Magnesium in PDB 7oob: Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2)

Enzymatic activity of Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2)

All present enzymatic activity of Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2):
2.7.7.6;

Other elements in 7oob:

The structure of Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2) also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2) (pdb code 7oob). 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-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2), PDB code: 7oob:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7oob

Go back to Magnesium Binding Sites List in 7oob
Magnesium binding site 1 out of 2 in the Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:10.3
occ:1.00
OD1 A:ASP495 1.9 8.5 1.0
OD1 A:ASP499 1.9 11.3 1.0
O3' P:A10 2.1 11.3 1.0
OD1 A:ASP497 2.1 9.1 1.0
OD2 A:ASP499 2.2 11.3 1.0
CG A:ASP499 2.3 11.3 1.0
HO2' P:A10 2.7 11.3 1.0
CG A:ASP495 3.0 8.5 1.0
CG A:ASP497 3.2 9.1 1.0
H A:ASP495 3.3 8.5 1.0
C3' P:A10 3.4 11.3 1.0
OD2 A:ASP497 3.5 9.1 1.0
O2' P:A10 3.5 11.3 1.0
H4' P:A10 3.5 11.3 1.0
OD2 A:ASP495 3.5 8.5 1.0
H A:ASP497 3.7 9.1 1.0
O A:ASP495 3.7 8.5 1.0
CB A:ASP499 3.8 11.3 1.0
C4' P:A10 3.9 11.3 1.0
HH21 A:ARG460 3.9 11.3 1.0
C2' P:A10 4.0 11.3 1.0
H A:ASP499 4.1 11.3 1.0
H3' P:A10 4.1 11.3 1.0
N A:ASP495 4.1 8.5 1.0
H5'' P:A10 4.1 11.3 1.0
C A:ASP495 4.2 8.5 1.0
HB2 A:ASP499 4.2 11.3 1.0
CB A:ASP495 4.3 8.5 1.0
HB3 A:ASP499 4.3 11.3 1.0
CA A:ASP495 4.4 8.5 1.0
N A:ASP499 4.4 11.3 1.0
HA A:ASP499 4.4 11.3 1.0
N A:ASP497 4.5 9.1 1.0
CA A:ASP499 4.5 11.3 1.0
H2' P:A10 4.5 11.3 1.0
CB A:ASP497 4.5 9.1 1.0
C5' P:A10 4.6 11.3 1.0
NH2 A:ARG460 4.6 11.3 1.0
O A:ASP497 4.6 9.1 1.0
HA A:ALA494 4.7 8.7 1.0
C A:ASP497 4.7 9.1 1.0
HE A:ARG460 4.7 11.3 1.0
HB2 A:ASP495 4.8 8.5 1.0
CA A:ASP497 4.8 9.1 1.0
HB3 A:ASP495 4.9 8.5 1.0
HB3 A:ASP497 5.0 9.1 1.0
HH22 A:ARG460 5.0 11.3 1.0

Magnesium binding site 2 out of 2 in 7oob

Go back to Magnesium Binding Sites List in 7oob
Magnesium binding site 2 out of 2 in the Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pol II-Csb-Csa-DDB1-Uvssa-ADPBEF3 (STRUCTURE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg1503

b:12.1
occ:1.00
O3B b:ADP1501 2.0 11.3 1.0
F3 b:BEF1502 2.0 13.6 1.0
PB b:ADP1501 3.3 11.3 1.0
BE b:BEF1502 3.5 13.6 1.0
HA2 b:GLY920 3.6 13.0 1.0
OG1 b:THR539 3.6 9.2 1.0
O1B b:ADP1501 3.6 11.3 1.0
HG1 b:THR539 3.8 9.2 1.0
HA3 b:GLY920 3.9 13.0 1.0
O1A b:ADP1501 3.9 11.3 1.0
OD2 b:ASP646 3.9 11.3 1.0
OD1 b:ASP646 4.0 11.3 1.0
O3A b:ADP1501 4.1 11.3 1.0
HH12 b:ARG950 4.1 13.6 1.0
CA b:GLY920 4.2 13.0 1.0
O2A b:ADP1501 4.2 11.3 1.0
HE22 b:GLN580 4.2 10.2 1.0
O b:GLY920 4.2 13.0 1.0
HB2 b:LYS538 4.2 9.8 1.0
PA b:ADP1501 4.2 11.3 1.0
HE2 b:LYS538 4.2 9.8 1.0
HE21 b:GLN580 4.2 10.2 1.0
H b:THR539 4.2 9.2 1.0
F2 b:BEF1502 4.3 13.6 1.0
OE2 b:GLU647 4.3 12.5 1.0
F1 b:BEF1502 4.3 13.6 1.0
CG b:ASP646 4.4 11.3 1.0
O2B b:ADP1501 4.4 11.3 1.0
NE2 b:GLN580 4.6 10.2 1.0
H b:LYS538 4.6 9.8 1.0
C b:GLY920 4.7 13.0 1.0
HZ3 b:LYS538 4.7 9.8 1.0
NH1 b:ARG950 4.8 13.6 1.0
HH11 b:ARG950 4.8 13.6 1.0
HD12 b:LEU673 4.9 10.5 1.0
N b:THR539 4.9 9.2 1.0
CB b:THR539 4.9 9.2 1.0
HZ1 b:LYS538 4.9 9.8 1.0
CD b:GLU647 4.9 12.5 1.0
HE1 b:TRP581 4.9 9.5 1.0
HZ2 b:TRP581 4.9 9.5 1.0
HB b:THR539 4.9 9.2 1.0

Reference:

G.Kokic, F.R.Wagner, A.Chernev, H.Urlaub, P.Cramer. Structural Basis of Human Transcription-Dna Repair Coupling. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 34526721
DOI: 10.1038/S41586-021-03906-4
Page generated: Fri Nov 5 15:31:15 2021

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