Zinc in PDB 4a3f: Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp

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

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

Protein crystallography data

The structure of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp, PDB code: 4a3f 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) 49.89 / 3.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.600, 391.300, 283.340, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.5

Other elements in 4a3f:

The structure of Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp 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 and Soaked with Ampcpp (pdb code 4a3f). 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 and Soaked with Ampcpp, PDB code: 4a3f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4a3f

Go back to Zinc Binding Sites List in 4a3f
Zinc binding site 1 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.6
occ:1.00
 SG A:CYS148 2.3 0.5 1.0
SG A:CYS107 2.3 0.3 1.0
SG A:CYS110 2.3 0.7 1.0
SG A:CYS167 2.4 0.8 1.0
CB A:CYS167 2.8 0.4 1.0
CB A:CYS148 3.0 0.6 1.0
CB A:CYS107 3.3 0.9 1.0
CB A:CYS110 3.3 0.1 1.0
N A:CYS110 3.8 0.1 1.0
CA A:CYS167 4.0 0.1 1.0
O A:CYS167 4.0 0.2 1.0
CA A:CYS110 4.1 0.1 1.0
C A:CYS167 4.2 0.0 1.0
O A:GLY166 4.3 0.1 1.0
CA A:CYS148 4.5 0.9 1.0
CA A:CYS107 4.7 0.9 1.0
CB A:HIS109 4.8 0.1 1.0
N A:CYS167 4.9 0.6 1.0
C A:HIS109 4.9 0.6 1.0
NE2 A:GLN171 4.9 0.8 1.0
C A:GLY166 4.9 0.6 1.0

Zinc binding site 2 out of 8 in 4a3f

Go back to Zinc Binding Sites List in 4a3f
Zinc binding site 2 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:74.9
occ:1.00
 NE2 A:HIS80 2.3 0.8 1.0
SG A:CYS77 2.4 96.7 1.0
SG A:CYS70 2.4 99.8 1.0
CD2 A:HIS80 2.4 0.8 1.0
SG A:CYS67 2.4 0.4 1.0
CB A:CYS67 3.2 97.6 1.0
CB A:CYS70 3.3 97.3 1.0
CE1 A:HIS80 3.6 0.6 1.0
CB A:CYS77 3.7 92.4 1.0
N A:CYS70 3.8 98.2 1.0
CG A:HIS80 3.8 98.7 1.0
OG1 A:THR69 3.9 96.4 1.0
CA A:CYS70 4.1 98.3 1.0
O A:PRO78 4.2 99.0 1.0
O A:CYS70 4.3 0.7 1.0
ND1 A:HIS80 4.4 0.7 1.0
C A:CYS70 4.5 0.2 1.0
CA A:CYS77 4.5 91.9 1.0
O A:LEU58 4.7 0.3 1.0
CA A:CYS67 4.7 98.7 1.0
CD A:PRO78 4.8 92.8 1.0
CB A:HIS80 4.9 95.4 1.0
C A:THR69 4.9 0.2 1.0

Zinc binding site 3 out of 8 in 4a3f

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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 and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:82.0
occ:1.00
 SG B:CYS1166 2.2 97.5 1.0
SG B:CYS1163 2.4 98.2 1.0
SG B:CYS1182 2.4 96.1 1.0
SG B:CYS1185 2.5 94.5 1.0
CB B:CYS1163 3.1 92.7 1.0
CB B:CYS1185 3.1 92.6 1.0
CB B:CYS1166 3.6 92.7 1.0
N B:CYS1166 3.6 90.2 1.0
O B:CYS1166 3.6 89.5 1.0
CB B:CYS1182 3.8 93.2 1.0
CA B:CYS1166 4.0 90.2 1.0
C B:CYS1166 4.2 90.0 1.0
O B:GLY1184 4.5 0.1 1.0
CA B:CYS1185 4.5 95.6 1.0
CA B:CYS1163 4.5 91.2 1.0
OG1 B:THR1170 4.7 0.3 1.0
C B:ILE1165 4.7 92.3 1.0
CB B:ILE1165 4.7 89.9 1.0
CB B:THR1170 4.8 0.2 1.0
O B:CYS1182 4.8 0.1 1.0
CG2 B:THR1170 4.9 0.8 1.0
N B:ILE1165 4.9 87.9 1.0
CA B:ILE1165 5.0 87.0 1.0
N B:CYS1185 5.0 98.5 1.0

Zinc binding site 4 out of 8 in 4a3f

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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 and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:93.5
occ:1.00
 SG C:CYS88 2.2 95.4 1.0
SG C:CYS86 2.3 95.8 1.0
SG C:CYS92 2.3 0.2 1.0
SG C:CYS95 2.3 91.4 1.0
CB C:CYS86 3.3 90.6 1.0
CB C:CYS95 3.3 87.7 1.0
CB C:CYS92 3.4 98.6 1.0
N C:CYS92 3.4 97.4 1.0
CB C:CYS88 3.5 92.6 1.0
CA C:CYS92 3.9 97.8 1.0
N C:CYS95 4.0 89.8 1.0
C C:HIS91 4.0 0.5 1.0
N C:CYS88 4.2 90.1 1.0
CA C:CYS95 4.3 88.2 1.0
CA C:HIS91 4.3 98.1 1.0
CA C:CYS88 4.4 92.0 1.0
C C:CYS92 4.5 0.8 1.0
CA C:CYS86 4.6 90.1 1.0
CB C:LYS94 4.7 94.2 1.0
C C:LYS94 4.7 95.7 1.0
O C:HIS91 4.8 0.9 1.0
N C:PHE87 4.8 87.9 1.0
C C:CYS86 4.8 91.3 1.0
N C:LYS94 4.8 94.1 1.0
O C:ASP90 4.9 0.2 1.0
O C:CYS88 4.9 0.1 1.0
O C:CYS92 5.0 99.8 1.0

Zinc binding site 5 out of 8 in 4a3f

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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 and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.6
occ:1.00
 SG I:CYS29 2.3 0.3 1.0
SG I:CYS7 2.3 0.2 1.0
SG I:CYS10 2.3 0.5 1.0
SG I:CYS32 2.4 0.7 1.0
CB I:CYS10 2.5 0.2 1.0
CB I:CYS29 3.3 0.4 1.0
CB I:CYS7 3.4 1.0 1.0
CB I:CYS32 3.6 0.3 1.0
CA I:CYS10 3.8 0.2 1.0
N I:CYS32 3.9 1.0 1.0
N I:CYS10 4.0 0.8 1.0
O I:ARG8 4.3 0.7 1.0
CA I:CYS32 4.3 0.8 1.0
OG1 I:THR31 4.3 0.7 1.0
CB I:THR31 4.3 0.5 1.0
CB I:TYR34 4.4 0.5 1.0
C I:THR31 4.7 0.5 1.0
CA I:CYS29 4.7 0.6 1.0
CA I:CYS7 4.8 0.8 1.0
C I:CYS10 4.9 0.6 1.0
CA I:THR31 5.0 0.4 1.0
C I:CYS32 5.0 0.4 1.0
C I:CYS7 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 4a3f

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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 and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.3
occ:1.00
 SG I:CYS106 2.3 0.5 1.0
SG I:CYS75 2.3 1.0 1.0
SG I:CYS78 2.4 0.1 1.0
SG I:CYS103 2.5 0.9 1.0
CB I:CYS103 3.1 0.5 1.0
CB I:CYS75 3.2 0.1 1.0
CB I:CYS106 3.2 0.5 1.0
CB I:CYS78 3.5 0.7 1.0
N I:CYS78 3.7 0.4 1.0
N I:CYS106 3.9 0.9 1.0
OG I:SER105 3.9 0.6 1.0
CA I:CYS106 4.1 0.4 1.0
CA I:CYS78 4.1 0.5 1.0
CB I:LYS77 4.6 0.2 1.0
CA I:CYS75 4.6 0.8 1.0
CA I:CYS103 4.6 0.1 1.0
CB I:SER80 4.6 0.9 1.0
C I:CYS78 4.7 0.7 1.0
N I:HIS79 4.7 0.3 1.0
CB I:HIS108 4.7 0.3 1.0
N I:SER80 4.8 0.5 1.0
C I:CYS106 4.8 0.2 1.0
C I:LYS77 4.8 0.2 1.0
C I:SER105 4.9 0.6 1.0
N I:SER107 4.9 0.0 1.0
CB I:SER105 5.0 0.6 1.0

Zinc binding site 7 out of 8 in 4a3f

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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 and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:95.5
occ:1.00
 SG J:CYS7 2.2 0.6 1.0
SG J:CYS46 2.3 95.7 1.0
SG J:CYS45 2.4 92.4 1.0
SG J:CYS10 2.5 98.3 1.0
CB J:CYS7 3.1 0.2 1.0
N J:CYS46 3.3 91.1 1.0
CB J:CYS10 3.5 94.4 1.0
CB J:CYS45 3.5 88.9 1.0
CB J:CYS46 3.6 91.6 1.0
N J:CYS10 3.6 93.5 1.0
CA J:CYS46 3.7 91.0 1.0
C J:CYS45 3.8 93.2 1.0
CA J:CYS10 4.0 93.2 1.0
CA J:CYS45 4.3 89.5 1.0
NE J:ARG43 4.4 0.6 1.0
CA J:CYS7 4.5 99.9 1.0
N J:GLY11 4.5 93.4 1.0
O J:CYS45 4.6 91.9 1.0
CB J:SER9 4.6 98.8 1.0
C J:SER9 4.6 98.4 1.0
C J:CYS10 4.7 96.1 1.0
CB J:ARG43 4.8 0.7 1.0
N J:LYS12 4.8 97.7 1.0
C J:CYS7 4.8 0.3 1.0
CA J:SER9 4.9 94.2 1.0
N J:SER9 4.9 93.9 1.0
N J:CYS45 4.9 91.6 1.0
CB J:LYS12 5.0 0.7 1.0

Zinc binding site 8 out of 8 in 4a3f

Go back to Zinc Binding Sites List in 4a3f
Zinc binding site 8 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 6NT Dna-Rna Hybrid and Soaked with Ampcpp


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 and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.2
occ:1.00
 SG L:CYS34 2.3 0.4 1.0
SG L:CYS48 2.3 0.2 1.0
SG L:CYS51 2.4 0.4 1.0
SG L:CYS31 2.5 0.9 1.0
CB L:CYS51 2.6 0.4 1.0
CB L:CYS48 3.0 1.0 1.0
CB L:CYS31 3.3 0.8 1.0
CB L:CYS34 3.6 0.2 1.0
O L:CYS51 3.7 0.1 1.0
CA L:CYS51 3.8 0.7 1.0
C L:CYS51 4.1 0.1 1.0
N L:CYS34 4.4 1.0 1.0
OG L:SER36 4.5 0.9 1.0
CA L:CYS48 4.5 0.2 1.0
N L:CYS51 4.5 0.9 1.0
CA L:CYS34 4.6 0.7 1.0
OE2 L:GLU33 4.7 1.0 1.0
CA L:CYS31 4.8 0.1 1.0
C L:CYS48 4.9 0.1 1.0
CG L:GLU33 4.9 0.9 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 18:55:09 2024

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