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Zinc in PDB 3s1r: Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp, PDB code: 3s1r 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) 29.97 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.670, 221.320, 193.210, 90.00, 98.31, 90.00
R / Rfree (%) 17.7 / 22.6

Other elements in 3s1r:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp 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 A 5-Nt 3'-Deoxy Rna Soaked with Gtp (pdb code 3s1r). 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 3'-Deoxy Rna Soaked with Gtp, PDB code: 3s1r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s1r

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.1
occ:1.00
 SG A:CYS107 2.3 0.9 1.0
SG A:CYS167 2.3 0.7 1.0
SG A:CYS110 2.4 0.7 1.0
SG A:CYS148 2.4 0.6 1.0
CB A:CYS107 3.1 0.6 1.0
CB A:CYS148 3.2 0.8 1.0
CB A:CYS167 3.8 0.6 1.0
N A:CYS167 3.9 0.6 1.0
CB A:CYS110 4.0 0.4 1.0
N A:CYS110 4.2 0.7 1.0
CA A:CYS167 4.3 0.4 1.0
N A:GLY168 4.5 0.6 1.0
CA A:CYS110 4.6 0.2 1.0
CA A:CYS107 4.6 0.7 1.0
CA A:CYS148 4.7 1.0 1.0
C A:CYS167 4.7 0.0 1.0

Zinc binding site 2 out of 8 in 3s1r

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.1
occ:1.00
 NE2 A:HIS80 2.2 0.7 1.0
SG A:CYS77 2.3 0.2 1.0
SG A:CYS67 2.4 0.7 1.0
SG A:CYS70 2.5 0.0 1.0
CD2 A:HIS80 2.7 0.0 1.0
CE1 A:HIS80 3.4 0.2 1.0
CB A:CYS67 3.6 0.8 1.0
CB A:CYS77 3.8 0.0 1.0
CG A:HIS80 4.0 0.2 1.0
CB A:CYS70 4.2 0.3 1.0
ND1 A:HIS80 4.3 0.8 1.0
O A:GLN71 4.4 0.1 1.0
CG A:GLN68 4.5 0.3 1.0
CD A:GLN68 4.6 0.1 1.0
O A:LEU58 4.6 0.2 1.0
O A:CYS67 4.8 0.7 1.0
CA A:CYS67 4.9 0.2 1.0
OE1 A:GLN68 4.9 0.2 1.0
CA A:CYS77 4.9 0.4 1.0
NE2 A:GLN68 5.0 0.9 1.0
C A:CYS67 5.0 0.9 1.0

Zinc binding site 3 out of 8 in 3s1r

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.0
occ:1.00
 SG B:CYS1166 2.3 0.0 1.0
SG B:CYS1163 2.4 0.3 1.0
SG B:CYS1185 2.4 0.7 1.0
SG B:CYS1182 2.4 0.7 1.0
CB B:CYS1163 3.0 0.2 1.0
CB B:CYS1185 3.1 0.0 1.0
CB B:CYS1166 3.5 0.2 1.0
CB B:CYS1182 3.7 0.2 1.0
N B:CYS1166 3.7 0.5 1.0
CA B:CYS1166 4.2 0.3 1.0
CA B:CYS1185 4.5 0.9 1.0
CA B:CYS1163 4.5 0.7 1.0
CB B:ILE1165 4.6 0.1 1.0
N B:CYS1185 4.8 0.9 1.0
C B:ILE1165 4.9 0.2 1.0
N B:GLY1167 5.0 0.2 1.0

Zinc binding site 4 out of 8 in 3s1r

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:89.3
occ:1.00
 SG C:CYS86 2.3 76.9 1.0
SG C:CYS92 2.3 81.7 1.0
SG C:CYS95 2.3 77.6 1.0
SG C:CYS88 2.3 72.5 1.0
CB C:CYS86 3.1 71.9 1.0
CB C:CYS95 3.3 74.2 1.0
CB C:CYS92 3.4 78.3 1.0
N C:CYS92 3.5 78.7 1.0
CB C:CYS88 3.5 70.1 1.0
CA C:CYS92 3.9 78.2 1.0
C C:HIS91 3.9 82.9 1.0
N C:CYS95 4.0 75.1 1.0
CA C:HIS91 4.2 78.1 1.0
CA C:CYS95 4.2 74.1 1.0
N C:CYS88 4.5 71.3 1.0
O C:ASP90 4.5 83.5 1.0
CA C:CYS86 4.5 71.5 1.0
C C:CYS92 4.5 82.2 1.0
CA C:CYS88 4.6 70.9 1.0
CE C:LYS94 4.6 0.8 1.0
O C:HIS91 4.6 82.6 1.0
CB C:LYS94 4.7 79.2 1.0
C C:LYS94 4.8 79.6 1.0
C C:CYS86 4.9 73.9 1.0
N C:LYS94 5.0 77.4 1.0

Zinc binding site 5 out of 8 in 3s1r

Go back to Zinc Binding Sites List in 3s1r
Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.5
occ:1.00
 SG I:CYS29 2.2 0.9 1.0
SG I:CYS10 2.3 0.5 1.0
SG I:CYS7 2.3 0.4 1.0
SG I:CYS32 2.5 0.5 1.0
CB I:CYS10 2.8 0.6 1.0
CB I:CYS7 3.1 0.0 1.0
CB I:CYS29 3.2 0.4 1.0
CB I:CYS32 3.5 0.4 1.0
N I:CYS10 3.8 0.3 1.0
N I:CYS32 3.8 0.3 1.0
CA I:CYS10 3.9 0.3 1.0
CA I:CYS32 4.1 0.0 1.0
CB I:TYR34 4.2 0.1 1.0
CB I:THR31 4.4 0.6 1.0
CA I:CYS7 4.6 0.6 1.0
OG1 I:THR31 4.6 0.7 1.0
C I:THR31 4.6 0.6 1.0
CA I:CYS29 4.6 0.0 1.0
C I:CYS32 4.7 0.9 1.0
N I:THR31 4.9 0.3 1.0
CA I:THR31 4.9 0.4 1.0
O I:CYS32 4.9 0.7 1.0
C I:ASP9 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 3s1r

Go back to Zinc Binding Sites List in 3s1r
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:82.2
occ:1.00
 SG I:CYS103 2.2 81.8 1.0
SG I:CYS106 2.3 82.9 1.0
SG I:CYS78 2.3 78.8 1.0
SG I:CYS75 2.4 74.1 1.0
CB I:CYS75 3.1 70.1 1.0
CB I:CYS103 3.1 76.1 1.0
CB I:CYS78 3.3 76.2 1.0
CB I:CYS106 3.6 80.3 1.0
N I:CYS78 3.6 76.9 1.0
O I:CYS78 3.7 78.8 1.0
N I:CYS106 3.8 80.1 1.0
CA I:CYS78 3.9 76.5 1.0
C I:CYS78 4.1 78.9 1.0
CA I:CYS106 4.2 79.7 1.0
CB I:HIS108 4.3 75.9 1.0
CB I:SER80 4.4 68.0 1.0
CA I:CYS103 4.5 72.9 1.0
CA I:CYS75 4.6 70.4 1.0
CB I:LYS77 4.6 79.0 1.0
N I:SER80 4.7 67.7 1.0
CB I:SER105 4.8 82.5 1.0
C I:LYS77 4.8 80.7 1.0
C I:SER105 4.9 84.6 1.0
C I:CYS106 4.9 83.6 1.0

Zinc binding site 7 out of 8 in 3s1r

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:78.8
occ:1.00
 SG J:CYS10 2.3 66.2 1.0
SG J:CYS45 2.3 65.2 1.0
SG J:CYS7 2.3 62.2 1.0
SG J:CYS46 2.4 76.4 1.0
N J:CYS46 3.1 68.2 1.0
CB J:CYS10 3.1 62.0 1.0
CB J:CYS7 3.3 58.6 1.0
CB J:CYS45 3.5 60.5 1.0
CA J:CYS46 3.5 69.6 1.0
CB J:CYS46 3.5 71.7 1.0
C J:CYS45 3.5 68.6 1.0
N J:CYS10 3.7 59.5 1.0
CA J:CYS10 3.9 60.5 1.0
CA J:CYS45 4.0 60.7 1.0
CG J:ARG43 4.1 61.5 1.0
O J:CYS45 4.3 68.4 1.0
N J:CYS45 4.7 61.6 1.0
C J:CYS10 4.7 62.8 1.0
N J:GLY11 4.7 58.8 1.0
CA J:CYS7 4.7 57.9 1.0
O J:ARG43 4.8 62.4 1.0
CB J:LYS12 4.8 65.4 1.0
C J:SER9 4.9 61.4 1.0
CB J:SER9 5.0 56.8 1.0

Zinc binding site 8 out of 8 in 3s1r

Go back to Zinc Binding Sites List in 3s1r
Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:99.3
occ:1.00
 CB L:CYS51 2.3 0.7 1.0
SG L:CYS34 2.3 0.5 1.0
SG L:CYS51 2.4 0.5 1.0
SG L:CYS48 2.4 0.1 1.0
SG L:CYS31 2.5 0.9 1.0
CB L:CYS31 3.2 0.1 1.0
CB L:CYS34 3.2 0.5 1.0
CB L:CYS48 3.2 0.4 1.0
CA L:CYS51 3.7 0.1 1.0
N L:CYS34 3.7 0.2 1.0
CA L:CYS34 4.0 0.2 1.0
N L:CYS51 4.3 0.3 1.0
C L:CYS51 4.4 0.3 1.0
OG L:SER36 4.5 0.9 1.0
N L:GLY52 4.6 0.1 1.0
CA L:CYS31 4.7 0.1 1.0
CA L:CYS48 4.7 0.9 1.0
O L:ASP50 4.7 0.1 1.0
C L:ASP50 4.8 0.7 1.0
N L:HIS53 4.9 1.0 1.0
C L:CYS34 4.9 0.2 1.0
C L:GLU33 4.9 0.9 1.0
CB L:HIS53 5.0 0.6 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 15:20:32 2024

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