Atomistry » Zinc » PDB 2n9o-2nwo » 2nvy
Atomistry »
  Zinc »
    PDB 2n9o-2nwo »
      2nvy »

Zinc in PDB 2nvy: Rna Polymerase II Form II in 150 Mm Mn+2

Enzymatic activity of Rna Polymerase II Form II in 150 Mm Mn+2

All present enzymatic activity of Rna Polymerase II Form II in 150 Mm Mn+2:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Form II in 150 Mm Mn+2, PDB code: 2nvy was solved by D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.036, 218.914, 369.549, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 32.3

Other elements in 2nvy:

The structure of Rna Polymerase II Form II in 150 Mm Mn+2 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Form II in 150 Mm Mn+2 (pdb code 2nvy). 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 Form II in 150 Mm Mn+2, PDB code: 2nvy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 1 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:68.8
occ:1.00
SG J:CYS7 2.0 59.7 1.0
SG J:CYS45 2.1 66.3 1.0
SG J:CYS46 2.1 63.4 1.0
SG J:CYS10 2.3 60.2 1.0
N J:CYS46 3.1 64.0 1.0
CB J:CYS7 3.3 58.7 1.0
C J:CYS45 3.3 64.5 1.0
CB J:CYS46 3.3 63.1 1.0
CA J:CYS46 3.4 63.3 1.0
CB J:CYS45 3.4 65.3 1.0
CB J:CYS10 3.6 60.6 1.0
O J:CYS45 3.6 64.6 1.0
N J:CYS10 3.7 60.4 1.0
CA J:CYS45 4.0 65.0 1.0
NE J:ARG43 4.2 72.2 1.0
CB J:SER9 4.2 59.6 1.0
CA J:CYS10 4.2 60.6 1.0
CG J:ARG43 4.5 71.1 1.0
N J:GLY11 4.6 61.4 1.0
CD J:ARG43 4.6 72.0 1.0
CA J:CYS7 4.6 58.5 1.0
C J:SER9 4.6 60.0 1.0
CA J:SER9 4.7 59.6 1.0
N J:SER9 4.8 59.0 1.0
C J:CYS7 4.8 58.3 1.0
C J:CYS46 4.9 62.9 1.0
N J:CYS45 4.9 65.5 1.0
C J:CYS10 4.9 61.0 1.0
O J:CYS7 4.9 58.2 1.0
O J:ARG43 4.9 69.0 1.0
OG J:SER9 4.9 60.1 1.0
CB J:LYS12 5.0 63.1 1.0

Zinc binding site 2 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 2 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:79.3
occ:1.00
SG C:CYS88 2.0 81.9 1.0
SG C:CYS86 2.1 79.0 1.0
SG C:CYS95 2.5 74.9 1.0
SG C:CYS92 2.7 84.5 1.0
CB C:CYS88 3.1 81.0 1.0
CB C:CYS86 3.3 78.4 1.0
CB C:CYS95 3.4 75.4 1.0
N C:CYS92 3.6 83.7 1.0
CB C:CYS92 3.6 83.3 1.0
N C:CYS95 3.8 77.0 1.0
O C:CYS92 4.1 82.1 1.0
CA C:CYS92 4.1 83.0 1.0
C C:HIS91 4.2 84.5 1.0
CA C:CYS95 4.2 75.7 1.0
N C:CYS88 4.2 80.1 1.0
CA C:CYS88 4.3 81.0 1.0
CA C:HIS91 4.3 84.7 1.0
CB C:LYS94 4.3 78.3 1.0
C C:CYS92 4.4 82.2 1.0
CA C:CYS86 4.6 78.2 1.0
C C:CYS86 4.6 78.2 1.0
C C:LYS94 4.6 78.0 1.0
O C:CYS86 4.7 78.1 1.0
N C:LYS94 4.7 79.3 1.0
CA C:LYS94 4.8 78.5 1.0
N C:HIS91 4.9 84.7 1.0
O C:ASP90 5.0 85.1 1.0

Zinc binding site 3 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 3 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:97.5
occ:1.00
SG I:CYS10 1.9 96.0 1.0
SG I:CYS32 2.1 83.1 1.0
SG I:CYS29 2.3 83.1 1.0
SG I:CYS7 2.5 99.5 1.0
CB I:CYS32 3.1 81.8 1.0
CB I:CYS7 3.1 99.6 1.0
CB I:CYS29 3.2 83.0 1.0
N I:CYS32 3.3 81.8 1.0
CB I:CYS10 3.4 95.5 1.0
CA I:CYS32 3.7 81.7 1.0
N I:CYS10 3.9 96.1 1.0
CA I:CYS10 4.1 95.2 1.0
CB I:TYR34 4.3 75.4 1.0
C I:CYS32 4.4 81.2 1.0
CB I:THR31 4.4 82.8 1.0
C I:THR31 4.5 82.3 1.0
CA I:CYS7 4.6 99.7 1.0
O I:CYS32 4.6 81.3 1.0
N I:ASN11 4.6 93.0 1.0
CA I:CYS29 4.7 83.0 1.0
C I:CYS10 4.7 94.3 1.0
CA I:THR31 4.8 82.6 1.0
N I:THR31 4.8 82.5 1.0
CG2 I:THR31 4.9 83.3 1.0
N I:ASN12 5.0 90.9 1.0

Zinc binding site 4 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 4 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:0.5
occ:1.00
SG I:CYS75 2.2 0.0 1.0
SG I:CYS106 2.5 0.3 1.0
SG I:CYS103 2.7 0.4 1.0
CB I:CYS75 2.7 0.4 1.0
CB I:CYS103 3.0 0.4 1.0
SG I:CYS78 3.1 0.4 1.0
N I:CYS78 3.6 0.3 1.0
CB I:HIS108 3.6 0.8 1.0
CB I:CYS78 3.9 0.6 1.0
CB I:LYS77 4.0 0.5 1.0
CA I:CYS75 4.1 0.6 1.0
CA I:CYS78 4.2 0.6 1.0
CB I:CYS106 4.2 0.5 1.0
CG I:HIS108 4.3 0.0 1.0
O I:CYS75 4.3 0.6 1.0
CD2 I:HIS108 4.3 0.6 1.0
C I:CYS75 4.4 0.3 1.0
N I:LYS77 4.4 0.9 1.0
C I:LYS77 4.4 0.9 1.0
CA I:LYS77 4.5 0.5 1.0
CA I:CYS103 4.5 0.4 1.0
N I:HIS79 4.6 0.2 1.0
N I:HIS108 4.6 0.8 1.0
CA I:HIS108 4.6 0.8 1.0
C I:CYS78 4.7 0.9 1.0
OG I:SER80 4.8 0.6 1.0
O I:HIS108 4.9 0.7 1.0
N I:CYS75 4.9 0.8 1.0
N I:CYS106 5.0 0.8 1.0

Zinc binding site 5 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 5 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:0.2
occ:1.00
SG L:CYS34 2.1 0.6 1.0
SG L:CYS48 2.6 0.7 1.0
CB L:CYS51 2.6 0.5 1.0
O L:CYS51 2.8 0.2 1.0
CB L:CYS48 3.0 0.1 1.0
SG L:CYS31 3.3 0.4 1.0
CB L:CYS34 3.5 0.2 1.0
CA L:CYS51 3.5 0.4 1.0
C L:CYS51 3.6 0.4 1.0
SG L:CYS51 3.6 0.8 1.0
CD2 L:HIS53 3.6 0.4 1.0
OG L:SER36 3.9 0.7 1.0
N L:CYS51 3.9 0.2 1.0
CB L:CYS31 4.0 0.0 1.0
N L:CYS34 4.2 0.8 1.0
CA L:CYS48 4.3 0.3 1.0
CG L:HIS53 4.3 0.5 1.0
CA L:CYS34 4.5 0.4 1.0
O L:LYS49 4.5 0.3 1.0
C L:CYS48 4.5 0.3 1.0
NE2 L:HIS53 4.5 0.1 1.0
CB L:HIS53 4.6 0.2 1.0
N L:LYS49 4.6 0.2 1.0
N L:HIS53 4.8 0.8 1.0
N L:GLY52 4.9 0.3 1.0
C L:LYS49 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 6 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:95.4
occ:1.00
SG A:CYS110 2.0 98.2 1.0
SG A:CYS148 2.4 0.5 1.0
SG A:CYS107 2.8 96.3 1.0
SG A:CYS167 3.0 0.6 1.0
CB A:CYS148 3.0 0.6 1.0
O A:CYS167 3.0 0.7 1.0
CB A:CYS167 3.2 0.3 1.0
CB A:CYS107 3.3 96.6 1.0
CB A:CYS110 3.6 99.0 1.0
C A:CYS167 3.8 0.7 1.0
CA A:CYS167 4.1 0.2 1.0
N A:CYS110 4.3 99.1 1.0
CA A:CYS148 4.5 0.7 1.0
O A:CYS148 4.5 0.9 1.0
CA A:CYS110 4.6 99.0 1.0
CB A:LYS112 4.6 0.2 1.0
N A:CYS167 4.7 0.7 1.0
CA A:CYS107 4.8 96.6 1.0
C A:CYS148 4.9 1.0 1.0
N A:GLY168 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 7 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:87.2
occ:1.00
SG B:CYS1182 2.2 0.9 1.0
SG B:CYS1166 2.5 100.0 1.0
SG B:CYS1163 2.6 97.4 1.0
CB B:CYS1163 2.7 97.6 1.0
SG B:CYS1185 2.9 0.9 1.0
CB B:CYS1185 3.0 0.6 1.0
CB B:CYS1182 3.5 0.1 1.0
OG1 B:THR1170 4.1 0.2 1.0
O B:CYS1166 4.1 0.8 1.0
CB B:CYS1166 4.1 0.5 1.0
CA B:CYS1163 4.3 97.6 1.0
CA B:CYS1185 4.3 0.5 1.0
N B:CYS1185 4.3 0.2 1.0
N B:CYS1166 4.4 0.3 1.0
O B:LYS1183 4.5 0.9 1.0
O B:CYS1182 4.7 0.1 1.0
CA B:CYS1182 4.7 0.1 1.0
ND2 B:ASN1187 4.7 0.9 1.0
CA B:CYS1166 4.8 0.7 1.0
C B:CYS1182 4.8 0.1 1.0
C B:CYS1166 4.9 0.3 1.0
N B:CYS1163 5.0 97.4 1.0

Zinc binding site 8 out of 8 in 2nvy

Go back to Zinc Binding Sites List in 2nvy
Zinc binding site 8 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:0.4
occ:1.00
NE2 A:HIS80 2.0 0.3 1.0
SG A:CYS77 2.0 0.1 1.0
SG A:CYS70 2.1 0.7 1.0
SG A:CYS67 2.4 0.8 1.0
CD2 A:HIS80 2.8 0.9 1.0
CE1 A:HIS80 3.1 0.6 1.0
CB A:CYS67 3.2 0.6 1.0
O A:CYS67 3.4 0.2 1.0
CB A:CYS77 3.4 0.6 1.0
CB A:CYS70 3.8 0.5 1.0
CG A:HIS80 4.0 0.6 1.0
ND1 A:HIS80 4.1 0.4 1.0
C A:CYS67 4.2 0.2 1.0
CA A:CYS67 4.3 0.5 1.0
CA A:CYS77 4.4 0.4 1.0
O A:GLN71 4.6 0.8 1.0
CA A:CYS70 4.9 0.5 1.0
CA A:GLY59 4.9 1.0 1.0
CD A:PRO78 4.9 0.6 1.0
C A:CYS70 4.9 0.7 1.0
C A:CYS77 5.0 0.0 1.0

Reference:

D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg. Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis Cell(Cambridge,Mass.) V. 127 941 2006.
ISSN: ISSN 0092-8674
PubMed: 17129781
DOI: 10.1016/J.CELL.2006.11.023
Page generated: Wed Dec 16 03:44:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy