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Zinc in PDB 1twh: Rna Polymerase II Complexed with 2'Datp

Enzymatic activity of Rna Polymerase II Complexed with 2'Datp

All present enzymatic activity of Rna Polymerase II Complexed with 2'Datp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Complexed with 2'Datp, PDB code: 1twh was solved by K.D.Westover, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.000, 223.000, 374.000, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.2

Other elements in 1twh:

The structure of Rna Polymerase II Complexed with 2'Datp also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Complexed with 2'Datp (pdb code 1twh). 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 Complexed with 2'Datp, PDB code: 1twh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1twh

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Zinc binding site 1 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:34.2
occ:1.00
 SG J:CYS45 1.6 77.6 1.0
SG J:CYS10 1.6 38.8 1.0
SG J:CYS7 1.6 19.2 1.0
SG J:CYS46 2.0 1.0 1.0
CB J:CYS10 2.9 42.1 1.0
CB J:CYS7 3.0 20.7 1.0
N J:CYS46 3.0 30.7 1.0
CB J:CYS45 3.3 72.9 1.0
CB J:CYS46 3.6 1.0 1.0
CA J:CYS46 3.8 27.4 1.0
C J:CYS45 3.9 8.4 1.0
N J:CYS10 3.9 44.9 1.0
CA J:CYS10 4.0 43.4 1.0
CA J:CYS45 4.1 3.4 1.0
NE J:ARG43 4.1 30.2 1.0
CG J:ARG43 4.6 35.6 1.0
CA J:CYS7 4.6 12.3 1.0
O J:CYS45 4.7 4.3 1.0
CZ J:ARG43 4.8 31.7 1.0
N J:CYS45 4.8 2.9 1.0
C J:CYS10 4.8 42.9 1.0
CB J:LYS12 4.9 1.0 1.0
NH2 J:ARG43 4.9 21.9 1.0
C J:SER9 4.9 4.7 1.0
CD J:ARG43 4.9 28.4 1.0

Zinc binding site 2 out of 8 in 1twh

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Zinc binding site 2 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:42.6
occ:1.00
 SG C:CYS86 1.3 11.6 1.0
SG C:CYS95 1.6 26.1 1.0
SG C:CYS88 1.9 4.9 1.0
SG C:CYS92 2.2 9.0 1.0
CB C:CYS88 2.9 10.2 1.0
CB C:CYS95 3.1 20.9 1.0
CB C:CYS86 3.2 20.1 1.0
CB C:CYS92 3.3 15.1 1.0
N C:CYS92 3.7 35.8 1.0
C C:HIS91 4.0 38.0 1.0
N C:CYS95 4.0 36.5 1.0
CA C:CYS88 4.1 11.3 1.0
N C:CYS88 4.2 9.2 1.0
CA C:CYS92 4.2 35.8 1.0
CA C:CYS95 4.3 36.5 1.0
CA C:HIS91 4.3 37.3 1.0
N C:LYS94 4.5 13.8 1.0
CA C:CYS86 4.5 33.0 1.0
C C:CYS92 4.6 36.9 1.0
C C:LYS94 4.6 17.1 1.0
C C:CYS86 4.6 30.6 1.0
O C:CYS92 4.7 38.7 1.0
CB C:LYS94 4.7 84.0 1.0
CA C:LYS94 4.8 20.1 1.0
C C:CYS88 4.8 8.5 1.0
O C:HIS91 4.8 38.1 1.0
O C:ASP90 4.9 14.3 1.0
O C:CYS86 4.9 26.2 1.0
N C:PHE87 5.0 13.6 1.0

Zinc binding site 3 out of 8 in 1twh

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Zinc binding site 3 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:46.2
occ:1.00
 SG I:CYS32 0.9 0.5 1.0
SG I:CYS7 1.6 19.4 1.0
SG I:CYS10 1.6 78.8 1.0
SG I:CYS29 2.0 31.2 1.0
CB I:CYS32 2.4 0.1 1.0
CB I:CYS7 3.0 28.7 1.0
CB I:CYS29 3.2 32.5 1.0
CB I:CYS10 3.4 77.3 1.0
CA I:CYS32 3.5 59.6 1.0
N I:CYS32 3.7 61.0 1.0
N I:CYS10 3.8 36.3 1.0
CG2 I:THR31 4.0 31.2 1.0
CA I:CYS10 4.1 32.7 1.0
CA I:CYS7 4.4 14.6 1.0
CB I:THR31 4.4 20.4 1.0
C I:CYS32 4.6 58.6 1.0
CB I:TYR34 4.6 1.0 1.0
C I:THR31 4.6 29.9 1.0
CA I:CYS29 4.7 26.3 1.0
CA I:THR31 4.9 27.4 1.0
N I:THR31 5.0 23.8 1.0
CB I:ASP9 5.0 40.9 1.0

Zinc binding site 4 out of 8 in 1twh

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Zinc binding site 4 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:66.7
occ:1.00
 SG I:CYS78 1.1 74.9 1.0
SG I:CYS106 1.4 28.6 1.0
SG I:CYS75 1.5 58.6 1.0
SG I:CYS103 2.4 60.8 1.0
CB I:CYS78 2.8 94.6 1.0
CB I:CYS103 3.1 52.3 1.0
CB I:CYS75 3.1 70.1 1.0
CB I:CYS106 3.3 34.5 1.0
N I:CYS78 3.3 62.2 1.0
CA I:CYS78 3.7 57.3 1.0
CB I:HIS108 4.1 48.2 1.0
CB I:LYS77 4.3 32.4 1.0
C I:LYS77 4.4 45.2 1.0
N I:LYS77 4.5 45.1 1.0
CA I:CYS75 4.5 48.2 1.0
N I:CYS106 4.5 31.8 1.0
CA I:CYS106 4.5 29.9 1.0
CA I:LYS77 4.6 45.0 1.0
CA I:CYS103 4.6 10.2 1.0
C I:CYS78 4.6 60.5 1.0
CB I:SER80 4.8 63.9 1.0
C I:CYS75 4.9 51.0 1.0
N I:HIS79 4.9 65.1 1.0
C I:CYS106 4.9 32.7 1.0
N I:CYS75 4.9 47.1 1.0
O I:CYS75 4.9 54.0 1.0
N I:HIS108 4.9 22.9 1.0
N I:SER107 5.0 10.2 1.0

Zinc binding site 5 out of 8 in 1twh

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Zinc binding site 5 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:90.5
occ:1.00
 SG L:CYS34 1.8 30.6 1.0
SG L:CYS31 1.8 0.1 1.0
SG L:CYS48 2.0 43.9 1.0
SG L:CYS51 2.1 78.5 1.0
CB L:CYS34 2.7 56.4 1.0
CB L:CYS51 2.7 93.1 1.0
CB L:CYS31 3.0 0.7 1.0
OG L:SER36 3.5 83.3 1.0
O L:CYS51 3.6 99.7 1.0
CA L:CYS34 3.6 55.9 1.0
N L:CYS34 3.6 62.2 1.0
CB L:CYS48 3.7 62.3 1.0
CA L:CYS51 3.9 99.9 1.0
N L:CYS51 4.1 0.6 1.0
C L:CYS34 4.2 57.2 1.0
C L:CYS51 4.2 98.8 1.0
N L:SER35 4.5 63.7 1.0
CA L:CYS31 4.5 77.1 1.0
O L:CYS34 4.7 55.0 1.0
N L:HIS53 4.9 0.1 1.0
CB L:SER36 4.9 77.2 1.0
C L:GLU33 5.0 78.8 1.0

Zinc binding site 6 out of 8 in 1twh

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Zinc binding site 6 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:47.9
occ:1.00
 SG A:CYS110 1.2 96.1 1.0
SG A:CYS148 1.4 53.7 1.0
SG A:CYS107 2.0 85.2 1.0
SG A:CYS167 2.2 1.0 1.0
CB A:CYS167 2.6 0.2 1.0
CB A:CYS148 2.7 71.0 1.0
CB A:CYS110 3.0 0.4 1.0
CB A:CYS107 3.2 85.0 1.0
O A:GLY166 3.4 40.1 1.0
CA A:CYS167 4.1 72.1 1.0
CA A:CYS148 4.2 39.3 1.0
N A:CYS110 4.3 34.3 1.0
CA A:CYS110 4.4 33.4 1.0
C A:GLY166 4.4 40.4 1.0
O A:CYS148 4.5 41.4 1.0
N A:GLY168 4.6 48.1 1.0
CA A:CYS107 4.7 24.7 1.0
C A:CYS167 4.7 66.9 1.0
C A:CYS148 4.7 40.3 1.0
N A:CYS167 4.8 72.6 1.0

Zinc binding site 7 out of 8 in 1twh

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Zinc binding site 7 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:57.4
occ:1.00
 SG B:CYS1185 1.0 0.9 1.0
SG B:CYS1166 1.8 47.1 1.0
SG B:CYS1163 2.0 58.4 1.0
SG B:CYS1182 2.1 59.6 1.0
CB B:CYS1185 2.1 0.7 1.0
CB B:CYS1163 2.7 47.0 1.0
CB B:CYS1166 2.9 51.9 1.0
CB B:CYS1182 3.2 73.5 1.0
CA B:CYS1185 3.7 52.0 1.0
N B:CYS1185 4.2 54.9 1.0
N B:CYS1166 4.3 29.6 1.0
OG1 B:THR1170 4.3 26.8 1.0
CA B:CYS1166 4.3 29.0 1.0
CA B:CYS1163 4.4 36.7 1.0
CG1 B:ILE1165 4.7 45.4 1.0
CA B:CYS1182 4.7 83.3 1.0

Zinc binding site 8 out of 8 in 1twh

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Zinc binding site 8 out of 8 in the Rna Polymerase II Complexed with 2'Datp


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 Complexed with 2'Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:91.8
occ:1.00
 SG A:CYS70 1.2 91.5 1.0
NE2 A:HIS80 1.7 0.4 1.0
SG A:CYS77 1.8 52.2 1.0
CD2 A:HIS80 2.4 0.2 1.0
CE1 A:HIS80 2.9 0.0 1.0
SG A:CYS67 3.0 0.5 1.0
CB A:CYS70 3.2 0.1 1.0
CB A:CYS77 3.5 65.3 1.0
CB A:CYS67 3.6 0.7 1.0
CG A:HIS80 3.7 0.1 1.0
ND1 A:HIS80 3.9 0.9 1.0
CA A:CYS77 4.2 64.6 1.0
CA A:CYS70 4.6 0.7 1.0
OE1 A:GLU72 4.6 0.1 1.0
C A:CYS70 4.6 0.1 1.0
O A:GLN71 4.7 97.9 1.0
O A:CYS70 4.8 1.0 1.0
CD A:PRO78 4.9 68.8 1.0
C A:CYS77 4.9 62.6 1.0

Reference:

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016
Page generated: Wed Oct 16 19:21:25 2024

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