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Zinc in PDB 4a3i: Rna Polymerase II Binary Complex with Dna

Enzymatic activity of Rna Polymerase II Binary Complex with Dna

All present enzymatic activity of Rna Polymerase II Binary Complex with Dna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Binary Complex with Dna, PDB code: 4a3i 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) 49.80 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.140, 393.180, 282.480, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Other elements in 4a3i:

The structure of Rna Polymerase II Binary Complex with Dna 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 Binary Complex with Dna (pdb code 4a3i). 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 Binary Complex with Dna, PDB code: 4a3i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4a3i

Go back to Zinc Binding Sites List in 4a3i
Zinc binding site 1 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.6
occ:1.00
 SG A:CYS107 2.3 0.6 1.0
SG A:CYS110 2.3 0.3 1.0
SG A:CYS148 2.4 0.9 1.0
SG A:CYS167 2.5 0.3 1.0
CB A:CYS167 2.8 0.6 1.0
CB A:CYS148 3.2 0.1 1.0
CB A:CYS107 3.3 0.2 1.0
CB A:CYS110 3.5 0.9 1.0
N A:CYS110 3.8 0.9 1.0
O A:GLY166 4.0 0.1 1.0
CA A:CYS167 4.0 0.9 1.0
CA A:CYS110 4.2 0.1 1.0
C A:CYS167 4.3 0.1 1.0
O A:CYS167 4.4 0.7 1.0
CB A:HIS109 4.4 0.1 1.0
CD2 A:HIS109 4.6 0.4 1.0
CA A:CYS148 4.7 0.1 1.0
C A:GLY166 4.7 0.1 1.0
N A:CYS167 4.7 0.2 1.0
C A:HIS109 4.7 0.9 1.0
CA A:CYS107 4.7 0.2 1.0
NE2 A:GLN171 4.7 0.9 1.0
CG A:HIS109 4.9 0.1 1.0
CA A:HIS109 4.9 0.7 1.0
N A:HIS109 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 4a3i

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Zinc binding site 2 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:89.0
occ:1.00
 NE2 A:HIS80 2.2 0.3 1.0
SG A:CYS77 2.3 0.1 1.0
SG A:CYS67 2.3 0.3 1.0
CD2 A:HIS80 2.5 0.6 1.0
SG A:CYS70 2.5 0.7 1.0
CB A:CYS67 3.1 1.0 1.0
CE1 A:HIS80 3.5 0.1 1.0
CB A:CYS77 3.5 97.7 1.0
CB A:CYS70 3.7 0.3 1.0
CG A:HIS80 3.8 0.1 1.0
N A:CYS70 3.8 0.2 1.0
OG1 A:THR69 4.2 0.8 1.0
CA A:CYS70 4.2 0.1 1.0
O A:PRO78 4.3 0.1 1.0
ND1 A:HIS80 4.3 0.6 1.0
CA A:CYS77 4.5 97.1 1.0
C A:CYS70 4.5 0.4 1.0
CA A:CYS67 4.6 0.9 1.0
O A:CYS70 4.7 0.1 1.0
O A:LEU58 4.9 0.0 1.0
N A:THR69 4.9 0.5 1.0
C A:THR69 5.0 0.6 1.0
CA A:GLY59 5.0 0.4 1.0
CB A:HIS80 5.0 0.4 1.0

Zinc binding site 3 out of 8 in 4a3i

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Zinc binding site 3 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:92.7
occ:1.00
 SG B:CYS1166 2.4 0.7 1.0
SG B:CYS1182 2.4 0.2 1.0
SG B:CYS1185 2.4 0.3 1.0
SG B:CYS1163 2.5 0.7 1.0
CB B:CYS1185 2.9 0.9 1.0
CB B:CYS1163 2.9 99.2 1.0
O B:CYS1166 3.7 0.6 1.0
CB B:CYS1182 3.8 0.6 1.0
N B:CYS1166 3.8 95.8 1.0
CB B:CYS1166 3.8 96.5 1.0
CA B:CYS1185 4.2 0.6 1.0
CA B:CYS1166 4.3 95.4 1.0
C B:CYS1166 4.4 0.7 1.0
CA B:CYS1163 4.4 97.3 1.0
N B:CYS1185 4.5 0.5 1.0
CB B:ILE1165 4.6 99.0 1.0
OG1 B:THR1170 4.7 0.4 1.0
O B:CYS1182 4.7 0.5 1.0
CB B:THR1170 4.7 0.9 1.0
C B:ILE1165 4.9 99.0 1.0
CG2 B:THR1170 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 4a3i

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Zinc binding site 4 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:88.8
occ:1.00
 SG C:CYS88 2.2 91.8 1.0
SG C:CYS95 2.3 95.1 1.0
SG C:CYS86 2.3 98.4 1.0
SG C:CYS92 2.4 0.7 1.0
N C:CYS92 3.2 96.3 1.0
CB C:CYS86 3.3 93.2 1.0
CB C:CYS92 3.3 97.9 1.0
CB C:CYS95 3.4 92.2 1.0
CB C:CYS88 3.7 88.6 1.0
CA C:CYS92 3.7 97.0 1.0
N C:CYS95 3.8 94.8 1.0
C C:HIS91 3.8 0.8 1.0
O C:CYS92 4.0 97.5 1.0
CA C:HIS91 4.1 97.2 1.0
C C:CYS92 4.1 0.1 1.0
CA C:CYS95 4.2 93.6 1.0
CB C:LYS94 4.4 97.7 1.0
N C:CYS88 4.5 86.2 1.0
O C:ASP90 4.6 99.1 1.0
C C:LYS94 4.6 98.9 1.0
CA C:CYS88 4.6 87.5 1.0
CA C:CYS86 4.7 92.4 1.0
O C:HIS91 4.7 0.6 1.0
N C:LYS94 4.7 97.8 1.0
CA C:LYS94 4.8 96.4 1.0

Zinc binding site 5 out of 8 in 4a3i

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Zinc binding site 5 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.5
occ:1.00
 SG I:CYS29 2.3 0.2 1.0
SG I:CYS7 2.3 0.2 1.0
SG I:CYS32 2.4 0.3 1.0
SG I:CYS10 2.4 1.0 1.0
CB I:CYS10 3.0 0.7 1.0
CB I:CYS29 3.1 0.6 1.0
CB I:CYS7 3.2 0.6 1.0
CB I:CYS32 3.3 0.7 1.0
N I:CYS32 3.7 0.5 1.0
N I:CYS10 3.8 0.5 1.0
CA I:CYS32 4.0 0.7 1.0
CA I:CYS10 4.0 0.2 1.0
CB I:TYR34 4.5 0.8 1.0
C I:THR31 4.5 0.5 1.0
OG1 I:THR31 4.5 0.4 1.0
CB I:THR31 4.6 0.2 1.0
CA I:CYS29 4.6 0.7 1.0
C I:CYS32 4.6 0.6 1.0
CA I:CYS7 4.6 0.1 1.0
CB I:ASP9 4.8 0.8 1.0
N I:THR31 4.8 0.5 1.0
C I:ASP9 4.9 0.7 1.0
CA I:THR31 4.9 0.9 1.0

Zinc binding site 6 out of 8 in 4a3i

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Zinc binding site 6 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS106 2.3 0.2 1.0
SG I:CYS78 2.3 0.4 1.0
SG I:CYS75 2.3 0.6 1.0
SG I:CYS103 2.6 0.8 1.0
CB I:CYS75 3.0 0.5 1.0
CB I:CYS103 3.1 0.3 1.0
CB I:CYS106 3.3 0.5 1.0
CB I:CYS78 3.5 0.3 1.0
N I:CYS78 3.9 0.8 1.0
OG I:SER105 3.9 0.2 1.0
N I:CYS106 4.0 0.6 1.0
CA I:CYS106 4.1 0.4 1.0
CA I:CYS78 4.2 0.4 1.0
CA I:CYS75 4.5 0.3 1.0
CA I:CYS103 4.6 0.0 1.0
C I:CYS106 4.7 0.6 1.0
N I:HIS79 4.7 0.2 1.0
CB I:SER80 4.7 0.9 1.0
C I:CYS78 4.7 0.1 1.0
N I:SER80 4.7 0.9 1.0
N I:SER107 4.8 0.6 1.0
CB I:LYS77 4.8 0.7 1.0
CB I:HIS108 4.9 0.5 1.0
CD2 I:HIS108 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 4a3i

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Zinc binding site 7 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:90.2
occ:1.00
 SG J:CYS46 2.3 0.8 1.0
SG J:CYS7 2.4 0.6 1.0
SG J:CYS10 2.4 0.4 1.0
SG J:CYS45 2.4 0.1 1.0
CB J:CYS7 3.1 99.3 1.0
N J:CYS46 3.2 0.7 1.0
CB J:CYS10 3.4 0.5 1.0
CB J:CYS46 3.5 0.7 1.0
CA J:CYS46 3.6 0.3 1.0
CB J:CYS45 3.6 0.4 1.0
C J:CYS45 3.8 0.3 1.0
N J:CYS10 3.8 99.8 1.0
NH2 J:ARG43 4.0 0.3 1.0
CA J:CYS10 4.1 0.4 1.0
CA J:CYS45 4.3 0.6 1.0
O J:CYS45 4.4 0.0 1.0
O J:ARG43 4.5 0.4 1.0
CZ J:ARG43 4.5 0.6 1.0
CA J:CYS7 4.5 98.4 1.0
NE J:ARG43 4.6 0.9 1.0
N J:GLY11 4.7 0.1 1.0
C J:CYS10 4.7 0.5 1.0
OG J:SER9 4.7 0.7 1.0
CB J:ARG43 4.7 0.6 1.0
CB J:LYS12 4.8 0.7 1.0
N J:LYS12 4.8 0.7 1.0
N J:CYS45 4.9 0.5 1.0
C J:SER9 4.9 0.4 1.0
C J:CYS7 5.0 0.4 1.0
CB J:SER9 5.0 0.0 1.0

Zinc binding site 8 out of 8 in 4a3i

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Zinc binding site 8 out of 8 in the Rna Polymerase II Binary Complex with Dna


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 Binary Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.4
occ:1.00
 SG L:CYS48 2.3 0.1 1.0
SG L:CYS34 2.3 0.6 1.0
SG L:CYS31 2.3 0.8 1.0
SG L:CYS51 2.4 1.0 1.0
CB L:CYS51 2.4 0.9 1.0
CB L:CYS34 2.9 0.6 1.0
CB L:CYS48 3.1 0.4 1.0
CB L:CYS31 3.4 0.9 1.0
CA L:CYS51 3.7 0.5 1.0
CA L:CYS34 3.9 0.7 1.0
N L:CYS34 3.9 0.0 1.0
N L:CYS51 4.1 0.5 1.0
C L:CYS51 4.2 0.5 1.0
O L:CYS51 4.4 0.1 1.0
OG L:SER36 4.4 0.0 1.0
C L:CYS34 4.5 0.6 1.0
CA L:CYS48 4.6 0.3 1.0
N L:SER35 4.7 0.3 1.0
CG L:GLU33 4.8 0.4 1.0
CA L:CYS31 4.8 0.6 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 18:55:11 2024

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