Atomistry » Magnesium » PDB 2mtk-2o52 » 2nvz
Atomistry »
  Magnesium »
    PDB 2mtk-2o52 »
      2nvz »

Magnesium in PDB 2nvz: Rna Polymerase II Elongation Complex with Utp, Updated 11/2006

Enzymatic activity of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006

All present enzymatic activity of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006, PDB code: 2nvz 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 / 4.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.647, 222.338, 194.316, 90.00, 101.67, 90.00
R / Rfree (%) 27 / 33.2

Other elements in 2nvz:

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 (pdb code 2nvz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006, PDB code: 2nvz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2nvz

Go back to Magnesium Binding Sites List in 2nvz
Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:97.5
occ:1.00
OD1 A:ASP485 2.2 95.1 1.0
OD1 A:ASP483 2.2 100.0 1.0
O2A B:UTP3000 2.6 0.6 1.0
O1A B:UTP3000 2.6 0.5 1.0
CG A:ASP483 2.9 99.4 1.0
OD2 A:ASP483 2.9 100.0 1.0
CG A:ASP485 3.0 94.3 1.0
PA B:UTP3000 3.0 0.6 1.0
OD2 A:ASP485 3.1 94.0 1.0
C3' R:A10 3.4 87.6 1.0
MG A:MG2002 3.6 0.4 1.0
OD1 A:ASP481 3.8 0.4 1.0
C5' R:A10 3.9 90.6 1.0
C4' R:A10 3.9 88.7 1.0
O3A B:UTP3000 3.9 0.2 1.0
CB A:ASP481 4.1 0.3 1.0
CG A:ASP481 4.1 0.8 1.0
O3G B:UTP3000 4.3 0.6 1.0
CB A:ASP483 4.3 98.8 1.0
O5' B:UTP3000 4.4 0.1 1.0
CB A:ASP485 4.4 94.4 1.0
C4' B:UTP3000 4.5 0.4 1.0
N A:ASP481 4.6 0.2 1.0
O5' R:A10 4.6 93.1 1.0
C2' R:A10 4.7 87.3 1.0
C5' B:UTP3000 4.7 0.5 1.0
O A:ASP481 4.8 0.5 1.0
N A:ASP485 4.8 95.1 1.0
CA A:ASP481 4.8 0.1 1.0
O4' B:UTP3000 4.8 0.7 1.0
CA A:ASP485 4.9 94.4 1.0
O2' R:A10 4.9 87.1 1.0
C A:ASP481 5.0 0.7 1.0
OD2 A:ASP481 5.0 0.9 1.0
N A:ASP483 5.0 98.9 1.0

Magnesium binding site 2 out of 2 in 2nvz

Go back to Magnesium Binding Sites List in 2nvz
Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:0.4
occ:1.00
O3G B:UTP3000 2.0 0.6 1.0
OD1 B:ASP837 2.2 0.0 1.0
OD1 A:ASP483 2.2 100.0 1.0
OD1 A:ASP481 2.2 0.4 1.0
CG A:ASP481 3.1 0.8 1.0
O3A B:UTP3000 3.2 0.2 1.0
CB A:ASP481 3.2 0.3 1.0
NH1 B:ARG1020 3.3 0.6 1.0
CG A:ASP483 3.3 99.4 1.0
CG B:ASP837 3.3 0.7 1.0
MG A:MG2001 3.6 97.5 1.0
PG B:UTP3000 3.6 0.0 1.0
O1A B:UTP3000 3.6 0.5 1.0
CB A:ASP483 3.8 98.8 1.0
PA B:UTP3000 3.8 0.6 1.0
CB B:ASP837 3.9 0.2 1.0
O2B B:UTP3000 3.9 0.5 1.0
NH2 B:ARG1020 4.1 0.5 1.0
PB B:UTP3000 4.1 0.7 1.0
CZ B:ARG1020 4.1 0.1 1.0
O2A B:UTP3000 4.2 0.6 1.0
O3B B:UTP3000 4.3 0.3 1.0
OD2 A:ASP481 4.3 0.9 1.0
OD2 B:ASP837 4.4 0.1 1.0
O2G B:UTP3000 4.4 0.1 1.0
OD2 A:ASP483 4.4 100.0 1.0
O1G B:UTP3000 4.4 0.3 1.0
CA A:ASP481 4.7 0.1 1.0
N A:ASP483 4.9 98.9 1.0
OD1 A:ASP485 4.9 95.1 1.0
CA A:ASP483 5.0 98.5 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: Mon Dec 14 07:31:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy