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

Zinc in PDB 3rzd: Rna Polymerase II Initiation Complex with A 5-Nt Rna

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

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

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna, PDB code: 3rzd 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) 45.14 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.538, 221.266, 192.175, 90.00, 97.44, 90.00
R / Rfree (%) 18.8 / 23

Other elements in 3rzd:

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

Zinc binding site 1 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.6
occ:1.00
 SG A:CYS107 2.3 1.0 1.0
SG A:CYS167 2.4 0.0 1.0
SG A:CYS110 2.4 0.5 1.0
SG A:CYS148 2.4 0.0 1.0
CB A:CYS107 3.0 0.5 1.0
CB A:CYS148 3.5 0.2 1.0
CB A:CYS110 3.5 0.8 1.0
N A:CYS110 3.8 0.5 1.0
N A:CYS167 3.8 0.1 1.0
CB A:CYS167 3.9 0.3 1.0
O A:CYS167 4.0 0.6 1.0
CA A:CYS110 4.2 0.0 1.0
CA A:CYS167 4.3 0.3 1.0
CA A:CYS107 4.5 0.9 1.0
C A:CYS167 4.6 0.1 1.0
CB A:HIS109 4.6 0.8 1.0
C A:GLY166 4.8 0.6 1.0
C A:HIS109 4.8 0.5 1.0
N A:HIS109 4.9 0.6 1.0
CA A:GLY166 4.9 0.7 1.0
CA A:CYS148 4.9 1.0 1.0
CA A:HIS109 5.0 0.2 1.0

Zinc binding site 2 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.2
occ:1.00
 CE1 A:HIS80 2.0 0.1 1.0
NE2 A:HIS80 2.2 0.8 1.0
SG A:CYS77 2.4 0.8 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS70 2.4 0.1 1.0
ND1 A:HIS80 3.2 0.8 1.0
CD2 A:HIS80 3.6 0.6 1.0
CG A:GLN68 3.8 0.4 1.0
CB A:CYS77 3.8 0.1 1.0
CB A:CYS67 3.8 0.1 1.0
CB A:CYS70 4.0 0.2 1.0
CG A:HIS80 4.0 0.5 1.0
O A:CYS67 4.1 0.7 1.0
C A:CYS67 4.4 0.2 1.0
CD A:GLN68 4.6 0.0 1.0
CA A:CYS67 4.8 1.0 1.0
O A:GLN71 4.8 0.8 1.0
CB A:GLN68 4.9 0.8 1.0
CA A:CYS77 4.9 0.1 1.0

Zinc binding site 3 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1185 2.3 0.6 1.0
SG B:CYS1166 2.3 0.3 1.0
SG B:CYS1163 2.3 0.8 1.0
SG B:CYS1182 2.4 0.1 1.0
CB B:CYS1185 3.2 0.8 1.0
CB B:CYS1166 3.3 0.9 1.0
N B:CYS1166 3.4 0.7 1.0
CB B:CYS1163 3.6 0.2 1.0
CB B:CYS1182 3.8 0.1 1.0
CA B:CYS1166 3.9 0.4 1.0
CB B:ILE1165 4.3 0.3 1.0
C B:ILE1165 4.5 0.7 1.0
CA B:CYS1185 4.6 0.3 1.0
N B:GLY1167 4.8 0.5 1.0
C B:CYS1166 4.8 0.8 1.0
CA B:ILE1165 4.8 0.4 1.0
N B:CYS1185 4.9 0.3 1.0
CA B:CYS1163 4.9 0.4 1.0
N B:ILE1165 4.9 0.6 1.0

Zinc binding site 4 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:64.5
occ:1.00
 SG C:CYS92 2.3 75.7 1.0
SG C:CYS95 2.3 69.6 1.0
SG C:CYS86 2.4 68.8 1.0
SG C:CYS88 2.4 63.0 1.0
CB C:CYS86 3.3 63.4 1.0
CB C:CYS88 3.4 60.7 1.0
CB C:CYS92 3.4 72.5 1.0
N C:CYS92 3.4 70.7 1.0
CB C:CYS95 3.5 65.9 1.0
C C:HIS91 3.9 74.1 1.0
CA C:CYS92 4.0 71.8 1.0
N C:CYS95 4.1 68.5 1.0
CA C:HIS91 4.1 69.7 1.0
CA C:CYS95 4.4 66.7 1.0
N C:CYS88 4.5 60.7 1.0
CA C:CYS88 4.5 60.7 1.0
O C:HIS91 4.6 73.9 1.0
C C:CYS92 4.7 76.0 1.0
CA C:CYS86 4.7 63.0 1.0
CB C:LYS94 4.8 72.3 1.0
C C:LYS94 4.9 73.3 1.0
N C:LYS94 4.9 70.1 1.0
C C:CYS86 5.0 66.2 1.0
N C:HIS91 5.0 69.9 1.0

Zinc binding site 5 out of 8 in 3rzd

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

b:94.9
occ:1.00
 SG I:CYS32 2.3 0.5 1.0
SG I:CYS7 2.3 0.3 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS29 2.4 0.5 1.0
CB I:CYS10 2.8 0.3 1.0
CB I:CYS7 3.1 97.6 1.0
OG1 I:THR31 3.3 0.2 1.0
CB I:CYS29 3.5 0.7 1.0
CB I:CYS32 3.5 0.2 1.0
N I:CYS10 3.7 0.0 1.0
CA I:CYS10 3.9 0.9 1.0
N I:CYS32 4.1 0.3 1.0
CB I:TYR34 4.3 0.2 1.0
CA I:CYS32 4.3 0.9 1.0
CA I:CYS7 4.5 96.9 1.0
CB I:THR31 4.6 0.1 1.0
C I:THR31 4.6 0.4 1.0
CA I:CYS29 4.9 0.3 1.0
CB I:ASP9 4.9 0.6 1.0
C I:ASP9 4.9 0.2 1.0
C I:CYS32 5.0 0.3 1.0
C I:CYS10 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:67.8
occ:1.00
 SG I:CYS78 2.3 78.2 1.0
SG I:CYS106 2.3 79.8 1.0
SG I:CYS75 2.4 71.3 1.0
SG I:CYS103 2.4 81.0 1.0
CB I:CYS103 3.1 75.5 1.0
CB I:CYS75 3.2 66.8 1.0
CB I:CYS78 3.5 76.4 1.0
CB I:CYS106 3.6 77.7 1.0
N I:CYS78 3.7 75.5 1.0
O I:CYS78 3.9 79.7 1.0
N I:CYS106 4.0 77.1 1.0
CA I:CYS78 4.0 76.2 1.0
C I:CYS78 4.3 80.6 1.0
CA I:CYS106 4.3 77.2 1.0
CB I:HIS108 4.5 72.5 1.0
CB I:LYS77 4.5 75.8 1.0
CB I:SER80 4.6 77.0 1.0
CA I:CYS103 4.6 73.8 1.0
CA I:CYS75 4.7 66.2 1.0
C I:LYS77 4.8 79.4 1.0
CB I:SER105 4.8 82.2 1.0
C I:SER105 4.9 82.3 1.0
C I:CYS106 5.0 80.8 1.0
N I:SER80 5.0 75.5 1.0
N I:HIS108 5.0 72.1 1.0

Zinc binding site 7 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:63.1
occ:1.00
 SG J:CYS10 2.3 58.4 1.0
SG J:CYS7 2.3 60.3 1.0
SG J:CYS45 2.4 56.4 1.0
SG J:CYS46 2.4 63.0 1.0
CB J:CYS7 3.2 57.4 1.0
N J:CYS46 3.3 56.6 1.0
CB J:CYS10 3.4 53.5 1.0
CB J:CYS45 3.6 51.5 1.0
CB J:CYS46 3.6 59.2 1.0
CA J:CYS46 3.7 57.3 1.0
C J:CYS45 3.7 58.5 1.0
N J:CYS10 3.7 51.5 1.0
NE J:ARG43 4.1 77.7 1.0
CA J:CYS10 4.1 52.1 1.0
CD J:ARG43 4.1 70.6 1.0
CA J:CYS45 4.2 52.3 1.0
CG J:ARG43 4.2 65.6 1.0
O J:CYS45 4.4 58.1 1.0
CA J:CYS7 4.6 56.3 1.0
N J:GLY11 4.7 52.9 1.0
CB J:SER9 4.7 54.8 1.0
CB J:LYS12 4.7 64.4 1.0
C J:CYS10 4.8 56.3 1.0
C J:SER9 4.9 55.0 1.0
N J:LYS12 4.9 59.4 1.0
N J:CYS45 4.9 53.9 1.0
O J:CYS7 4.9 57.5 1.0

Zinc binding site 8 out of 8 in 3rzd

Go back to Zinc Binding Sites List in 3rzd
Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-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 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:96.9
occ:1.00
 SG L:CYS51 2.3 0.0 1.0
SG L:CYS34 2.3 0.0 1.0
SG L:CYS48 2.3 0.1 1.0
SG L:CYS31 2.4 0.1 1.0
CB L:CYS48 3.1 0.9 1.0
CB L:CYS31 3.1 0.8 1.0
CB L:CYS51 3.1 0.6 1.0
CB L:CYS34 3.5 0.5 1.0
N L:CYS51 3.6 0.1 1.0
N L:CYS34 3.8 0.8 1.0
CA L:CYS51 3.9 0.6 1.0
CA L:CYS34 4.2 0.9 1.0
N L:GLY52 4.5 0.8 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 0.2 1.0
C L:ASP50 4.7 0.8 1.0
CB L:ASP50 4.8 0.6 1.0
C L:CYS34 4.8 0.7 1.0
N L:HIS53 4.9 0.9 1.0
N L:ASP50 5.0 0.2 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

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy