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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

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