Magnesium in PDB 5wm1: Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex

The structure of Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex, PDB code: 5wm1 was solved by O.Rechkoblit, A.Kolbanovsky, H.Landes, N.E.Geacintov, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.33 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.002, 64.879, 130.652, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.6

The binding sites of Magnesium atom in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex (pdb code 5wm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex, PDB code: 5wm1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:24.0 occ:1.00 O P:HOH212 2.1 27.2 1.0 O A:ASP548 2.2 18.2 1.0 O A:VAL553 2.2 19.0 1.0 O A:HOH915 2.3 49.8 1.0 OP1 P:DA11 2.6 22.9 0.7 O A:LEU550 2.8 22.9 1.0 OP1 P:DA11 2.8 21.6 0.3 C A:ASP548 3.3 18.9 1.0 OP2 P:DA11 3.3 23.0 0.7 C A:VAL553 3.3 19.0 1.0 P P:DA11 3.4 20.8 0.7 OP2 P:DA11 3.5 21.4 0.3 P P:DA11 3.6 21.4 0.3 C A:LEU550 3.8 24.0 1.0 CA A:ASP548 3.9 18.5 1.0 N A:VAL553 4.0 19.6 1.0 CA A:VAL553 4.1 19.2 1.0 CB A:ASP548 4.2 19.6 1.0 O A:HOH1027 4.2 40.7 1.0 C A:ASP549 4.2 19.9 1.0 N A:ASP549 4.3 17.6 1.0 N A:LEU550 4.3 19.7 1.0 N A:GLY554 4.3 18.3 1.0 CB A:VAL553 4.5 19.0 1.0 CA A:ASP549 4.5 18.9 1.0 O5' P:DA11 4.5 21.7 0.7 O3' P:DT10 4.5 20.4 1.0 CA A:PRO551 4.6 26.9 1.0 NH2 A:ARG518 4.6 32.7 1.0 O A:ASP549 4.6 21.3 1.0 N A:GLY552 4.6 23.0 1.0 N A:PRO551 4.6 27.1 1.0 CA A:GLY554 4.7 19.6 1.0 CA A:LEU550 4.7 22.8 1.0 C A:PRO551 4.9 24.9 1.0 NH1 A:ARG518 4.9 32.0 1.0 O5' P:DA11 4.9 22.2 0.3

Magnesium binding site 2 out of 4 in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:28.0 occ:1.00 OD1 A:ASP467 2.2 17.7 1.0 OE2 A:GLU468 2.5 22.9 1.0 O2A A:DCP804 2.6 14.2 1.0 CG A:ASP467 2.9 14.4 1.0 OD2 A:ASP467 2.9 15.5 1.0 OD2 A:ASP362 3.1 20.3 1.0 C3' P:DDG12 3.2 23.4 0.6 MG A:MG802 3.3 13.4 1.0 CB A:GLU468 3.6 16.0 1.0 C3' P:DDG12 3.6 25.1 0.4 O A:HOH1001 3.6 30.6 1.0 CD A:GLU468 3.6 19.5 1.0 PA A:DCP804 3.7 15.7 1.0 OG A:SER465 3.7 13.7 0.5 MG A:MG803 3.8 24.3 1.0 C5' A:DCP804 3.8 13.7 1.0 O5' A:DCP804 3.8 14.2 1.0 CB A:ASP362 3.9 19.0 1.0 CG A:ASP362 3.9 20.9 1.0 C4' P:DDG12 3.9 23.6 0.6 CG A:GLU468 4.1 17.3 1.0 C5' P:DDG12 4.2 23.6 0.6 C2' P:DDG12 4.2 24.9 0.4 C4' P:DDG12 4.3 25.6 0.4 CB A:ASP467 4.4 14.4 1.0 O A:ASP467 4.4 12.0 1.0 C A:ASP467 4.4 13.2 1.0 O1A A:DCP804 4.4 15.3 1.0 C2' P:DDG12 4.5 23.8 0.6 OE1 A:GLU468 4.6 18.4 1.0 CA A:GLU468 4.7 14.4 1.0 N A:GLU468 4.7 13.2 1.0 CB A:SER465 4.8 13.8 0.5 O1B A:DCP804 4.8 14.3 1.0 CB A:SER465 4.8 13.5 0.5 CA A:ASP467 4.9 13.3 1.0 O3G A:DCP804 5.0 16.8 1.0 C5' P:DDG12 5.0 26.2 0.4

Magnesium binding site 3 out of 4 in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:13.4 occ:1.00 O1B A:DCP804 2.2 14.3 1.0 OD2 A:ASP362 2.2 20.3 1.0 O A:PHE363 2.2 12.9 1.0 OD2 A:ASP467 2.3 15.5 1.0 O2A A:DCP804 2.3 14.2 1.0 O3G A:DCP804 2.5 16.8 1.0 MG A:MG803 3.1 24.3 1.0 CG A:ASP362 3.2 20.9 1.0 MG A:MG801 3.3 28.0 1.0 PB A:DCP804 3.4 14.8 1.0 CG A:ASP467 3.5 14.4 1.0 C A:PHE363 3.5 13.1 1.0 PA A:DCP804 3.5 15.7 1.0 PG A:DCP804 3.7 16.1 1.0 O3A A:DCP804 3.8 14.6 1.0 O3B A:DCP804 3.9 16.1 1.0 NZ A:LYS525 4.0 22.7 1.0 OD1 A:ASP362 4.0 28.3 1.0 OD1 A:ASP467 4.0 17.7 1.0 C5' A:DCP804 4.0 13.7 1.0 CB A:ASP362 4.1 19.0 1.0 N A:PHE363 4.1 13.3 1.0 CA A:PHE363 4.2 13.8 1.0 O5' A:DCP804 4.3 14.2 1.0 O2G A:DCP804 4.4 15.2 1.0 CB A:PHE366 4.5 12.6 1.0 CB A:PHE363 4.5 13.5 1.0 C A:ASP362 4.5 14.8 1.0 N A:ASP364 4.5 13.8 1.0 N A:PHE366 4.6 12.4 1.0 N A:CYS365 4.6 14.9 1.0 CE A:LYS525 4.7 23.5 1.0 CB A:ASP467 4.7 14.4 1.0 O A:HOH1115 4.7 43.6 1.0 CA A:ASP364 4.7 14.7 1.0 O2B A:DCP804 4.7 14.6 1.0 C A:ASP364 4.8 14.7 1.0 O1A A:DCP804 4.8 15.3 1.0 O1G A:DCP804 4.9 17.2 1.0 CA A:ASP362 4.9 15.9 1.0 O A:HOH1001 4.9 30.6 1.0 O A:ASP467 5.0 12.0 1.0

Magnesium binding site 4 out of 4 in the Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the 10S (+)-Trans-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:24.3 occ:1.00 O A:HOH1115 2.1 43.6 1.0 O3G A:DCP804 2.2 16.8 1.0 OD2 A:ASP362 2.2 20.3 1.0 O2A A:DCP804 2.5 14.2 1.0 O A:HOH1001 2.5 30.6 1.0 O A:HOH1150 2.6 44.9 1.0 MG A:MG802 3.1 13.4 1.0 CG A:ASP362 3.3 20.9 1.0 PA A:DCP804 3.5 15.7 1.0 PG A:DCP804 3.5 16.1 1.0 CE A:LYS525 3.7 23.5 1.0 OD1 A:ASP362 3.7 28.3 1.0 MG A:MG801 3.8 28.0 1.0 O1A A:DCP804 3.8 15.3 1.0 O1G A:DCP804 3.8 17.2 1.0 O3A A:DCP804 4.1 14.6 1.0 NZ A:LYS525 4.1 22.7 1.0 O A:HOH1068 4.2 37.1 1.0 OE2 A:GLU468 4.4 22.9 1.0 O1B A:DCP804 4.4 14.3 1.0 O3B A:DCP804 4.4 16.1 1.0 CB A:ASP362 4.5 19.0 1.0 CD A:LYS525 4.5 23.9 1.0 PB A:DCP804 4.6 14.8 1.0 O A:PHE363 4.6 12.9 1.0 O2G A:DCP804 4.7 15.2 1.0 O P:HOH221 4.8 46.3 1.0 OD2 A:ASP467 4.9 15.5 1.0 O5' A:DCP804 4.9 14.2 1.0

O.Rechkoblit, A.Kolbanovskiy, H.Landes, N.E.Geacintov, A.K.Aggarwal. Mechanism of Error-Free Replication Across Benzo[A]Pyrene Stereoisomers By REV1 Dna Polymerase. Nat Commun V. 8 965 2017.
ISSN: ESSN 2041-1723
PubMed: 29042535
DOI: 10.1038/S41467-017-01013-5