Magnesium in PDB 5wm8: Structure of the 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex

The structure of Structure of the 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex, PDB code: 5wm8 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)	45.00 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.551, 180.358, 54.586, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.4

The binding sites of Magnesium atom in the Structure of the 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex (pdb code 5wm8). 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 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex, PDB code: 5wm8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the 10R (+)-Cis-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 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:30.8 occ:1.00 O A:ASP548 2.2 28.4 1.0 O A:VAL553 2.2 26.1 1.0 O P:HOH209 2.3 32.4 1.0 OP1 P:DA11 2.5 25.2 0.3 O A:LEU550 2.7 28.3 1.0 OP1 P:DA11 2.7 25.0 0.7 O A:HOH1125 2.8 38.4 1.0 C A:ASP548 3.2 28.2 1.0 C A:VAL553 3.3 26.4 1.0 OP2 P:DA11 3.4 26.1 0.3 P P:DA11 3.4 25.6 0.3 P P:DA11 3.6 25.4 0.7 OP2 P:DA11 3.7 25.7 0.7 C A:LEU550 3.7 31.1 1.0 CA A:ASP548 3.9 28.5 1.0 N A:VAL553 3.9 27.9 1.0 O A:HOH1104 4.0 53.9 1.0 CA A:VAL553 4.1 27.0 1.0 C A:ASP549 4.2 26.6 1.0 CB A:ASP548 4.2 29.6 1.0 N A:LEU550 4.2 28.0 1.0 N A:ASP549 4.3 26.5 1.0 O A:HOH1030 4.3 37.8 1.0 N A:GLY554 4.3 27.1 1.0 CB A:VAL553 4.4 27.0 1.0 CA A:ASP549 4.4 26.9 1.0 O5' P:DA11 4.5 24.7 0.3 N A:GLY552 4.5 31.0 1.0 O A:ASP549 4.5 28.2 1.0 N A:PRO551 4.5 34.0 1.0 O3' P:DT10 4.6 25.2 1.0 CA A:GLY554 4.6 28.4 1.0 CA A:LEU550 4.6 29.5 1.0 CA A:PRO551 4.6 34.4 1.0 C A:PRO551 4.9 33.5 1.0 O5' P:DA11 4.9 25.6 0.7 C A:GLY552 4.9 28.7 1.0

Magnesium binding site 2 out of 4 in the Structure of the 10R (+)-Cis-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 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:29.9 occ:1.00 OD1 A:ASP467 2.0 20.4 1.0 OE2 A:GLU468 2.8 23.5 1.0 CG A:ASP467 2.8 18.4 1.0 O2A A:DCP804 2.9 18.1 1.0 OD2 A:ASP467 3.0 19.5 1.0 C3' P:DDG12 3.1 23.1 0.3 OD2 A:ASP362 3.5 24.8 1.0 C3' P:DDG12 3.5 26.8 0.7 C5' A:DCP804 3.5 18.7 1.0 CB A:GLU468 3.6 19.9 1.0 MG A:MG802 3.6 16.8 1.0 PA A:DCP804 3.7 19.0 1.0 O5' A:DCP804 3.8 18.1 1.0 CD A:GLU468 3.9 22.4 1.0 O A:HOH1019 3.9 27.2 1.0 MG A:MG803 4.0 22.4 1.0 C2' P:DDG12 4.1 26.7 0.7 C4' P:DDG12 4.2 22.8 0.3 CB A:SER465 4.2 19.2 1.0 C2' P:DDG12 4.2 23.5 0.3 C4' P:DDG12 4.2 27.4 0.7 CB A:ASP467 4.3 18.1 1.0 CG A:ASP362 4.3 23.8 1.0 CG A:GLU468 4.3 20.9 1.0 CB A:ASP362 4.3 23.1 1.0 C A:ASP467 4.3 17.0 1.0 O A:ASP467 4.4 16.9 1.0 OG A:SER465 4.5 20.8 1.0 O1A A:DCP804 4.5 19.0 1.0 N A:GLU468 4.5 16.1 1.0 C5' P:DDG12 4.5 22.6 0.3 CA A:GLU468 4.6 18.0 1.0 CA A:ASP467 4.7 17.2 1.0 O2B A:DCP804 4.7 17.6 1.0 N A:ASP467 4.8 17.0 1.0 C5' P:DDG12 4.9 29.3 0.7 OE1 A:GLU468 4.9 22.7 1.0 C4' A:DCP804 5.0 18.8 1.0

Magnesium binding site 3 out of 4 in the Structure of the 10R (+)-Cis-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 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:16.8 occ:1.00 OD2 A:ASP362 2.0 24.8 1.0 O2B A:DCP804 2.0 17.6 1.0 O2A A:DCP804 2.0 18.1 1.0 OD2 A:ASP467 2.2 19.5 1.0 O A:PHE363 2.2 18.4 1.0 O3G A:DCP804 2.5 18.9 1.0 MG A:MG803 2.9 22.4 1.0 CG A:ASP362 3.2 23.8 1.0 PB A:DCP804 3.2 17.0 1.0 PA A:DCP804 3.4 19.0 1.0 CG A:ASP467 3.5 18.4 1.0 C A:PHE363 3.5 17.6 1.0 MG A:MG801 3.6 29.9 1.0 PG A:DCP804 3.6 19.6 1.0 O3A A:DCP804 3.7 17.7 1.0 O3B A:DCP804 3.8 17.4 1.0 OD1 A:ASP362 4.0 28.0 1.0 OD1 A:ASP467 4.0 20.4 1.0 NZ A:LYS525 4.0 24.1 1.0 N A:PHE363 4.1 17.8 1.0 C5' A:DCP804 4.1 18.7 1.0 CB A:ASP362 4.1 23.1 1.0 O5' A:DCP804 4.2 18.1 1.0 CA A:PHE363 4.3 17.7 1.0 O2G A:DCP804 4.3 18.1 1.0 CB A:PHE366 4.5 16.4 1.0 N A:ASP364 4.5 17.6 1.0 C A:ASP362 4.6 19.8 1.0 CB A:PHE363 4.6 18.6 1.0 N A:PHE366 4.6 16.7 1.0 O1B A:DCP804 4.6 17.5 1.0 N A:CYS365 4.7 16.8 1.0 CB A:ASP467 4.7 18.1 1.0 O1A A:DCP804 4.7 19.0 1.0 CA A:ASP364 4.7 18.7 1.0 O A:HOH1091 4.8 50.6 1.0 C A:ASP364 4.8 18.1 1.0 CE A:LYS525 4.9 26.9 1.0 O A:HOH1097 4.9 37.6 1.0 O1G A:DCP804 4.9 18.2 1.0 O A:HOH1019 4.9 27.2 1.0 CA A:ASP362 5.0 20.7 1.0 O A:ASP467 5.0 16.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the 10R (+)-Cis-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 10R (+)-Cis-Bp-Dg Modified REV1 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:22.4 occ:1.00 O3G A:DCP804 2.0 18.9 1.0 O2A A:DCP804 2.0 18.1 1.0 O A:HOH1097 2.3 37.6 1.0 OD2 A:ASP362 2.5 24.8 1.0 O A:HOH1091 2.5 50.6 1.0 O A:HOH1019 2.6 27.2 1.0 MG A:MG802 2.9 16.8 1.0 PA A:DCP804 3.1 19.0 1.0 PG A:DCP804 3.4 19.6 1.0 CG A:ASP362 3.4 23.8 1.0 O1A A:DCP804 3.5 19.0 1.0 O3A A:DCP804 3.8 17.7 1.0 O1G A:DCP804 3.8 18.2 1.0 OD1 A:ASP362 3.8 28.0 1.0 CE A:LYS525 4.0 26.9 1.0 MG A:MG801 4.0 29.9 1.0 O A:HOH1075 4.1 49.0 1.0 O2B A:DCP804 4.1 17.6 1.0 NZ A:LYS525 4.1 24.1 1.0 O3B A:DCP804 4.2 17.4 1.0 PB A:DCP804 4.3 17.0 1.0 OE2 A:GLU468 4.4 23.5 1.0 O A:HOH1050 4.5 27.3 1.0 O A:PHE363 4.6 18.4 1.0 O5' A:DCP804 4.6 18.1 1.0 O2G A:DCP804 4.6 18.1 1.0 NH2 A:ARG518 4.6 42.7 1.0 CB A:ASP362 4.7 23.1 1.0 OD2 A:ASP467 4.7 19.5 1.0 CD A:LYS525 4.9 25.5 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