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Zinc in PDB 3s16: Rna Polymerase II Initiation Complex with An 8-Nt Rna

Enzymatic activity of Rna Polymerase II Initiation Complex with An 8-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with An 8-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with An 8-Nt Rna, PDB code: 3s16 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) 29.86 / 3.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.843, 221.125, 192.746, 90.00, 97.61, 90.00
R / Rfree (%) 18.3 / 22.7

Other elements in 3s16:

The structure of Rna Polymerase II Initiation Complex with An 8-Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Initiation Complex with An 8-Nt Rna (pdb code 3s16). 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 An 8-Nt Rna, PDB code: 3s16:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s16

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS110 2.3 0.9 1.0
SG A:CYS107 2.4 0.1 1.0
SG A:CYS148 2.4 0.7 1.0
SG A:CYS167 2.4 0.3 1.0
CB A:CYS148 3.5 0.4 1.0
N A:CYS167 3.5 1.0 1.0
CB A:CYS110 3.6 0.7 1.0
O A:MET108 3.7 0.9 1.0
CB A:CYS167 3.8 0.5 1.0
O A:CYS167 3.9 0.5 1.0
CB A:CYS107 4.1 0.1 1.0
CA A:CYS167 4.1 0.5 1.0
N A:CYS110 4.2 0.5 1.0
CA A:CYS110 4.4 0.3 1.0
C A:CYS167 4.5 0.0 1.0
N A:GLY111 4.5 0.2 1.0
C A:GLY166 4.5 0.3 1.0
CA A:GLY166 4.6 0.6 1.0
CA A:CYS148 4.9 0.3 1.0
C A:CYS110 4.9 0.8 1.0
CG A:LYS112 4.9 0.9 1.0
C A:MET108 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 3s16

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.3
occ:1.00
 NE2 A:HIS80 2.2 0.7 1.0
SG A:CYS77 2.3 0.8 1.0
SG A:CYS67 2.4 0.7 1.0
SG A:CYS70 2.4 0.9 1.0
CD2 A:HIS80 2.8 0.1 1.0
CE1 A:HIS80 3.4 0.8 1.0
CB A:CYS67 3.7 1.0 1.0
CB A:CYS70 3.7 0.0 1.0
CB A:CYS77 3.8 0.3 1.0
O A:CYS67 4.0 0.6 1.0
CG A:HIS80 4.1 0.9 1.0
O A:GLN71 4.3 0.7 1.0
ND1 A:HIS80 4.4 0.2 1.0
CG A:GLN68 4.4 0.1 1.0
NE2 A:GLN68 4.4 0.2 1.0
C A:CYS67 4.6 0.9 1.0
CD A:GLN68 4.6 0.6 1.0
O A:LEU58 4.7 0.1 1.0
CA A:CYS67 4.8 0.6 1.0
CA A:CYS77 4.8 0.9 1.0
N A:GLN71 4.9 0.2 1.0
CA A:CYS70 4.9 0.5 1.0

Zinc binding site 3 out of 8 in 3s16

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.5
occ:1.00
 SG B:CYS1182 2.4 0.3 1.0
SG B:CYS1166 2.4 0.2 1.0
SG B:CYS1163 2.4 0.7 1.0
SG B:CYS1185 2.4 0.5 1.0
CB B:CYS1166 2.9 0.9 1.0
CB B:CYS1185 3.1 0.3 1.0
CB B:CYS1163 3.3 0.2 1.0
N B:CYS1166 3.5 0.1 1.0
CB B:CYS1182 3.7 0.2 1.0
CA B:CYS1166 3.7 0.5 1.0
CA B:CYS1185 4.4 0.9 1.0
CB B:ILE1165 4.5 0.1 1.0
C B:ILE1165 4.5 0.2 1.0
N B:CYS1185 4.6 0.2 1.0
CA B:CYS1163 4.7 0.3 1.0
OG1 B:THR1170 4.7 0.5 1.0
CB B:THR1170 4.8 0.2 1.0
CA B:ILE1165 4.9 0.2 1.0
CA B:CYS1182 5.0 0.9 1.0

Zinc binding site 4 out of 8 in 3s16

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:91.1
occ:1.00
 SG C:CYS92 2.3 93.7 1.0
SG C:CYS95 2.3 88.7 1.0
SG C:CYS86 2.3 82.8 1.0
SG C:CYS88 2.4 73.6 1.0
CB C:CYS92 3.0 90.4 1.0
CB C:CYS86 3.2 77.6 1.0
CB C:CYS95 3.2 85.1 1.0
N C:CYS92 3.5 88.8 1.0
CB C:CYS88 3.7 72.3 1.0
CA C:CYS92 3.8 90.1 1.0
C C:HIS91 3.9 92.4 1.0
N C:CYS95 3.9 87.6 1.0
CA C:CYS95 4.2 85.8 1.0
O C:HIS91 4.4 91.8 1.0
CA C:HIS91 4.4 89.5 1.0
O C:ASP90 4.5 93.5 1.0
C C:CYS92 4.5 96.0 1.0
N C:CYS88 4.6 74.6 1.0
CA C:CYS86 4.6 78.0 1.0
CA C:CYS88 4.8 73.8 1.0
CB C:LYS94 4.8 93.0 1.0
C C:LYS94 4.9 92.9 1.0
N C:LYS94 4.9 92.0 1.0
N C:ASP93 5.0 94.5 1.0

Zinc binding site 5 out of 8 in 3s16

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.8
occ:1.00
 SG I:CYS29 2.3 0.7 1.0
SG I:CYS32 2.3 0.8 1.0
SG I:CYS10 2.4 0.5 1.0
SG I:CYS7 2.4 0.7 1.0
CB I:CYS10 2.7 0.2 1.0
CB I:CYS7 3.1 1.0 1.0
CB I:CYS29 3.4 0.5 1.0
CB I:CYS32 3.5 0.7 1.0
N I:CYS10 3.8 0.2 1.0
CA I:CYS10 3.8 0.5 1.0
N I:CYS32 4.0 0.5 1.0
CB I:THR31 4.2 0.2 1.0
CA I:CYS32 4.3 0.7 1.0
C I:THR31 4.4 0.2 1.0
CB I:TYR34 4.5 0.6 1.0
CA I:CYS7 4.6 0.5 1.0
CA I:THR31 4.7 0.1 1.0
CA I:CYS29 4.8 0.7 1.0
OG1 I:THR31 4.8 0.9 1.0
N I:THR31 4.8 0.5 1.0
C I:CYS10 4.9 0.5 1.0
O I:CYS29 5.0 0.7 1.0
O I:THR31 5.0 0.5 1.0
C I:CYS32 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 3s16

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Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:79.8
occ:1.00
 SG I:CYS106 2.3 0.2 1.0
SG I:CYS103 2.3 91.0 1.0
SG I:CYS75 2.4 90.7 1.0
SG I:CYS78 2.4 96.5 1.0
CB I:CYS106 3.0 96.7 1.0
CB I:CYS103 3.2 85.2 1.0
CB I:CYS75 3.2 86.0 1.0
CB I:CYS78 3.5 94.8 1.0
N I:CYS78 3.6 94.7 1.0
O I:CYS78 3.9 97.3 1.0
CA I:CYS78 4.0 94.9 1.0
N I:CYS106 4.0 96.0 1.0
CA I:CYS106 4.1 96.9 1.0
OG I:SER80 4.2 0.9 1.0
C I:SER105 4.2 98.7 1.0
C I:CYS78 4.3 99.2 1.0
O I:SER105 4.5 99.4 1.0
CB I:HIS108 4.6 93.7 1.0
CB I:LYS77 4.6 97.0 1.0
CA I:CYS103 4.6 83.2 1.0
CB I:SER105 4.7 96.7 1.0
CA I:CYS75 4.7 85.5 1.0
C I:LYS77 4.8 99.4 1.0
CA I:SER105 4.8 93.0 1.0
N I:SER105 4.9 90.8 1.0
O I:CYS103 4.9 88.2 1.0
C I:CYS103 5.0 88.2 1.0

Zinc binding site 7 out of 8 in 3s16

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:71.7
occ:1.00
 SG J:CYS45 2.3 71.6 1.0
SG J:CYS7 2.3 73.5 1.0
SG J:CYS46 2.4 80.2 1.0
SG J:CYS10 2.4 70.9 1.0
CB J:CYS7 3.2 71.0 1.0
CB J:CYS10 3.2 65.5 1.0
N J:CYS46 3.3 73.0 1.0
CB J:CYS45 3.6 66.6 1.0
N J:CYS10 3.7 61.3 1.0
CB J:CYS46 3.7 76.2 1.0
CD J:ARG43 3.7 85.1 1.0
C J:CYS45 3.7 73.8 1.0
CA J:CYS46 3.7 73.9 1.0
CA J:CYS10 3.9 63.2 1.0
CG J:ARG43 3.9 81.0 1.0
CA J:CYS45 4.2 67.0 1.0
O J:CYS45 4.3 72.5 1.0
NE J:ARG43 4.5 88.3 1.0
N J:GLY11 4.6 64.2 1.0
CA J:CYS7 4.6 70.4 1.0
CB J:SER9 4.7 58.5 1.0
C J:CYS10 4.7 66.5 1.0
C J:SER9 4.8 62.0 1.0
N J:CYS45 4.8 68.3 1.0
O J:CYS7 4.8 71.4 1.0
CB J:LYS12 5.0 77.6 1.0
C J:CYS7 5.0 70.6 1.0
N J:LYS12 5.0 72.7 1.0

Zinc binding site 8 out of 8 in 3s16

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Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with An 8-Nt Rna


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 An 8-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.4
occ:1.00
 SG L:CYS48 2.3 0.6 1.0
SG L:CYS51 2.3 0.2 1.0
SG L:CYS31 2.3 0.2 1.0
SG L:CYS34 2.3 0.2 1.0
CB L:CYS48 3.1 0.1 1.0
CB L:CYS51 3.2 0.1 1.0
CB L:CYS31 3.3 1.0 1.0
CB L:CYS34 3.5 0.1 1.0
N L:CYS51 3.6 0.6 1.0
CA L:CYS51 3.9 0.3 1.0
N L:CYS34 4.0 1.0 1.0
CA L:CYS34 4.3 0.9 1.0
OG L:SER36 4.4 0.0 1.0
CB L:ASP50 4.5 0.7 1.0
CA L:CYS48 4.6 0.2 1.0
N L:GLY52 4.6 0.4 1.0
C L:ASP50 4.7 0.2 1.0
C L:CYS51 4.7 0.4 1.0
CA L:CYS31 4.7 0.5 1.0
CD1 L:LEU38 4.9 0.5 1.0
CA L:ASP50 4.9 0.3 1.0
N L:ASP50 5.0 0.8 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 15:12:30 2024

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