Atomistry » Magnesium » PDB 2dlc-2e74 » 2e2j
Atomistry »
  Magnesium »
    PDB 2dlc-2e74 »
      2e2j »

Magnesium in PDB 2e2j: Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp

Enzymatic activity of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp

All present enzymatic activity of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp, PDB code: 2e2j 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) 50.00 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.142, 222.017, 194.652, 90.00, 101.36, 90.00
R / Rfree (%) 24.2 / 30.6

Other elements in 2e2j:

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp 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 in 5 Mm Mg+2 with Gmpcpp (pdb code 2e2j). 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 in 5 Mm Mg+2 with Gmpcpp, PDB code: 2e2j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2e2j

Go back to Magnesium Binding Sites List in 2e2j
Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp


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 in 5 Mm Mg+2 with Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:67.3
occ:1.00
O3' R:G10 2.0 96.9 1.0
OD1 A:ASP481 2.4 80.8 1.0
OD2 A:ASP483 2.8 73.4 1.0
O2A T:G2P3000 2.8 0.9 1.0
OD2 A:ASP481 2.9 83.4 1.0
OD1 A:ASP483 2.9 76.8 1.0
OD1 A:ASP485 2.9 74.7 1.0
CG A:ASP481 3.0 79.9 1.0
CG A:ASP483 3.2 74.1 1.0
C3' R:G10 3.3 97.6 1.0
O1A T:G2P3000 3.4 0.8 1.0
PA T:G2P3000 3.7 0.6 1.0
CG A:ASP485 3.7 74.1 1.0
OD2 A:ASP485 3.8 73.8 1.0
MG A:MG2002 3.8 76.2 1.0
C4' R:G10 3.9 96.2 1.0
NH2 A:ARG446 4.2 75.5 1.0
C5' R:G10 4.2 94.8 1.0
C2' R:G10 4.5 99.2 1.0
O2' R:G10 4.6 0.9 1.0
CB A:ASP481 4.6 77.4 1.0
CB A:ASP483 4.7 72.9 1.0
O4' T:G2P3000 4.7 0.2 1.0
O5' T:G2P3000 4.8 0.2 1.0
C4' T:G2P3000 4.9 0.8 1.0

Magnesium binding site 2 out of 2 in 2e2j

Go back to Magnesium Binding Sites List in 2e2j
Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with Gmpcpp


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 in 5 Mm Mg+2 with Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:76.2
occ:1.00
OD1 A:ASP483 2.2 76.8 1.0
O3G T:G2P3000 3.0 0.9 1.0
OD2 A:ASP481 3.2 83.4 1.0
CG A:ASP483 3.4 74.1 1.0
O2A T:G2P3000 3.4 0.9 1.0
OD2 B:ASP837 3.6 85.9 1.0
O3B T:G2P3000 3.6 0.6 1.0
PG T:G2P3000 3.7 0.3 1.0
MG A:MG2001 3.8 67.3 1.0
O1G T:G2P3000 3.8 0.7 1.0
C3A T:G2P3000 4.0 0.0 1.0
PA T:G2P3000 4.1 0.6 1.0
CB A:ASP483 4.1 72.9 1.0
OD2 A:ASP483 4.3 73.4 1.0
PB T:G2P3000 4.3 0.8 1.0
CG A:ASP481 4.3 79.9 1.0
O1A T:G2P3000 4.3 0.8 1.0
O1B T:G2P3000 4.4 0.7 1.0
CE B:LYS987 4.4 83.1 1.0
NH1 B:ARG1020 4.4 83.7 1.0
NH2 B:ARG1020 4.8 82.8 1.0
OD1 A:ASP481 4.8 80.8 1.0
CG B:ASP837 4.8 82.5 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 07:20:57 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