Magnesium in PDB 6x71: REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp

The structure of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp, PDB code: 6x71 was solved by T.M.Weaver, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.63 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.269, 73.713, 117.221, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.2

The binding sites of Magnesium atom in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp (pdb code 6x71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp, PDB code: 6x71:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg102 b:21.4 occ:0.50 O3' P:DG12 2.1 23.2 0.5 OP1 P:DC13 2.2 20.1 0.3 OD1 A:ASP362 2.2 28.4 1.0 O1A P:DCP106 2.2 20.7 0.7 O3' P:DG12 2.3 23.1 0.5 OD1 A:ASP467 2.4 22.6 1.0 OE2 A:GLU468 2.5 30.4 1.0 P P:DC13 2.6 19.9 0.3 O A:HOH1170 2.9 35.3 1.0 CG A:ASP467 3.1 20.7 1.0 OD2 A:ASP467 3.2 20.7 1.0 CG A:ASP362 3.3 20.1 1.0 C3' P:DG12 3.3 22.9 0.5 C3' P:DG12 3.3 23.1 0.5 PA P:DCP106 3.4 18.1 0.7 MG P:MG103 3.4 16.9 0.9 CD A:GLU468 3.5 27.3 1.0 CB A:GLU468 3.6 25.8 1.0 C4' P:DG12 3.7 22.7 0.5 OP2 P:DC13 3.7 22.8 0.3 O5' P:DCP106 3.7 18.8 0.7 OD2 A:ASP362 3.8 28.3 1.0 O5' P:DC13 3.8 18.9 0.3 C5' P:DCP106 3.8 17.9 0.7 OG A:SER465 3.8 24.8 1.0 O2A P:DCP106 3.9 23.5 0.7 C5' P:DC13 4.0 17.5 0.3 C5' P:DG12 4.1 25.5 0.5 CG A:GLU468 4.1 23.5 1.0 C2' P:DG12 4.3 19.8 0.5 O A:ASP467 4.4 14.1 1.0 C2' P:DG12 4.4 25.4 0.5 MG P:MG104 4.4 33.5 0.5 C4' P:DG12 4.4 26.2 0.5 C A:ASP467 4.5 15.0 1.0 OE1 A:GLU468 4.5 26.0 1.0 CB A:ASP467 4.6 16.8 1.0 CB A:ASP362 4.6 17.6 1.0 CA A:GLU468 4.7 16.0 1.0 O2 P:POP107 4.8 21.5 0.1 N A:GLU468 4.8 16.4 1.0 O2B P:DCP106 4.8 15.1 0.7 O3A P:DCP106 4.8 21.9 0.7 O6 P:POP107 4.8 20.3 0.1 C5' P:DG12 4.9 27.4 0.5 O3G P:DCP106 4.9 20.1 0.7 O3 P:POP107 4.9 15.6 0.1 O5' P:DG12 4.9 27.1 0.5 CB A:SER465 4.9 19.3 1.0 O5' P:DG12 5.0 26.7 0.5 CA A:ASP467 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg103 b:16.9 occ:0.95 OD2 A:ASP362 2.1 28.3 1.0 OP1 P:DC13 2.1 20.1 0.3 O2B P:DCP106 2.1 15.1 0.7 O1A P:DCP106 2.2 20.7 0.7 O3 P:POP107 2.2 15.6 0.1 O6 P:POP107 2.3 20.3 0.1 O A:PHE363 2.3 16.4 1.0 O3G P:DCP106 2.4 20.1 0.7 OD2 A:ASP467 2.4 20.7 1.0 CG A:ASP362 2.8 20.1 1.0 OD1 A:ASP362 3.0 28.4 1.0 P1 P:POP107 3.3 20.2 0.1 PB P:DCP106 3.3 20.3 0.7 PA P:DCP106 3.4 18.1 0.7 MG P:MG102 3.4 21.4 0.5 O2 P:POP107 3.4 21.5 0.1 P P:DC13 3.5 19.9 0.3 P2 P:POP107 3.5 21.6 0.1 C A:PHE363 3.5 20.0 1.0 CG A:ASP467 3.5 20.7 1.0 PG P:DCP106 3.5 21.6 0.7 O3A P:DCP106 3.6 21.9 0.7 O P:POP107 3.8 20.6 0.1 O3B P:DCP106 3.8 20.7 0.7 OD1 A:ASP467 4.0 22.6 1.0 C5' P:DCP106 4.0 17.9 0.7 N A:PHE363 4.0 14.3 1.0 MG P:MG104 4.1 33.5 0.5 NZ A:LYS525 4.1 23.3 1.0 O4 P:POP107 4.2 20.2 0.1 O1G P:DCP106 4.2 20.1 0.7 CB A:ASP362 4.2 17.6 1.0 CA A:PHE363 4.2 14.3 1.0 OP2 P:DC13 4.3 22.8 0.3 O5' P:DCP106 4.3 18.8 0.7 O5' P:DC13 4.3 18.9 0.3 C5' P:DC13 4.4 17.5 0.3 C A:ASP362 4.4 15.3 1.0 O A:HOH1170 4.4 35.3 1.0 O3' P:DG12 4.5 23.2 0.5 CB A:PHE363 4.5 14.3 1.0 O2A P:DCP106 4.5 23.5 0.7 CB A:PHE366 4.5 14.2 1.0 N A:ASP364 4.6 16.5 1.0 N A:CYS365 4.6 17.9 1.0 N A:PHE366 4.6 14.8 1.0 O1 P:POP107 4.6 17.5 0.1 O1B P:DCP106 4.6 17.3 0.7 CE A:LYS525 4.7 24.4 1.0 O5 P:POP107 4.7 22.1 0.1 CA A:ASP364 4.8 14.2 1.0 CA A:ASP362 4.8 17.2 1.0 O2G P:DCP106 4.8 22.1 0.7 CB A:ASP467 4.8 16.8 1.0 O A:ASP467 4.8 14.1 1.0 C A:ASP364 4.8 15.8 1.0 O A:ASP362 4.9 20.6 1.0

Magnesium binding site 3 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg104 b:33.5 occ:0.52 O A:HOH1170 2.4 35.3 1.0 O3G P:DCP106 2.9 20.1 0.7 O A:HOH1102 2.9 27.1 1.0 O6 P:POP107 3.0 20.3 0.1 NH2 A:ARG518 3.4 38.2 0.5 OD2 A:ASP362 3.5 28.3 1.0 O1A P:DCP106 3.5 20.7 0.7 O P:HOH205 3.7 28.1 1.0 O2G P:DCP106 3.8 22.1 0.7 OP2 P:DC13 3.8 22.8 0.3 O5 P:POP107 3.8 22.1 0.1 O2A P:DCP106 3.8 23.5 0.7 CE A:LYS525 3.9 24.4 1.0 CG A:ASP362 3.9 20.1 1.0 PG P:DCP106 3.9 21.6 0.7 P2 P:POP107 3.9 21.6 0.1 OP1 P:DC13 4.0 20.1 0.3 MG P:MG103 4.1 16.9 0.9 OD1 A:ASP362 4.1 28.4 1.0 PA P:DCP106 4.1 18.1 0.7 CZ A:ARG518 4.3 36.0 0.5 P P:DC13 4.3 19.9 0.3 MG P:MG102 4.4 21.4 0.5 O2 P:POP107 4.4 21.5 0.1 O3A P:DCP106 4.5 21.9 0.7 CD A:LYS525 4.6 28.7 1.0 O P:HOH209 4.6 33.1 1.0 OP1 P:DG12 4.7 31.6 0.5 NZ A:LYS525 4.7 23.3 1.0 CB A:ASP362 4.8 17.6 1.0 CD2 A:LEU521 4.8 18.1 1.0 NH1 A:ARG518 4.8 14.8 0.5 O3' P:DG12 4.9 23.2 0.5

Magnesium binding site 4 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg105 b:33.0 occ:1.00 O A:HOH932 2.4 43.6 1.0 OP1 P:DA11 2.6 30.3 0.4 OP1 P:DA11 2.7 30.5 0.6 O A:LEU550 2.8 25.0 1.0 O A:HOH1163 2.8 42.4 1.0 O A:ASP548 2.8 24.4 1.0 O A:VAL553 3.1 23.2 1.0 P P:DA11 3.6 27.2 0.4 OP2 P:DA11 3.7 26.9 0.4 P P:DA11 3.7 27.1 0.6 C A:LEU550 3.7 27.4 1.0 OP2 P:DA11 3.8 26.8 0.6 C A:ASP548 3.8 22.7 1.0 C A:VAL553 3.9 25.8 1.0 N A:VAL553 4.0 24.2 1.0 CA A:PRO551 4.2 26.7 1.0 C A:ASP549 4.2 25.5 1.0 N A:GLY552 4.3 28.4 1.0 N A:PRO551 4.3 24.9 1.0 O A:ASP549 4.3 24.3 1.0 N A:LEU550 4.4 25.8 1.0 CA A:VAL553 4.5 26.4 1.0 CA A:ASP548 4.5 29.3 1.0 C A:PRO551 4.6 27.6 1.0 CA A:ASP549 4.6 20.1 1.0 N A:ASP549 4.7 19.6 1.0 CA A:LEU550 4.7 25.2 1.0 O5' P:DA11 4.7 26.0 0.4 O3' P:DT10 4.8 24.8 1.0 O A:HOH928 4.8 52.2 1.0 CB A:ASP548 4.8 28.9 1.0 N A:GLY554 4.9 21.4 1.0 CB A:VAL553 4.9 25.8 1.0 O5' P:DA11 4.9 25.9 0.6 C A:GLY552 5.0 25.7 1.0

T.M.Weaver, L.M.Cortez, T.H.Khoang, M.T.Washington, P.K.Agarwal, B.D.Freudenthal. Visualizing REV1 Catalyze Protein-Template Dna Synthesis. Proc.Natl.Acad.Sci.Usa V. 117 25494 2020.
ISSN: ESSN 1091-6490
PubMed: 32999062
DOI: 10.1073/PNAS.2010484117