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Zinc in PDB 3s2d: Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.286, 220.768, 192.241, 90.00, 97.69, 90.00
R / Rfree (%) 18.3 / 23.1

Other elements in 3s2d:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U 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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U (pdb code 3s2d). 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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s2d

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS110 2.3 0.8 1.0
SG A:CYS167 2.3 0.0 1.0
SG A:CYS107 2.4 0.9 1.0
SG A:CYS148 2.4 0.4 1.0
CB A:CYS148 3.0 0.0 1.0
CB A:CYS107 3.4 1.0 1.0
CB A:CYS110 3.5 0.8 1.0
CB A:CYS167 3.7 0.9 1.0
N A:CYS167 3.8 0.8 1.0
O A:MET108 3.8 0.9 1.0
CA A:CYS167 4.2 0.8 1.0
N A:CYS110 4.4 0.1 1.0
CA A:CYS148 4.4 0.7 1.0
CA A:CYS110 4.5 0.7 1.0
C A:CYS167 4.7 1.0 1.0
CA A:CYS107 4.7 0.5 1.0
O A:CYS167 4.9 0.3 1.0
C A:CYS107 4.9 0.6 1.0
C A:GLY166 4.9 0.9 1.0

Zinc binding site 2 out of 8 in 3s2d

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.0
occ:1.00
 NE2 A:HIS80 2.1 0.0 1.0
SG A:CYS77 2.4 1.0 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS70 2.5 0.1 1.0
CD2 A:HIS80 3.1 0.6 1.0
CE1 A:HIS80 3.1 0.3 1.0
CB A:CYS70 3.4 0.5 1.0
NE2 A:GLN68 3.6 0.3 1.0
CB A:CYS77 3.7 0.3 1.0
CB A:CYS67 3.8 0.5 1.0
O A:GLN71 4.2 0.6 1.0
CG A:HIS80 4.2 0.6 1.0
ND1 A:HIS80 4.3 1.0 1.0
O A:CYS67 4.4 0.9 1.0
CA A:CYS77 4.7 0.5 1.0
CD A:GLN68 4.7 0.9 1.0
CA A:CYS70 4.7 0.7 1.0
C A:CYS67 4.9 0.7 1.0
C A:CYS70 4.9 0.2 1.0
CG A:GLN68 4.9 0.5 1.0
CA A:CYS67 4.9 0.9 1.0
N A:GLN71 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 3s2d

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.5
occ:1.00
 SG B:CYS1163 2.3 0.4 1.0
SG B:CYS1166 2.3 0.8 1.0
SG B:CYS1185 2.4 0.9 1.0
SG B:CYS1182 2.4 0.6 1.0
CB B:CYS1185 3.1 0.4 1.0
CB B:CYS1163 3.1 0.7 1.0
CB B:CYS1166 3.3 0.3 1.0
N B:CYS1166 3.6 0.5 1.0
CB B:CYS1182 3.6 0.9 1.0
CA B:CYS1166 4.0 0.6 1.0
CB B:ILE1165 4.5 0.7 1.0
CA B:CYS1185 4.5 0.8 1.0
CA B:CYS1163 4.5 0.3 1.0
C B:ILE1165 4.7 0.9 1.0
N B:CYS1185 4.8 0.2 1.0
O B:CYS1182 4.9 0.0 1.0
C B:CYS1166 4.9 0.6 1.0
CA B:CYS1182 4.9 0.8 1.0
CA B:ILE1165 4.9 0.9 1.0
N B:GLY1167 4.9 0.9 1.0

Zinc binding site 4 out of 8 in 3s2d

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:67.5
occ:1.00
 SG C:CYS88 2.3 57.8 1.0
SG C:CYS92 2.3 69.6 1.0
SG C:CYS95 2.3 63.9 1.0
SG C:CYS86 2.4 68.1 1.0
CB C:CYS86 3.1 62.5 1.0
CB C:CYS92 3.2 66.1 1.0
CB C:CYS95 3.3 59.9 1.0
CB C:CYS88 3.4 56.1 1.0
N C:CYS92 3.5 64.6 1.0
CA C:CYS92 3.9 65.5 1.0
C C:HIS91 4.0 68.2 1.0
N C:CYS95 4.0 61.1 1.0
CA C:CYS95 4.3 59.9 1.0
CA C:HIS91 4.3 65.1 1.0
O C:ASP90 4.4 72.4 1.0
N C:CYS88 4.4 58.0 1.0
C C:CYS92 4.5 69.9 1.0
CA C:CYS86 4.5 61.9 1.0
CA C:CYS88 4.5 57.2 1.0
O C:HIS91 4.6 67.7 1.0
O C:CYS92 4.7 68.4 1.0
C C:LYS94 4.8 66.1 1.0
CB C:LYS94 4.8 67.2 1.0
C C:CYS86 4.9 63.6 1.0
N C:LYS94 4.9 65.9 1.0

Zinc binding site 5 out of 8 in 3s2d

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:87.4
occ:1.00
 SG I:CYS29 2.3 99.0 1.0
SG I:CYS10 2.3 1.0 1.0
SG I:CYS7 2.4 1.0 1.0
SG I:CYS32 2.4 0.1 1.0
CB I:CYS10 2.7 98.9 1.0
CB I:CYS7 3.1 98.8 1.0
CB I:CYS29 3.3 95.7 1.0
CB I:CYS32 3.5 0.3 1.0
OG1 I:THR31 3.5 0.2 1.0
N I:CYS10 3.8 99.5 1.0
CA I:CYS10 3.8 98.4 1.0
N I:CYS32 4.0 0.1 1.0
CA I:CYS32 4.2 0.7 1.0
CB I:TYR34 4.4 94.4 1.0
C I:THR31 4.6 0.7 1.0
CA I:CYS7 4.6 98.6 1.0
CA I:CYS29 4.7 95.7 1.0
CB I:THR31 4.8 0.5 1.0
C I:CYS32 4.9 0.8 1.0
C I:ASP9 5.0 0.1 1.0
C I:CYS10 5.0 99.7 1.0

Zinc binding site 6 out of 8 in 3s2d

Go back to Zinc Binding Sites List in 3s2d
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:67.0
occ:1.00
 SG I:CYS106 2.3 72.6 1.0
SG I:CYS103 2.3 71.2 1.0
SG I:CYS78 2.4 75.2 1.0
SG I:CYS75 2.4 70.5 1.0
CB I:CYS103 3.1 65.8 1.0
CB I:CYS75 3.2 65.7 1.0
CB I:CYS106 3.2 70.1 1.0
O I:CYS78 3.7 77.0 1.0
CB I:CYS78 3.7 73.3 1.0
N I:CYS78 3.7 74.5 1.0
N I:CYS106 4.1 69.4 1.0
CA I:CYS78 4.1 73.7 1.0
CA I:CYS106 4.2 69.7 1.0
CB I:HIS108 4.3 70.4 1.0
C I:CYS78 4.3 77.3 1.0
CB I:LYS77 4.5 77.8 1.0
CB I:SER80 4.5 70.4 1.0
CA I:CYS103 4.6 63.6 1.0
CA I:CYS75 4.7 65.3 1.0
C I:SER105 4.7 74.7 1.0
OG I:SER105 4.7 86.2 1.0
C I:CYS106 4.8 74.3 1.0
C I:LYS77 4.8 80.0 1.0
N I:HIS108 4.9 69.3 1.0
C I:CYS103 5.0 66.4 1.0

Zinc binding site 7 out of 8 in 3s2d

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:58.1
occ:1.00
 SG J:CYS46 2.3 57.0 1.0
SG J:CYS45 2.3 49.4 1.0
SG J:CYS10 2.3 57.7 1.0
SG J:CYS7 2.4 56.0 1.0
CB J:CYS7 3.3 53.6 1.0
N J:CYS46 3.3 52.0 1.0
CB J:CYS10 3.4 52.9 1.0
CB J:CYS46 3.6 53.5 1.0
CB J:CYS45 3.6 45.1 1.0
CA J:CYS46 3.7 52.6 1.0
C J:CYS45 3.8 52.9 1.0
N J:CYS10 3.9 50.9 1.0
NE J:ARG43 3.9 74.9 1.0
CD J:ARG43 4.0 69.4 1.0
CG J:ARG43 4.1 64.6 1.0
CA J:CYS10 4.1 51.6 1.0
CA J:CYS45 4.2 46.2 1.0
O J:CYS45 4.4 52.3 1.0
N J:GLY11 4.6 50.5 1.0
CA J:CYS7 4.7 53.9 1.0
CB J:SER9 4.7 49.9 1.0
C J:CYS10 4.8 54.8 1.0
N J:CYS45 4.9 48.2 1.0
O J:CYS7 4.9 57.7 1.0
C J:SER9 5.0 53.0 1.0
CB J:LYS12 5.0 59.1 1.0

Zinc binding site 8 out of 8 in 3s2d

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Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.9
occ:1.00
 CB L:CYS51 2.0 0.4 1.0
SG L:CYS31 2.4 0.7 1.0
SG L:CYS34 2.4 0.6 1.0
SG L:CYS48 2.4 0.2 1.0
SG L:CYS51 2.5 0.4 1.0
CB L:CYS48 3.2 0.9 1.0
CB L:CYS31 3.3 0.7 1.0
CB L:CYS34 3.3 0.3 1.0
CA L:CYS51 3.5 0.1 1.0
N L:CYS34 3.7 0.8 1.0
N L:CYS51 4.0 0.2 1.0
CA L:CYS34 4.1 0.3 1.0
C L:CYS51 4.4 0.8 1.0
C L:ASP50 4.6 0.9 1.0
CA L:CYS48 4.6 0.8 1.0
CB L:GLU33 4.6 0.8 1.0
N L:GLY52 4.7 0.5 1.0
CA L:CYS31 4.8 0.9 1.0
C L:GLU33 4.8 0.6 1.0
O L:ASP50 4.9 0.3 1.0
C L:CYS34 4.9 0.3 1.0
N L:SER35 4.9 0.9 1.0

Reference:

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629
Page generated: Sat Oct 26 15:20:27 2024

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