Magnesium in PDB 6blp: Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp

Enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp

All present enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp, PDB code: 6blp was solved by W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.88 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.060, 222.180, 193.200, 90.00, 101.34, 90.00
R / Rfree (%) 21.4 / 25.7

Other elements in 6blp:

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp (pdb code 6blp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp, PDB code: 6blp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6blp

Go back to Magnesium Binding Sites List in 6blp
Magnesium binding site 1 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:6.8
occ:1.00
O3' R:G8 2.0 54.9 1.0
OD1 A:ASP481 2.1 37.6 1.0
OD1 A:ASP485 2.1 37.2 1.0
OD1 A:ASP483 2.4 40.7 1.0
CG A:ASP485 2.8 28.5 1.0
OD2 A:ASP485 2.9 23.7 1.0
CG A:ASP481 3.0 52.9 1.0
C3' R:G8 3.1 43.1 1.0
C4' R:G8 3.3 36.2 1.0
CG A:ASP483 3.4 37.3 1.0
OD2 A:ASP481 3.4 55.5 1.0
OD2 A:ASP483 3.5 33.3 1.0
O2' R:G8 3.7 45.5 1.0
C5' R:G8 3.8 54.3 1.0
C2' R:G8 4.0 32.9 1.0
CB A:ASP485 4.3 28.0 1.0
CB A:ASP481 4.3 49.5 1.0
N A:ASP481 4.4 46.3 1.0
NH2 A:ARG446 4.4 23.7 1.0
O5' A:APC1805 4.5 0.2 1.0
O4' R:G8 4.6 36.5 1.0
CA A:ASP481 4.7 38.7 1.0
CB A:ASP483 4.8 31.1 1.0
N A:ASP483 4.8 33.9 1.0
O5' R:G8 4.8 48.1 1.0
N A:ASP485 4.8 28.7 1.0
C A:ASP481 4.8 37.9 1.0
CA A:ASP485 4.9 24.6 1.0
O A:ASP481 4.9 29.5 1.0
C4' A:APC1805 5.0 0.9 1.0

Magnesium binding site 2 out of 2 in 6blp

Go back to Magnesium Binding Sites List in 6blp
Magnesium binding site 2 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1804

b:68.0
occ:1.00
O3G A:APC1805 1.8 0.6 1.0
OD2 A:ASP481 2.7 55.5 1.0
PG A:APC1805 3.3 0.9 1.0
OE1 B:GLU836 3.3 67.5 1.0
CG A:ASP481 3.4 52.9 1.0
CB A:ASP481 3.5 49.5 1.0
OD2 B:ASP837 3.8 81.5 1.0
O1G A:APC1805 3.9 0.9 1.0
NH2 B:ARG1020 4.1 75.6 1.0
O2G A:APC1805 4.1 0.6 1.0
O3B A:APC1805 4.3 0.4 1.0
CD B:GLU836 4.6 59.9 1.0
OD1 A:ASP481 4.6 37.6 1.0
CA A:ASP481 4.6 38.7 1.0
O2B A:APC1805 4.8 1.0 1.0
N A:ASP481 4.9 46.3 1.0
CG B:ASP837 5.0 71.4 1.0
NH1 B:ARG1020 5.0 81.4 1.0

Reference:

W.Wang, C.Walmacq, J.Chong, M.Kashlev, D.Wang. Structural Basis of Transcriptional Stalling and Bypass of Abasic Dna Lesion By Rna Polymerase II. Proc. Natl. Acad. Sci. V. 115 E2538 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29487211
DOI: 10.1073/PNAS.1722050115
Page generated: Mon Dec 14 22:24:11 2020

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