Magnesium in PDB 6bm4: Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp

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

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

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp, PDB code: 6bm4 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) 55.61 / 2.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.720, 220.430, 193.150, 90.00, 100.97, 90.00
R / Rfree (%) 23.4 / 26

Other elements in 6bm4:

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp 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 Umpnpp (pdb code 6bm4). 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 Umpnpp, PDB code: 6bm4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6bm4

Go back to Magnesium Binding Sites List in 6bm4
Magnesium binding site 1 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp


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 Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:9.7
occ:1.00
OD1 A:ASP481 2.0 35.1 1.0
OD1 A:ASP485 2.2 25.7 1.0
O3' R:A9 2.3 0.6 1.0
OD1 A:ASP483 2.3 21.2 1.0
CG A:ASP481 2.8 38.1 1.0
CG A:ASP485 3.0 24.5 1.0
OD2 A:ASP485 3.0 24.3 1.0
OD2 A:ASP481 3.1 38.7 1.0
CG A:ASP483 3.2 20.9 1.0
C3' R:A9 3.3 0.7 1.0
C4' R:A9 3.3 0.2 1.0
OD2 A:ASP483 3.4 20.9 1.0
C5' R:A9 3.7 0.4 1.0
O2' R:A9 4.1 0.7 1.0
CB A:ASP481 4.2 38.0 1.0
C2' R:A9 4.3 0.5 1.0
N A:ASP481 4.4 37.8 1.0
CB A:ASP485 4.4 24.7 1.0
NH2 A:ARG446 4.5 33.0 1.0
CB A:ASP483 4.7 21.1 1.0
CA A:ASP481 4.7 36.2 1.0
O5' R:A9 4.7 1.0 1.0
O4' R:A9 4.7 0.8 1.0
N A:ASP483 4.7 21.0 1.0
C A:ASP481 4.8 35.7 1.0
N A:ASP485 4.9 24.1 1.0
O A:ASP481 4.9 34.3 1.0
CA A:ASP485 5.0 23.3 1.0

Magnesium binding site 2 out of 2 in 6bm4

Go back to Magnesium Binding Sites List in 6bm4
Magnesium binding site 2 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp


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 Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1804

b:36.3
occ:1.00
O2' B:2KH1302 2.3 0.9 1.0
OD2 A:ASP481 3.0 38.7 1.0
O1B B:2KH1302 3.3 0.8 1.0
C2' B:2KH1302 3.6 0.1 1.0
CG A:ASP481 3.7 38.1 1.0
C1' B:2KH1302 3.8 0.8 1.0
O4' B:2KH1302 3.8 0.1 1.0
CB A:ASP481 3.9 38.0 1.0
C4' B:2KH1302 4.0 0.4 1.0
O3' B:2KH1302 4.2 0.7 1.0
OE1 B:GLU836 4.2 44.6 1.0
C3' B:2KH1302 4.2 0.3 1.0
OD2 B:ASP837 4.2 53.1 1.0
O3G B:2KH1302 4.4 0.6 1.0
NH2 B:ARG1020 4.6 38.0 1.0
OD1 A:ASP481 4.7 35.1 1.0
PB B:2KH1302 4.7 0.9 1.0
CA A:ASP481 5.0 36.2 1.0
NH1 B:ARG1020 5.0 39.4 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 22:24:20 2020

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