Atomistry » Zinc » PDB 3ryj-3s2q » 3rzo
Atomistry »
  Zinc »
    PDB 3ryj-3s2q »
      3rzo »

Zinc in PDB 3rzo: Rna Polymerase II Initiation Complex with A 4-Nt Rna

Enzymatic activity of Rna Polymerase II Initiation Complex with A 4-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 4-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 4-Nt Rna, PDB code: 3rzo 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) 40.01 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.038, 221.149, 192.875, 90.00, 98.34, 90.00
R / Rfree (%) 18.8 / 23.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS107 2.3 0.4 1.0
SG A:CYS110 2.3 0.7 1.0
SG A:CYS167 2.3 0.9 1.0
SG A:CYS148 2.4 0.2 1.0
CB A:CYS148 3.3 0.9 1.0
CB A:CYS107 3.4 0.9 1.0
CB A:CYS167 3.6 0.9 1.0
CB A:CYS110 3.6 0.3 1.0
N A:CYS167 3.8 0.4 1.0
CA A:CYS167 4.1 0.9 1.0
N A:CYS110 4.3 0.6 1.0
C A:CYS167 4.4 0.4 1.0
CA A:CYS110 4.4 0.6 1.0
O A:CYS167 4.5 0.7 1.0
O A:MET108 4.5 0.8 1.0
CA A:CYS148 4.7 0.8 1.0
CA A:CYS107 4.8 0.0 1.0
C A:GLY166 4.9 0.3 1.0
N A:GLY111 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.2
occ:1.00
 NE2 A:HIS80 2.1 0.4 1.0
SG A:CYS77 2.3 0.9 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS70 2.5 0.2 1.0
CD2 A:HIS80 3.0 0.9 1.0
CE1 A:HIS80 3.2 0.4 1.0
CB A:CYS67 3.4 0.2 1.0
NE2 A:GLN68 3.6 0.4 1.0
CB A:CYS77 3.7 0.6 1.0
O A:CYS67 3.9 0.8 1.0
CB A:CYS70 4.1 0.9 1.0
CG A:HIS80 4.1 0.6 1.0
ND1 A:HIS80 4.2 0.8 1.0
CA A:CYS67 4.6 0.3 1.0
C A:CYS67 4.6 0.4 1.0
O A:GLN71 4.7 0.3 1.0
CA A:CYS77 4.7 0.6 1.0
CD A:GLN68 4.8 0.3 1.0
O A:LEU58 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.9
occ:1.00
 SG B:CYS1166 2.3 0.0 1.0
SG B:CYS1163 2.4 0.8 1.0
SG B:CYS1185 2.5 0.8 1.0
SG B:CYS1182 2.5 0.0 1.0
CB B:CYS1185 2.8 0.8 1.0
CB B:CYS1163 3.0 0.3 1.0
CB B:CYS1166 3.4 0.5 1.0
CB B:CYS1182 3.4 1.0 1.0
N B:CYS1166 3.7 0.8 1.0
CA B:CYS1166 4.1 0.8 1.0
CA B:CYS1185 4.3 0.1 1.0
CA B:CYS1163 4.5 0.3 1.0
CB B:ILE1165 4.7 0.1 1.0
CA B:CYS1182 4.9 0.4 1.0
CB B:ASN1187 4.9 0.3 1.0
C B:ILE1165 4.9 0.7 1.0

Zinc binding site 4 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:79.6
occ:1.00
 SG C:CYS92 2.2 92.6 1.0
SG C:CYS86 2.3 87.3 1.0
SG C:CYS88 2.4 81.5 1.0
SG C:CYS95 2.4 84.6 1.0
CB C:CYS86 3.2 81.8 1.0
CB C:CYS88 3.3 79.1 1.0
CB C:CYS95 3.3 81.2 1.0
N C:CYS92 3.4 86.3 1.0
CB C:CYS92 3.4 88.6 1.0
C C:HIS91 3.8 88.4 1.0
CA C:CYS92 3.9 87.5 1.0
N C:CYS95 4.0 83.3 1.0
CA C:HIS91 4.1 83.6 1.0
CA C:CYS95 4.3 81.3 1.0
C C:CYS92 4.4 92.3 1.0
N C:CYS88 4.5 80.3 1.0
CA C:CYS88 4.5 79.9 1.0
CB C:LYS94 4.5 89.0 1.0
CA C:CYS86 4.6 81.4 1.0
O C:HIS91 4.6 87.2 1.0
C C:LYS94 4.6 90.6 1.0
O C:CYS92 4.6 90.9 1.0
O C:ASP90 4.7 92.0 1.0
N C:LYS94 4.8 89.6 1.0
CA C:LYS94 4.9 87.9 1.0
C C:CYS86 4.9 83.1 1.0
N C:HIS91 4.9 84.1 1.0

Zinc binding site 5 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.6
occ:1.00
 SG I:CYS29 2.2 1.0 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS32 2.4 0.2 1.0
SG I:CYS7 2.4 0.6 1.0
CB I:CYS10 2.8 0.0 1.0
CB I:CYS7 3.0 0.5 1.0
CB I:CYS29 3.2 0.4 1.0
CB I:CYS32 3.6 0.7 1.0
N I:CYS10 3.8 0.1 1.0
N I:CYS32 3.9 0.3 1.0
CA I:CYS10 3.9 0.7 1.0
CA I:CYS32 4.2 0.3 1.0
CB I:THR31 4.2 0.5 1.0
CB I:TYR34 4.3 0.8 1.0
CA I:CYS7 4.5 0.7 1.0
CA I:CYS29 4.7 0.6 1.0
C I:THR31 4.7 0.6 1.0
OG1 I:THR31 4.7 0.3 1.0
C I:CYS32 4.8 0.7 1.0
N I:THR31 4.9 0.0 1.0
CA I:THR31 4.9 0.8 1.0
C I:ASP9 5.0 0.8 1.0

Zinc binding site 6 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:90.8
occ:1.00
 SG I:CYS106 2.2 93.6 1.0
SG I:CYS103 2.3 95.1 1.0
SG I:CYS75 2.3 97.9 1.0
SG I:CYS78 2.3 94.0 1.0
CB I:CYS103 3.1 89.1 1.0
CB I:CYS75 3.2 93.4 1.0
CB I:CYS106 3.4 91.2 1.0
CB I:CYS78 3.6 92.5 1.0
N I:CYS78 3.7 94.3 1.0
N I:CYS106 4.1 90.4 1.0
CA I:CYS78 4.1 93.7 1.0
CA I:CYS106 4.3 90.7 1.0
CB I:HIS108 4.3 87.6 1.0
O I:CYS78 4.4 98.8 1.0
CB I:SER80 4.4 93.2 1.0
C I:CYS78 4.4 99.3 1.0
CB I:LYS77 4.4 96.5 1.0
CA I:CYS103 4.6 85.8 1.0
CA I:CYS75 4.6 93.6 1.0
C I:SER105 4.8 94.3 1.0
N I:SER80 4.8 93.7 1.0
C I:LYS77 4.8 98.6 1.0
CB I:SER105 4.9 92.1 1.0
C I:CYS106 4.9 94.5 1.0
N I:HIS108 5.0 87.7 1.0
C I:CYS103 5.0 87.7 1.0

Zinc binding site 7 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:88.8
occ:1.00
 SG J:CYS10 2.3 80.5 1.0
SG J:CYS46 2.3 82.3 1.0
SG J:CYS45 2.3 83.1 1.0
SG J:CYS7 2.4 70.9 1.0
CB J:CYS10 3.2 76.4 1.0
CB J:CYS7 3.2 67.7 1.0
N J:CYS46 3.4 77.6 1.0
CB J:CYS45 3.6 77.6 1.0
CB J:CYS46 3.6 78.2 1.0
C J:CYS45 3.7 81.5 1.0
CA J:CYS46 3.8 77.0 1.0
N J:CYS10 3.9 73.5 1.0
CA J:CYS10 4.0 74.9 1.0
CG J:ARG43 4.2 80.7 1.0
CA J:CYS45 4.2 77.0 1.0
O J:CYS45 4.3 82.0 1.0
CZ J:ARG43 4.5 96.6 1.0
CB J:LYS12 4.6 76.8 1.0
NH1 J:ARG43 4.6 84.8 1.0
N J:GLY11 4.6 73.2 1.0
CA J:CYS7 4.7 67.2 1.0
C J:CYS10 4.7 77.2 1.0
NE J:ARG43 4.8 80.1 1.0
NH2 J:ARG43 4.8 84.3 1.0
N J:CYS45 4.8 78.2 1.0
N J:LYS12 4.9 75.4 1.0
CB J:SER9 5.0 67.8 1.0

Zinc binding site 8 out of 8 in 3rzo

Go back to Zinc Binding Sites List in 3rzo
Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 4-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 A 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.7
occ:1.00
 CB L:CYS51 2.3 0.7 1.0
SG L:CYS48 2.3 0.8 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS51 2.4 0.8 1.0
SG L:CYS34 2.4 0.9 1.0
CB L:CYS48 3.2 0.2 1.0
CB L:CYS31 3.2 0.4 1.0
CB L:CYS34 3.7 0.7 1.0
CA L:CYS51 3.8 0.7 1.0
N L:CYS34 3.9 0.2 1.0
CB L:SER36 4.3 0.9 1.0
CA L:CYS34 4.3 0.4 1.0
O L:ASP50 4.5 0.4 1.0
N L:CYS51 4.5 0.5 1.0
C L:CYS51 4.6 0.5 1.0
CA L:CYS48 4.6 0.4 1.0
CA L:CYS31 4.6 1.0 1.0
N L:GLY52 4.8 0.6 1.0
C L:ASP50 4.9 0.9 1.0
O L:CYS48 4.9 0.2 1.0
CB L:HIS53 4.9 0.6 1.0
C L:CYS48 4.9 0.1 1.0
CB L:GLU33 5.0 0.3 1.0
C L:CYS34 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 15:10:39 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy