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Zinc in PDB 1twf: Rna Polymerase II Complexed with Utp at 2.3 A Resolution

Enzymatic activity of Rna Polymerase II Complexed with Utp at 2.3 A Resolution

All present enzymatic activity of Rna Polymerase II Complexed with Utp at 2.3 A Resolution:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Complexed with Utp at 2.3 A Resolution, PDB code: 1twf 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 / 2.30
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 (%) 24.7 / 29.4

Other elements in 1twf:

The structure of Rna Polymerase II Complexed with Utp at 2.3 A Resolution 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 Utp at 2.3 A Resolution (pdb code 1twf). 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 Utp at 2.3 A Resolution, PDB code: 1twf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1twf

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Zinc binding site 1 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:45.9
occ:1.00
 SG J:CYS10 2.3 43.1 1.0
SG J:CYS7 2.4 33.4 1.0
SG J:CYS45 2.5 37.3 1.0
SG J:CYS46 2.5 46.9 1.0
N J:CYS46 3.1 41.8 1.0
CB J:CYS45 3.4 39.8 1.0
CB J:CYS7 3.5 36.2 1.0
CA J:CYS46 3.5 41.8 1.0
C J:CYS45 3.5 40.4 1.0
CB J:CYS46 3.6 45.1 1.0
CB J:CYS10 3.7 39.9 1.0
N J:CYS10 3.9 39.7 1.0
NE J:ARG43 3.9 37.4 1.0
CA J:CYS45 4.0 40.1 1.0
O J:CYS45 4.1 42.0 1.0
CD J:ARG43 4.2 39.1 1.0
CG J:ARG43 4.4 42.4 1.0
CA J:CYS10 4.4 40.7 1.0
CB J:SER9 4.4 35.8 1.0
N J:CYS45 4.8 39.4 1.0
C J:SER9 4.9 37.5 1.0
O J:ARG43 4.9 37.5 1.0
CA J:CYS7 4.9 34.7 1.0
CA J:SER9 5.0 34.9 1.0

Zinc binding site 2 out of 8 in 1twf

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Zinc binding site 2 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:48.6
occ:1.00
 SG C:CYS86 2.4 48.3 1.0
SG C:CYS88 2.4 55.2 1.0
SG C:CYS95 2.4 52.4 1.0
SG C:CYS92 2.7 56.1 1.0
CB C:CYS86 3.3 48.5 1.0
N C:CYS92 3.4 59.9 1.0
CB C:CYS88 3.4 56.5 1.0
CB C:CYS95 3.5 57.3 1.0
CB C:CYS92 3.6 56.9 1.0
C C:HIS91 3.8 60.9 1.0
CA C:HIS91 4.0 62.3 1.0
CA C:CYS92 4.0 58.3 1.0
N C:CYS95 4.0 59.1 1.0
O C:CYS92 4.3 58.1 1.0
CA C:CYS95 4.4 57.5 1.0
C C:CYS92 4.4 58.5 1.0
N C:CYS88 4.5 53.2 1.0
CA C:CYS88 4.5 55.8 1.0
O C:ASP90 4.5 61.0 1.0
O C:HIS91 4.6 60.5 1.0
CA C:CYS86 4.6 50.2 1.0
CB C:LYS94 4.7 61.5 1.0
N C:HIS91 4.7 62.7 1.0
C C:LYS94 4.8 59.9 1.0
C C:ASP90 4.9 62.1 1.0
C C:CYS86 4.9 51.1 1.0

Zinc binding site 3 out of 8 in 1twf

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Zinc binding site 3 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:58.0
occ:1.00
 SG I:CYS10 2.3 57.9 1.0
SG I:CYS32 2.4 66.9 1.0
SG I:CYS29 2.5 55.2 1.0
SG I:CYS7 2.5 53.1 1.0
CB I:CYS32 3.0 65.0 1.0
N I:CYS32 3.3 66.0 1.0
CB I:CYS29 3.4 60.5 1.0
CB I:CYS7 3.6 57.8 1.0
CB I:CYS10 3.7 57.0 1.0
CA I:CYS32 3.7 64.4 1.0
CB I:THR31 3.9 66.7 1.0
N I:CYS10 4.1 58.2 1.0
CG2 I:THR31 4.3 67.1 1.0
C I:THR31 4.4 66.2 1.0
C I:CYS32 4.5 63.4 1.0
CA I:CYS10 4.5 56.4 1.0
CB I:TYR34 4.5 48.3 1.0
CA I:THR31 4.6 66.2 1.0
N I:THR31 4.7 66.1 1.0
CA I:CYS29 4.9 60.5 1.0
OG1 I:THR31 4.9 65.4 1.0
O I:CYS32 4.9 63.7 1.0
CB I:ASP9 5.0 61.4 1.0

Zinc binding site 4 out of 8 in 1twf

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Zinc binding site 4 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:74.9
occ:1.00
 SG I:CYS106 2.4 70.6 1.0
SG I:CYS78 2.6 89.5 1.0
SG I:CYS75 2.6 87.7 1.0
SG I:CYS103 2.7 65.9 1.0
CB I:CYS103 3.0 59.2 1.0
CB I:CYS75 3.4 89.0 1.0
N I:CYS78 3.5 95.5 1.0
CB I:CYS78 3.7 94.4 1.0
CB I:HIS108 3.9 64.6 1.0
CB I:LYS77 3.9 95.8 1.0
CB I:CYS106 4.0 70.0 1.0
CA I:CYS78 4.2 94.9 1.0
N I:CYS106 4.5 69.0 1.0
CA I:CYS103 4.5 58.1 1.0
OG I:SER80 4.5 0.6 1.0
C I:LYS77 4.5 95.5 1.0
CA I:LYS77 4.6 95.3 1.0
N I:HIS108 4.6 65.3 1.0
CG I:HIS108 4.6 65.7 1.0
N I:LYS77 4.7 94.3 1.0
CD2 I:HIS108 4.7 64.9 1.0
CA I:CYS75 4.7 88.9 1.0
N I:HIS79 4.7 96.3 1.0
CA I:CYS106 4.8 69.2 1.0
C I:CYS78 4.8 95.4 1.0
CA I:HIS108 4.8 64.1 1.0
C I:CYS75 5.0 89.8 1.0
O I:CYS75 5.0 89.1 1.0

Zinc binding site 5 out of 8 in 1twf

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Zinc binding site 5 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:89.9
occ:1.00
 SG L:CYS34 2.6 94.4 1.0
SG L:CYS31 2.8 0.0 1.0
SG L:CYS48 2.8 0.4 1.0
CB L:CYS51 2.8 0.3 1.0
CB L:CYS48 3.0 0.9 1.0
SG L:CYS51 3.3 0.0 1.0
O L:CYS51 3.6 0.2 1.0
CB L:CYS31 3.7 0.3 1.0
CA L:CYS51 3.8 0.8 1.0
O L:LYS49 3.8 0.6 1.0
N L:CYS51 4.0 0.3 1.0
CB L:CYS34 4.1 99.9 1.0
OG L:SER36 4.1 1.0 1.0
C L:CYS51 4.1 1.0 1.0
CA L:CYS48 4.3 0.3 1.0
N L:LYS49 4.5 0.3 1.0
C L:CYS48 4.5 0.7 1.0
CD2 L:HIS53 4.6 0.6 1.0
C L:LYS49 4.7 0.6 1.0
N L:CYS34 4.7 0.1 1.0
CA L:CYS34 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 1twf

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Zinc binding site 6 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:53.9
occ:1.00
 SG A:CYS110 2.4 54.5 1.0
SG A:CYS107 2.5 66.8 1.0
SG A:CYS148 2.5 80.6 1.0
SG A:CYS167 2.6 82.8 1.0
CB A:CYS167 3.0 85.9 1.0
CB A:CYS107 3.3 65.7 1.0
CB A:CYS148 3.3 86.9 1.0
CB A:CYS110 4.0 64.6 1.0
CA A:CYS167 4.2 87.1 1.0
N A:CYS110 4.2 69.5 1.0
C A:CYS167 4.2 87.0 1.0
O A:CYS167 4.4 86.7 1.0
CA A:CYS110 4.7 66.4 1.0
N A:GLY168 4.7 85.7 1.0
CA A:CYS107 4.7 65.9 1.0
CB A:HIS109 4.8 76.6 1.0
CA A:CYS148 4.8 89.2 1.0
N A:CYS167 5.0 89.2 1.0

Zinc binding site 7 out of 8 in 1twf

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Zinc binding site 7 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:55.4
occ:1.00
 SG B:CYS1166 2.6 72.1 1.0
SG B:CYS1185 2.7 100.0 1.0
SG B:CYS1182 2.8 0.9 1.0
SG B:CYS1163 2.8 68.0 1.0
CB B:CYS1163 3.1 65.8 1.0
CB B:CYS1185 3.3 0.8 1.0
CB B:CYS1166 3.6 67.8 1.0
CB B:CYS1182 3.9 0.8 1.0
N B:CYS1166 4.0 67.0 1.0
OG1 B:THR1170 4.3 69.7 1.0
CA B:CYS1166 4.4 68.0 1.0
O B:LYS1183 4.5 0.2 1.0
O B:CYS1166 4.6 68.4 1.0
CA B:CYS1163 4.7 65.9 1.0
CB B:ILE1165 4.7 68.6 1.0
CA B:CYS1185 4.7 0.6 1.0
O B:CYS1182 4.7 1.0 1.0
N B:CYS1185 4.9 0.9 1.0
C B:CYS1166 5.0 68.5 1.0

Zinc binding site 8 out of 8 in 1twf

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Zinc binding site 8 out of 8 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


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 Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:97.1
occ:1.00
 SG A:CYS77 2.6 0.5 1.0
NE2 A:HIS80 2.6 96.5 1.0
SG A:CYS70 2.7 0.4 1.0
SG A:CYS67 2.8 0.8 1.0
CD2 A:HIS80 3.3 95.7 1.0
CE1 A:HIS80 3.5 96.0 1.0
CB A:CYS67 3.6 0.3 1.0
O A:CYS67 3.8 0.2 1.0
CB A:CYS77 4.0 0.7 1.0
CB A:CYS70 4.2 0.7 1.0
CG A:HIS80 4.3 95.5 1.0
ND1 A:HIS80 4.4 95.1 1.0
OE1 A:GLU72 4.6 0.1 1.0
C A:CYS67 4.6 0.2 1.0
O A:PRO78 4.7 0.9 1.0
CA A:CYS67 4.8 0.4 1.0
CA A:CYS77 4.8 0.7 1.0
CD A:PRO78 4.9 1.0 1.0
N A:PRO78 4.9 0.5 1.0
O A:GLN71 4.9 0.3 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 19:19:04 2024

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