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Magnesium in PDB 5ot2: Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A

Enzymatic activity of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A

All present enzymatic activity of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A, PDB code: 5ot2 was solved by S.Malvezzi, L.Farnung, C.Aloisi, T.Angelov, P.Cramer, S.J.Sturla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.350, 394.930, 283.710, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.2

Other elements in 5ot2:

The structure of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A (pdb code 5ot2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A, PDB code: 5ot2:

Magnesium binding site 1 out of 1 in 5ot2

Go back to Magnesium Binding Sites List in 5ot2
Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:97.7
occ:1.00
 O3' P:G10 1.9 0.2 1.0
OD1 A:ASP483 1.9 0.4 1.0
OD1 A:ASP481 1.9 0.7 1.0
OD2 A:ASP483 2.1 0.6 1.0
CG A:ASP483 2.2 0.2 1.0
OD2 A:ASP481 2.4 1.0 1.0
CG A:ASP481 2.4 0.0 1.0
C3' P:G10 2.5 0.8 1.0
OD1 A:ASP485 2.9 0.2 1.0
C4' P:G10 3.5 0.3 1.0
C2' P:G10 3.6 0.6 1.0
CG A:ASP485 3.7 0.8 1.0
CB A:ASP483 3.8 80.8 1.0
O2' P:G10 3.8 0.3 1.0
OD2 A:ASP485 3.8 0.3 1.0
CB A:ASP481 3.9 0.8 1.0
C5' P:G10 4.3 0.6 1.0
N A:ASP483 4.3 0.1 1.0
CA A:ASP483 4.5 90.7 1.0
C1' P:G10 4.6 0.2 1.0
CA A:ASP481 4.7 93.2 1.0
O4' P:G10 4.7 0.0 1.0
C A:ASP481 4.7 0.7 1.0
N A:ASP481 4.7 85.2 1.0
C A:ASP483 4.8 91.1 1.0
O A:ASP481 4.8 0.2 1.0

Reference:

S.Malvezzi, L.Farnung, C.M.N.Aloisi, T.Angelov, P.Cramer, S.J.Sturla. Mechanism of Rna Polymerase II Stalling By Dna Alkylation. Proc. Natl. Acad. Sci. V. 114 12172 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29087308
DOI: 10.1073/PNAS.1706592114
Page generated: Tue Aug 12 17:50:23 2025

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