Atomistry » Zinc » PDB 3rx8-3s2m » 3s1q
Atomistry »
  Zinc »
    PDB 3rx8-3s2m »
      3s1q »

Zinc in PDB 3s1q: Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp

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

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

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp, PDB code: 3s1q 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) 29.67 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.940, 220.530, 193.720, 90.00, 98.48, 90.00
R / Rfree (%) 17.6 / 22.9

Other elements in 3s1q:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

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 Atp (pdb code 3s1q). 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 Atp, PDB code: 3s1q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS167 2.4 0.3 1.0
SG A:CYS107 2.4 0.7 1.0
SG A:CYS110 2.4 0.0 1.0
SG A:CYS148 2.5 0.9 1.0
CB A:CYS148 3.2 0.5 1.0
CB A:CYS107 3.4 0.6 1.0
O A:MET108 3.8 0.7 1.0
CB A:CYS167 3.9 0.7 1.0
CB A:CYS110 4.1 0.1 1.0
N A:CYS167 4.1 0.8 1.0
CA A:CYS167 4.5 0.7 1.0
CA A:CYS148 4.6 0.4 1.0
N A:CYS110 4.7 0.8 1.0
CA A:CYS107 4.7 0.3 1.0
C A:CYS107 4.9 0.7 1.0
ND2 A:ASN169 4.9 0.1 1.0
CA A:CYS110 4.9 0.1 1.0
O A:CYS167 5.0 0.1 1.0
C A:CYS167 5.0 0.1 1.0

Zinc binding site 2 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.4
occ:1.00
 NE2 A:HIS80 2.2 0.8 1.0
SG A:CYS77 2.3 0.2 1.0
SG A:CYS67 2.4 0.0 1.0
SG A:CYS70 2.5 0.8 1.0
CD2 A:HIS80 2.9 0.3 1.0
CE1 A:HIS80 3.4 0.2 1.0
OE1 A:GLN68 3.5 0.7 1.0
CB A:CYS77 3.5 0.7 1.0
CB A:CYS67 3.6 0.7 1.0
CB A:CYS70 4.0 0.4 1.0
CG A:HIS80 4.1 0.3 1.0
O A:GLN71 4.3 0.9 1.0
ND1 A:HIS80 4.4 0.8 1.0
CD A:GLN68 4.4 0.1 1.0
CA A:CYS77 4.6 0.6 1.0
O A:LEU58 4.6 0.3 1.0
CA A:CYS67 4.7 0.8 1.0
C A:CYS67 4.8 0.3 1.0
CD A:PRO78 4.8 0.7 1.0
O A:CYS67 4.9 0.2 1.0
C A:LEU58 5.0 0.9 1.0
CG A:GLN68 5.0 0.9 1.0

Zinc binding site 3 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1163 2.3 0.1 1.0
SG B:CYS1166 2.3 0.4 1.0
SG B:CYS1185 2.4 0.7 1.0
SG B:CYS1182 2.4 0.0 1.0
CB B:CYS1163 3.0 0.7 1.0
CB B:CYS1166 3.4 0.2 1.0
N B:CYS1166 3.6 0.3 1.0
CB B:CYS1182 3.7 0.8 1.0
CA B:CYS1166 4.0 0.9 1.0
CB B:CYS1185 4.2 0.4 1.0
CA B:CYS1163 4.5 0.8 1.0
CB B:ILE1165 4.6 0.1 1.0
CD1 A:ILE30 4.6 0.6 1.0
C B:ILE1165 4.7 0.6 1.0
N B:CYS1185 4.8 0.2 1.0
N B:GLY1167 4.8 0.7 1.0
CB B:ASN1187 4.8 0.1 1.0
C B:CYS1166 4.9 0.7 1.0
O B:CYS1182 4.9 0.7 1.0
CA B:CYS1182 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:1.0
occ:1.00
 SG C:CYS88 2.2 96.2 1.0
SG C:CYS92 2.2 99.2 1.0
SG C:CYS95 2.2 0.1 1.0
SG C:CYS86 2.4 96.4 1.0
CB C:CYS92 3.1 95.5 1.0
CB C:CYS95 3.2 0.5 1.0
N C:CYS92 3.3 95.7 1.0
CB C:CYS86 3.4 91.8 1.0
CB C:CYS88 3.6 93.5 1.0
CA C:CYS92 3.7 95.4 1.0
C C:HIS91 3.8 0.3 1.0
N C:CYS95 3.9 1.0 1.0
CA C:HIS91 4.2 97.5 1.0
CA C:CYS95 4.2 0.1 1.0
C C:CYS92 4.3 0.6 1.0
O C:ASP90 4.4 0.9 1.0
N C:CYS88 4.5 94.1 1.0
O C:HIS91 4.6 99.4 1.0
C C:LYS94 4.7 0.1 1.0
CA C:CYS88 4.7 94.1 1.0
CA C:CYS86 4.7 92.0 1.0
O C:CYS92 4.7 0.3 1.0
N C:LYS94 4.8 0.9 1.0
CB C:LYS94 4.8 0.4 1.0
N C:ASP93 4.9 0.1 1.0

Zinc binding site 5 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.4
occ:1.00
 SG I:CYS10 2.3 0.8 1.0
SG I:CYS29 2.3 0.2 1.0
SG I:CYS7 2.4 0.9 1.0
SG I:CYS32 2.4 0.9 1.0
CB I:CYS10 2.9 0.0 1.0
CB I:CYS7 3.1 0.7 1.0
CB I:CYS29 3.2 0.2 1.0
OG1 I:THR31 3.4 0.5 1.0
CB I:CYS32 3.4 0.3 1.0
N I:CYS10 3.8 0.8 1.0
N I:CYS32 3.9 0.5 1.0
CA I:CYS10 4.0 0.9 1.0
CB I:TYR34 4.1 0.9 1.0
CA I:CYS32 4.2 0.9 1.0
CA I:CYS7 4.6 0.2 1.0
CB I:THR31 4.6 0.6 1.0
CA I:CYS29 4.7 0.8 1.0
C I:THR31 4.7 0.6 1.0
C I:CYS32 4.8 0.4 1.0
N I:THR31 4.9 0.7 1.0
C I:ASP9 4.9 0.4 1.0
N I:TYR34 4.9 0.4 1.0
CG I:TYR34 4.9 0.5 1.0
CA I:THR31 5.0 0.7 1.0

Zinc binding site 6 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.3
occ:1.00
 SG I:CYS106 2.2 0.7 1.0
SG I:CYS75 2.3 0.8 1.0
SG I:CYS103 2.4 0.2 1.0
SG I:CYS78 2.4 0.4 1.0
CB I:CYS75 3.0 0.5 1.0
CB I:CYS106 3.1 0.3 1.0
CB I:CYS103 3.1 0.7 1.0
CB I:CYS78 3.5 0.2 1.0
OG I:SER80 3.6 0.6 1.0
N I:CYS78 3.7 1.0 1.0
N I:CYS106 3.8 0.0 1.0
CA I:CYS106 3.9 0.9 1.0
CA I:CYS78 4.0 0.1 1.0
C I:CYS78 4.2 0.3 1.0
O I:CYS78 4.2 0.5 1.0
CA I:CYS75 4.5 0.5 1.0
CB I:HIS108 4.5 0.9 1.0
CB I:LYS77 4.5 0.6 1.0
CA I:CYS103 4.6 0.1 1.0
C I:CYS106 4.6 0.6 1.0
C I:SER105 4.6 0.9 1.0
N I:SER80 4.8 0.6 1.0
C I:LYS77 4.8 0.8 1.0
N I:HIS79 4.9 0.2 1.0
CB I:SER80 4.9 0.7 1.0

Zinc binding site 7 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.8
occ:1.00
 SG J:CYS10 2.2 86.9 1.0
SG J:CYS46 2.3 99.0 1.0
SG J:CYS45 2.3 87.1 1.0
SG J:CYS7 2.4 84.7 1.0
CB J:CYS10 3.1 83.7 1.0
CB J:CYS7 3.3 81.5 1.0
N J:CYS46 3.3 90.6 1.0
CB J:CYS45 3.6 82.4 1.0
CB J:CYS46 3.6 94.4 1.0
C J:CYS45 3.7 90.4 1.0
CA J:CYS46 3.7 92.4 1.0
N J:CYS10 3.7 83.1 1.0
CA J:CYS10 3.9 83.5 1.0
CG J:ARG43 4.1 84.8 1.0
CA J:CYS45 4.2 82.4 1.0
O J:CYS45 4.2 89.7 1.0
N J:GLY11 4.6 83.8 1.0
C J:CYS10 4.6 87.0 1.0
CA J:CYS7 4.7 81.2 1.0
CB J:SER9 4.8 84.4 1.0
NE J:ARG43 4.8 84.6 1.0
CZ J:ARG43 4.8 0.0 1.0
N J:CYS45 4.8 83.3 1.0
CB J:LYS12 4.9 96.7 1.0
O J:CYS7 4.9 87.6 1.0
C J:SER9 4.9 85.1 1.0
N J:LYS12 4.9 92.1 1.0
NH1 J:ARG43 4.9 93.2 1.0

Zinc binding site 8 out of 8 in 3s1q

Go back to Zinc Binding Sites List in 3s1q
Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:1.00
 SG L:CYS34 2.3 0.7 1.0
CB L:CYS51 2.3 0.9 1.0
SG L:CYS51 2.4 0.2 1.0
SG L:CYS48 2.4 0.6 1.0
SG L:CYS31 2.5 1.0 1.0
CB L:CYS48 3.1 0.6 1.0
CB L:CYS31 3.2 0.9 1.0
CB L:CYS34 3.6 0.6 1.0
O L:CYS34 3.8 0.4 1.0
CA L:CYS51 3.8 0.9 1.0
N L:CYS34 3.9 0.6 1.0
CA L:CYS34 4.2 0.7 1.0
C L:CYS34 4.5 0.4 1.0
N L:CYS51 4.5 1.0 1.0
C L:CYS51 4.5 0.5 1.0
CA L:CYS48 4.6 0.2 1.0
O L:ASP50 4.6 0.2 1.0
CA L:CYS31 4.7 0.8 1.0
CB L:SER36 4.8 0.6 1.0
C L:ASP50 4.8 0.2 1.0
CB L:GLU33 4.8 0.8 1.0
N L:GLY52 4.9 0.3 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 15:19:50 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