Atomistry » Zinc » PDB 1tnz-1u1j » 1twf
Atomistry »
  Zinc »
    PDB 1tnz-1u1j »
      1twf »

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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Go back to Zinc Binding Sites List in 1twf
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy