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

Zinc in PDB 2nvq: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp

Enzymatic activity of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp

All present enzymatic activity of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp, PDB code: 2nvq 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) 48.45 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.646, 222.760, 195.281, 90.00, 101.31, 90.00
R / Rfree (%) 22.9 / 28.3

Other elements in 2nvq:

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp (pdb code 2nvq). 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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp, PDB code: 2nvq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:85.0
occ:1.00
 SG A:CYS110 2.4 72.8 1.0
SG A:CYS107 2.4 74.6 1.0
SG A:CYS148 2.4 74.2 1.0
SG A:CYS167 2.4 76.4 1.0
O A:CYS167 3.4 70.5 1.0
CB A:CYS107 3.4 73.8 1.0
CB A:CYS110 3.4 71.6 1.0
N A:CYS167 3.6 70.6 1.0
CB A:CYS148 3.6 73.0 1.0
O A:MET108 3.8 72.8 1.0
CB A:CYS167 3.8 72.0 1.0
CA A:CYS167 4.0 71.3 1.0
C A:CYS167 4.0 70.6 1.0
N A:CYS110 4.1 71.6 1.0
ND2 A:ASN169 4.2 65.8 1.0
CA A:CYS110 4.3 71.1 1.0
C A:GLY166 4.7 70.0 1.0
N A:GLY111 4.7 70.0 1.0
CA A:CYS107 4.8 73.2 1.0
C A:CYS110 4.9 70.5 1.0
CA A:GLY166 4.9 69.5 1.0
C A:MET108 5.0 72.9 1.0

Zinc binding site 2 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:78.3
occ:1.00
 NE2 A:HIS80 2.0 62.2 1.0
SG A:CYS67 2.3 78.6 1.0
SG A:CYS70 2.3 79.5 1.0
SG A:CYS77 2.4 75.7 1.0
CE1 A:HIS80 2.9 62.1 1.0
O A:CYS67 3.0 79.0 1.0
CD2 A:HIS80 3.1 61.8 1.0
CB A:CYS67 3.1 78.8 1.0
CB A:CYS70 3.2 79.5 1.0
CB A:CYS77 3.3 74.3 1.0
C A:CYS67 3.8 79.2 1.0
CA A:CYS67 4.0 79.0 1.0
CA A:CYS77 4.0 73.9 1.0
ND1 A:HIS80 4.1 61.6 1.0
CG A:HIS80 4.2 63.0 1.0
NE2 A:GLN68 4.4 73.8 1.0
CA A:CYS70 4.5 79.7 1.0
CD A:GLN68 4.6 75.7 1.0
O A:GLN71 4.6 80.0 1.0
N A:GLN71 4.6 79.9 1.0
CD A:PRO78 4.7 71.9 1.0
C A:CYS70 4.7 79.9 1.0
C A:CYS77 4.7 73.0 1.0
CG A:GLN68 4.7 77.9 1.0
N A:PRO78 4.9 72.0 1.0

Zinc binding site 3 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:80.9
occ:1.00
 SG B:CYS1163 2.3 69.8 1.0
SG B:CYS1185 2.3 72.1 1.0
SG B:CYS1182 2.4 69.0 1.0
SG B:CYS1166 2.4 70.2 1.0
CB B:CYS1185 3.3 71.3 1.0
CB B:CYS1163 3.3 68.4 1.0
CB B:CYS1182 3.3 69.0 1.0
CB B:ASN1187 3.7 64.4 1.0
O B:CYS1185 3.9 69.3 1.0
CB B:CYS1166 4.1 69.4 1.0
C B:CYS1185 4.1 69.5 1.0
N B:CYS1166 4.1 67.5 1.0
O B:CYS1182 4.2 69.6 1.0
CA B:CYS1163 4.3 67.4 1.0
CA B:CYS1185 4.3 70.6 1.0
ND2 B:ASN1187 4.3 64.9 1.0
CG B:ASN1187 4.6 63.8 1.0
CB B:ILE1165 4.6 66.2 1.0
N B:ASN1187 4.6 65.6 1.0
CA B:CYS1182 4.6 68.6 1.0
CA B:CYS1166 4.7 68.2 1.0
C B:CYS1182 4.8 69.6 1.0
CA B:ASN1187 4.8 64.5 1.0
N B:ILE1165 4.8 66.5 1.0
N B:ASP1186 4.8 68.3 1.0
C B:CYS1163 4.9 67.3 1.0

Zinc binding site 4 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:48.5
occ:1.00
 SG C:CYS86 2.3 49.1 1.0
SG C:CYS92 2.3 50.8 1.0
SG C:CYS88 2.3 37.0 1.0
SG C:CYS95 2.4 48.0 1.0
N C:CYS92 2.9 53.6 1.0
CB C:CYS95 3.2 46.9 1.0
CB C:CYS86 3.4 49.1 1.0
CB C:CYS88 3.4 43.8 1.0
CB C:CYS92 3.5 52.1 1.0
C C:HIS91 3.6 54.9 1.0
CA C:CYS92 3.6 52.5 1.0
CA C:HIS91 3.7 55.3 1.0
N C:CYS95 4.0 47.0 1.0
C C:CYS92 4.2 52.9 1.0
O C:CYS92 4.2 52.9 1.0
CA C:CYS95 4.2 46.4 1.0
C C:LYS94 4.5 48.2 1.0
O C:HIS91 4.5 55.5 1.0
N C:CYS88 4.6 45.7 1.0
CB C:LYS94 4.6 49.2 1.0
CA C:CYS88 4.6 45.2 1.0
CB C:HIS91 4.7 55.6 1.0
N C:HIS91 4.7 55.4 1.0
N C:LYS94 4.7 49.6 1.0
CA C:CYS86 4.8 49.4 1.0
CA C:LYS94 4.9 49.2 1.0

Zinc binding site 5 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:83.0
occ:1.00
 SG I:CYS10 2.3 50.8 1.0
SG I:CYS7 2.3 50.6 1.0
SG I:CYS29 2.3 50.3 1.0
SG I:CYS32 2.3 54.1 1.0
CB I:CYS10 3.1 50.2 1.0
CB I:CYS7 3.2 51.2 1.0
CB I:CYS29 3.3 49.0 1.0
CB I:CYS32 3.4 51.0 1.0
N I:CYS10 3.7 50.1 1.0
N I:CYS32 3.8 50.0 1.0
CA I:CYS10 4.0 50.2 1.0
CB I:TYR34 4.1 41.4 1.0
CA I:CYS32 4.1 50.5 1.0
N I:SER33 4.4 48.1 1.0
CB I:THR31 4.4 49.5 1.0
CA I:CYS7 4.6 51.3 1.0
N I:TYR34 4.6 43.4 1.0
CA I:CYS29 4.7 48.5 1.0
C I:THR31 4.7 49.7 1.0
C I:ASP9 4.8 49.7 1.0
CB I:ASP9 4.9 49.2 1.0
C I:CYS32 4.9 49.6 1.0
N I:THR31 4.9 49.0 1.0
CA I:THR31 5.0 49.4 1.0
C I:CYS29 5.0 48.3 1.0

Zinc binding site 6 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:57.1
occ:1.00
 SG I:CYS78 2.2 46.0 1.0
SG I:CYS75 2.3 52.0 1.0
SG I:CYS106 2.4 51.1 1.0
SG I:CYS103 2.6 41.6 1.0
CB I:CYS103 2.8 41.3 1.0
N I:CYS78 2.9 45.8 1.0
CB I:CYS78 3.1 45.1 1.0
O I:CYS78 3.2 43.6 1.0
CA I:CYS78 3.3 45.2 1.0
CB I:CYS75 3.4 49.3 1.0
CB I:HIS108 3.6 44.0 1.0
C I:CYS78 3.6 44.4 1.0
C I:LYS77 3.9 45.6 1.0
CG I:LYS77 4.0 48.5 1.0
CB I:CYS106 4.1 48.3 1.0
N I:LYS77 4.2 45.6 1.0
CG I:HIS108 4.3 43.2 1.0
CA I:CYS103 4.4 40.5 1.0
CA I:LYS77 4.4 46.1 1.0
CD2 I:HIS108 4.4 42.3 1.0
N I:CYS106 4.5 45.5 1.0
N I:HIS108 4.6 45.4 1.0
CA I:CYS75 4.7 48.8 1.0
CA I:HIS108 4.7 44.3 1.0
CA I:CYS106 4.7 47.1 1.0
CB I:LYS77 4.7 46.0 1.0
C I:CYS75 4.8 47.8 1.0
O I:CYS103 4.9 41.6 1.0
O I:CYS75 4.9 47.7 1.0
N I:HIS79 4.9 42.3 1.0
CD I:LYS77 4.9 48.4 1.0
O I:LYS77 4.9 45.3 1.0
C I:CYS106 5.0 47.2 1.0

Zinc binding site 7 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:50.2
occ:1.00
 SG J:CYS46 2.3 46.4 1.0
SG J:CYS10 2.3 45.3 1.0
SG J:CYS45 2.3 51.6 1.0
SG J:CYS7 2.4 42.0 1.0
N J:CYS46 2.7 45.7 1.0
CB J:CYS10 3.2 46.3 1.0
CA J:CYS46 3.3 45.0 1.0
CB J:CYS46 3.3 45.2 1.0
CB J:CYS7 3.4 43.3 1.0
CB J:CYS45 3.5 48.4 1.0
CD J:ARG43 3.5 57.3 1.0
C J:CYS45 3.5 47.2 1.0
OG J:SER9 3.7 46.4 1.0
CG J:ARG43 3.8 55.9 1.0
N J:CYS10 3.9 45.3 1.0
CA J:CYS45 4.0 48.2 1.0
CA J:CYS10 4.1 45.9 1.0
O J:CYS45 4.3 48.7 1.0
NE J:ARG43 4.3 55.6 1.0
N J:CYS45 4.7 48.8 1.0
C J:CYS46 4.8 44.9 1.0
CB J:SER9 4.8 46.8 1.0
CA J:CYS7 4.8 44.9 1.0
C J:SER9 4.9 46.1 1.0
O J:ARG43 4.9 53.1 1.0
N J:GLY11 5.0 46.3 1.0
C J:CYS10 5.0 45.4 1.0

Zinc binding site 8 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:91.6
occ:1.00
 SG L:CYS51 2.3 88.4 1.0
SG L:CYS34 2.3 87.5 1.0
SG L:CYS31 2.3 85.6 1.0
SG L:CYS48 2.4 88.3 1.0
CB L:CYS51 2.4 88.0 1.0
CB L:CYS31 3.1 85.3 1.0
CB L:CYS34 3.5 87.2 1.0
CB L:SER36 3.6 88.3 1.0
CA L:CYS51 3.6 88.5 1.0
N L:CYS51 3.7 88.8 1.0
CB L:CYS48 3.9 89.6 1.0
OG L:SER36 4.3 89.5 1.0
C L:ASP50 4.4 89.2 1.0
O L:ASP50 4.5 88.9 1.0
CA L:CYS34 4.6 87.5 1.0
CA L:CYS31 4.6 84.8 1.0
CD1 L:LEU38 4.6 90.8 1.0
N L:SER36 4.6 87.9 1.0
C L:CYS51 4.7 88.3 1.0
CA L:SER36 4.7 88.3 1.0
O L:LYS49 4.8 90.7 1.0
N L:CYS34 4.8 87.3 1.0
C L:CYS34 4.9 87.7 1.0
N L:LYS49 4.9 91.5 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: Thu Oct 17 02:17:54 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