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Magnesium in PDB 1r9t: Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide

Enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide

All present enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide, PDB code: 1r9t was solved by K.D.Westover, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.846, 222.958, 193.602, 90.00, 101.17, 90.00
R / Rfree (%) 23 / 31.7

Other elements in 1r9t:

The structure of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide (pdb code 1r9t). 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 Strand Separated Elongation Complex, Mismatched Nucleotide, PDB code: 1r9t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1r9t

Go back to Magnesium Binding Sites List in 1r9t
Magnesium binding site 1 out of 2 in the Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide


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 Strand Separated Elongation Complex, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:55.8
occ:1.00
OD1 A:ASP485 1.7 35.8 1.0
O3' R:A10 2.3 51.7 1.0
CG A:ASP485 2.5 35.6 1.0
OD1 A:ASP481 2.7 67.2 1.0
OD2 A:ASP483 2.7 69.9 1.0
OD2 A:ASP485 2.8 35.1 1.0
OD1 A:ASP483 3.2 72.8 1.0
CG A:ASP483 3.4 68.4 1.0
CG A:ASP481 3.5 65.8 1.0
C3' R:A10 3.6 47.7 1.0
CB A:ASP485 4.0 34.5 1.0
N A:ASP481 4.0 28.4 1.0
OD2 A:ASP481 4.2 67.8 1.0
C4' R:A10 4.2 43.9 1.0
CA A:ASP481 4.3 31.1 1.0
C A:ASP481 4.3 30.8 1.0
MG A:MG2002 4.3 63.8 1.0
C5' R:A10 4.4 38.9 1.0
CB A:ASP481 4.4 61.3 1.0
N A:ASP485 4.5 25.7 1.0
CA A:ASP485 4.6 24.1 1.0
O2' R:A10 4.6 48.5 1.0
N A:ASP483 4.6 25.7 1.0
O A:ASP481 4.6 29.9 1.0
C2' R:A10 4.7 48.3 1.0
N A:PHE482 4.9 42.7 1.0
O A:ASP483 4.9 23.0 1.0
CB A:ASP483 4.9 61.5 1.0
C A:ASP483 5.0 24.6 1.0

Magnesium binding site 2 out of 2 in 1r9t

Go back to Magnesium Binding Sites List in 1r9t
Magnesium binding site 2 out of 2 in the Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide


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 Strand Separated Elongation Complex, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:63.8
occ:1.00
OD1 A:ASP483 2.4 72.8 1.0
OD2 B:ASP837 2.4 79.1 1.0
OD1 A:ASP481 2.5 67.2 1.0
CG A:ASP483 2.6 68.4 1.0
CG B:ASP837 3.0 77.3 1.0
CB A:ASP483 3.2 61.5 1.0
O1G B:ATP1308 3.3 68.2 1.0
CG A:ASP481 3.3 65.8 1.0
OD2 A:ASP483 3.4 69.9 1.0
OD1 B:ASP837 3.5 77.2 1.0
OD2 A:ASP481 3.7 67.8 1.0
NH1 B:ARG1020 3.8 51.6 1.0
CB B:ASP837 4.0 74.6 1.0
N A:ASP483 4.2 25.7 1.0
CA A:ASP483 4.3 26.4 1.0
MG A:MG2001 4.3 55.8 1.0
CB A:ASP481 4.4 61.3 1.0
O B:LYS987 4.5 37.1 1.0
O B:GLU836 4.6 50.8 1.0
O2B B:ATP1308 4.7 73.8 1.0
PG B:ATP1308 4.7 73.0 1.0
CG B:LYS987 4.8 53.4 1.0

Reference:

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016
Page generated: Mon Dec 14 06:42:21 2020

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