 0.2 1.0
CA L:CYS34 4.6 0.3 1.0
O L:CYS51 4.6 0.0 1.0
C L:CYS51 4.7 0.9 1.0
CG L:GLU33 4.9 0.3 1.0
C L:CYS48 4.9 0.2 1.0

Reference:

A.C.Cheung, S.Sainsbury, P.Cramer. Structural Basis of Initial Rna Polymerase II Transcription. Embo J. V. 30 4755 2011.
ISSN: ESSN 1460-2075
PubMed: 22056778
DOI: 10.1038/EMBOJ.2011.396
Page generated: Sat Oct 26 18:52:09 2024

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