Manganese in PDB 6x76: REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound

The structure of REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound, PDB code: 6x76 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)	35.13 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.965, 73.626, 117.634, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 27.2

The binding sites of Manganese atom in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound (pdb code 6x76). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound, PDB code: 6x76:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:35.8 occ:1.00 OP2 P:DC13 1.7 52.2 1.0 OE2 A:GLU468 2.0 39.3 1.0 O1A A:DCP803 2.2 24.5 1.0 OD2 A:ASP362 2.2 28.0 1.0 OD1 A:ASP467 2.4 39.3 1.0 CD A:GLU468 2.8 47.5 1.0 OD2 A:ASP467 2.9 30.0 1.0 CG A:GLU468 2.9 40.4 1.0 CG A:ASP467 3.0 30.3 1.0 P P:DC13 3.3 39.7 1.0 PA A:DCP803 3.3 26.5 1.0 CG A:ASP362 3.3 31.3 1.0 MN A:MN801 3.4 33.6 1.0 O2A A:DCP803 3.6 42.6 1.0 OD1 A:ASP362 3.8 31.5 1.0 O5' A:DCP803 3.8 28.2 1.0 MN P:MN102 3.9 66.0 1.0 O3' P:DG12 3.9 49.2 1.0 OE1 A:GLU468 4.0 38.8 1.0 C5' A:DCP803 4.0 20.9 1.0 O5' P:DC13 4.1 65.0 1.0 O A:HOH901 4.1 36.3 1.0 OG A:SER465 4.2 38.4 1.0 CB A:GLU468 4.2 39.4 1.0 OP1 P:DC13 4.2 45.0 1.0 CB A:ASP362 4.5 33.9 1.0 CB A:ASP467 4.5 21.4 1.0 O3G A:DCP803 4.6 36.7 1.0 CB A:SER465 4.6 42.5 1.0 O A:ASP467 4.6 28.0 1.0 C A:ASP467 4.7 32.7 1.0 O3A A:DCP803 4.7 41.8 1.0 O2B A:DCP803 4.8 25.6 1.0 O P:HOH204 4.8 40.0 1.0 N A:GLU468 4.9 29.4 1.0

Manganese binding site 2 out of 4 in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn102 b:66.0 occ:1.00 O2A A:DCP803 2.2 42.6 1.0 O5' P:DC13 2.4 65.0 1.0 C5' P:DC13 3.2 71.2 1.0 OP2 P:DC13 3.4 52.2 1.0 P P:DC13 3.5 39.7 1.0 PA A:DCP803 3.6 26.5 1.0 OE2 A:GLU468 3.8 39.3 1.0 O P:HOH204 3.9 40.0 1.0 O A:HOH901 3.9 36.3 1.0 MN P:MN101 3.9 35.8 1.0 O1A A:DCP803 3.9 24.5 1.0 O3' P:DG12 4.2 49.2 1.0 NH2 A:ARG518 4.3 35.7 1.0 O5' A:DCP803 4.4 28.2 1.0 OP1 P:DC13 4.7 45.0 1.0 O3A A:DCP803 4.7 41.8 1.0 C4' P:DC13 4.7 58.7 1.0 C3' P:DG12 4.8 45.0 1.0 O5' P:DG12 4.8 45.9 1.0 CD A:GLU468 4.9 47.5 1.0

Manganese binding site 3 out of 4 in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:33.6 occ:1.00 OD1 A:ASP362 1.9 31.5 1.0 OD2 A:ASP467 2.2 30.0 1.0 O A:PHE363 2.2 23.1 1.0 O1A A:DCP803 2.3 24.5 1.0 O2B A:DCP803 2.3 25.6 1.0 O3G A:DCP803 2.4 36.7 1.0 CG A:ASP362 2.8 31.3 1.0 OD2 A:ASP362 3.1 28.0 1.0 PB A:DCP803 3.3 31.1 1.0 C A:PHE363 3.4 27.5 1.0 CG A:ASP467 3.4 30.3 1.0 MN P:MN101 3.4 35.8 1.0 PG A:DCP803 3.5 31.6 1.0 PA A:DCP803 3.5 26.5 1.0 O3A A:DCP803 3.7 41.8 1.0 O3B A:DCP803 3.8 32.3 1.0 O A:HOH901 3.8 36.3 1.0 N A:PHE363 3.8 27.8 1.0 OD1 A:ASP467 4.0 39.3 1.0 CA A:PHE363 4.0 28.6 1.0 O1G A:DCP803 4.0 38.1 1.0 NZ A:LYS525 4.1 35.2 1.0 CB A:ASP362 4.2 33.9 1.0 C A:ASP362 4.3 24.2 1.0 CB A:PHE363 4.3 24.4 1.0 C5' A:DCP803 4.3 20.9 1.0 CE A:LYS525 4.4 34.8 1.0 N A:ASP364 4.4 33.2 1.0 CB A:ASP467 4.5 21.4 1.0 O5' A:DCP803 4.5 28.2 1.0 CB A:PHE366 4.5 25.9 1.0 O2A A:DCP803 4.6 42.6 1.0 N A:PHE366 4.7 29.1 1.0 O1B A:DCP803 4.7 36.8 1.0 N A:CYS365 4.7 30.4 1.0 CA A:ASP364 4.7 30.2 1.0 CA A:ASP362 4.7 24.7 1.0 O2G A:DCP803 4.8 42.1 1.0 O A:ASP362 4.8 33.4 1.0 OP2 P:DC13 4.8 52.2 1.0 O A:ASP467 4.9 28.0 1.0 C A:ASP364 4.9 27.2 1.0

Manganese binding site 4 out of 4 in the REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of REV1 L325G MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:64.3 occ:1.00 O A:ASP548 2.0 66.8 1.0 O A:VAL553 2.1 51.8 1.0 C A:ASP548 3.0 48.9 1.0 CB A:ASP548 3.1 54.5 1.0 C A:VAL553 3.3 56.2 1.0 CA A:ASP548 3.4 45.4 1.0 CG A:ASP548 3.7 56.0 1.0 O A:LEU550 3.9 38.8 1.0 OD2 A:ASP548 4.0 49.4 1.0 OP1 P:DA11 4.0 49.4 1.0 OP2 P:DA11 4.0 33.3 1.0 N A:GLY554 4.2 54.0 1.0 N A:ASP549 4.2 39.2 1.0 CA A:GLY554 4.3 53.0 1.0 CA A:VAL553 4.3 56.9 1.0 CB A:VAL553 4.4 46.8 1.0 OD1 A:ASP548 4.5 57.4 1.0 P P:DA11 4.6 44.4 1.0 N A:VAL553 4.6 48.3 1.0 CA A:ASP549 4.7 37.6 1.0 C A:ASP549 4.8 38.2 1.0 N A:ASP548 4.8 47.7 1.0 N A:LEU550 4.9 37.9 1.0 C A:LEU550 5.0 44.8 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