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Magnesium in PDB 2e2h: Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp

Enzymatic activity of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp

All present enzymatic activity of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp, PDB code: 2e2h 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) 45.08 / 3.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 171.108, 222.005, 195.163, 90.00, 102.61, 90.00
R / Rfree (%) 29 / 36.8

Other elements in 2e2h:

The structure of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp 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 at 5 Mm MG2+ with Gtp (pdb code 2e2h). 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 at 5 Mm MG2+ with Gtp, PDB code: 2e2h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2e2h

Go back to Magnesium Binding Sites List in 2e2h
Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp


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 at 5 Mm MG2+ with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:96.2
occ:1.00
O2A T:GTP3000 2.0 0.4 1.0
OD1 A:ASP483 2.2 97.2 1.0
OD1 A:ASP485 2.2 93.4 1.0
OD2 A:ASP483 2.3 97.1 1.0
O1A T:GTP3000 2.5 0.9 1.0
CG A:ASP483 2.6 95.9 1.0
PA T:GTP3000 2.7 0.8 1.0
OD1 A:ASP481 2.9 99.9 1.0
CB A:ASP481 3.3 97.6 1.0
CG A:ASP481 3.4 98.8 1.0
CG A:ASP485 3.4 90.7 1.0
MG A:MG2002 3.4 0.0 1.0
O3A T:GTP3000 3.6 0.8 1.0
OD2 A:ASP485 3.9 91.6 1.0
O3G T:GTP3000 3.9 0.9 1.0
C3' R:A10 4.1 88.9 1.0
CB A:ASP483 4.1 95.0 1.0
O5' T:GTP3000 4.1 0.9 1.0
C4' R:A10 4.5 89.0 1.0
OD2 A:ASP481 4.5 0.4 1.0
C5' R:A10 4.5 88.9 1.0
C5' T:GTP3000 4.5 0.1 1.0
CA A:ASP481 4.5 97.3 1.0
O2G T:GTP3000 4.6 1.0 1.0
N A:ASP481 4.7 97.0 1.0
CB A:ASP485 4.7 89.7 1.0
C4' T:GTP3000 4.7 0.8 1.0
PG T:GTP3000 4.8 0.5 1.0
N A:ASP483 4.8 95.3 1.0
O5' R:A10 4.8 88.4 1.0
CA A:ASP483 4.9 94.6 1.0
PB T:GTP3000 5.0 0.7 1.0

Magnesium binding site 2 out of 2 in 2e2h

Go back to Magnesium Binding Sites List in 2e2h
Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp


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 at 5 Mm MG2+ with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:0.0
occ:1.00
O3G T:GTP3000 2.0 0.9 1.0
OD1 A:ASP481 2.2 99.9 1.0
OD1 A:ASP483 2.2 97.2 1.0
OD1 B:ASP837 2.3 0.6 1.0
O3A T:GTP3000 3.1 0.8 1.0
CG A:ASP481 3.1 98.8 1.0
NH1 B:ARG1020 3.1 99.9 1.0
O2B T:GTP3000 3.1 0.3 1.0
CG B:ASP837 3.3 0.4 1.0
CG A:ASP483 3.3 95.9 1.0
MG A:MG2001 3.4 96.2 1.0
PG T:GTP3000 3.4 0.5 1.0
CB A:ASP481 3.5 97.6 1.0
O1A T:GTP3000 3.5 0.9 1.0
PB T:GTP3000 3.6 0.7 1.0
PA T:GTP3000 3.7 0.8 1.0
CB B:ASP837 3.8 0.4 1.0
O3B T:GTP3000 4.1 0.0 1.0
CZ B:ARG1020 4.1 99.2 1.0
O2A T:GTP3000 4.1 0.4 1.0
CB A:ASP483 4.1 95.0 1.0
OD2 A:ASP481 4.2 0.4 1.0
NH2 B:ARG1020 4.2 99.0 1.0
O2G T:GTP3000 4.2 1.0 1.0
OD2 A:ASP483 4.3 97.1 1.0
O1G T:GTP3000 4.3 0.3 1.0
OD2 B:ASP837 4.4 0.5 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: Tue Aug 13 22:38:44 2024

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