Manganese in PDB 6x75: REV1 MN2+-Facilitated Product Complex with Second Dctp Bound

The structure of REV1 MN2+-Facilitated Product Complex with Second Dctp Bound, PDB code: 6x75 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)	42.69 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.199, 73.566, 117.390, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.8

The binding sites of Manganese atom in the REV1 MN2+-Facilitated Product Complex with Second Dctp Bound (pdb code 6x75). 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 MN2+-Facilitated Product Complex with Second Dctp Bound, PDB code: 6x75:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the REV1 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 MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:44.8 occ:1.00 O2A A:DCP804 2.0 17.1 1.0 O P:HOH207 2.5 12.5 1.0 O A:HOH1107 2.5 31.4 1.0 O A:HOH1177 2.5 25.2 1.0 OP2 P:DC13 2.5 50.2 1.0 O P:HOH214 2.6 38.9 1.0 PA A:DCP804 3.4 14.1 1.0 P P:DC13 3.5 32.9 1.0 O5' P:DC13 3.5 34.7 1.0 O A:HOH975 3.6 20.2 1.0 O1A A:DCP804 3.9 14.5 1.0 O A:HOH996 4.0 23.9 1.0 O A:HOH1017 4.0 20.5 1.0 OP1 P:DC13 4.1 23.1 1.0 MN A:MN801 4.1 18.4 1.0 C6 P:DC13 4.3 46.0 1.0 O5' A:DCP804 4.3 12.0 1.0 O P:HOH224 4.3 34.0 1.0 O3A A:DCP804 4.4 18.4 1.0 C5 P:DC13 4.5 50.7 1.0 NH2 A:ARG518 4.6 32.4 1.0 O A:HOH1000 4.7 32.6 1.0 C5' P:DG12 4.7 50.8 1.0 OE2 A:GLU468 4.8 18.1 1.0 O3' P:DG12 4.9 42.3 1.0 C5' P:DC13 4.9 29.7 1.0 OP2 P:DG12 5.0 39.9 1.0

Manganese binding site 2 out of 4 in the REV1 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 MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:18.4 occ:1.00 O1A A:DCP804 2.1 14.5 1.0 OD2 A:ASP362 2.2 11.3 1.0 OP1 P:DC13 2.2 23.1 1.0 O P:HOH207 2.2 12.5 1.0 OE2 A:GLU468 2.3 18.1 1.0 OD1 A:ASP467 2.4 11.0 1.0 P P:DC13 3.2 32.9 1.0 CG A:ASP362 3.2 11.4 1.0 CG A:ASP467 3.2 12.3 1.0 OP2 P:DC13 3.3 50.2 1.0 PA A:DCP804 3.3 14.1 1.0 OD2 A:ASP467 3.3 13.0 1.0 CD A:GLU468 3.4 22.7 1.0 MN A:MN802 3.6 9.2 0.8 OD1 A:ASP362 3.6 12.6 1.0 CB A:GLU468 3.7 17.5 1.0 O2A A:DCP804 3.7 17.1 1.0 O5' A:DCP804 3.9 12.0 1.0 OG A:SER465 4.0 17.0 1.0 O A:HOH975 4.0 20.2 1.0 C5' A:DCP804 4.1 12.7 1.0 MN P:MN101 4.1 44.8 1.0 CG A:GLU468 4.1 13.4 1.0 O3' P:DG12 4.2 42.3 1.0 OE1 A:GLU468 4.4 19.0 1.0 O5' P:DC13 4.4 34.7 1.0 O A:ASP467 4.5 8.9 1.0 CB A:ASP362 4.5 8.3 1.0 O A:HOH996 4.6 23.9 1.0 CB A:ASP467 4.7 10.9 1.0 C A:ASP467 4.7 11.5 1.0 O3G A:DCP804 4.7 11.5 1.0 O3A A:DCP804 4.8 18.4 1.0 CA A:GLU468 4.9 12.2 1.0 O2B A:DCP804 4.9 10.0 1.0

Manganese binding site 3 out of 4 in the REV1 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 MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:9.2 occ:0.76 OD1 A:ASP362 2.1 12.6 1.0 O2B A:DCP804 2.1 10.0 1.0 O A:PHE363 2.2 8.5 1.0 OD2 A:ASP467 2.3 13.0 1.0 O1A A:DCP804 2.3 14.5 1.0 O3G A:DCP804 2.3 11.5 1.0 CG A:ASP362 3.1 11.4 1.0 PB A:DCP804 3.2 16.6 1.0 OD2 A:ASP362 3.4 11.3 1.0 CG A:ASP467 3.4 12.3 1.0 PA A:DCP804 3.4 14.1 1.0 C A:PHE363 3.4 12.1 1.0 PG A:DCP804 3.4 17.3 1.0 O3A A:DCP804 3.5 18.4 1.0 MN A:MN801 3.6 18.4 1.0 O3B A:DCP804 3.7 19.9 1.0 OD1 A:ASP467 3.9 11.0 1.0 O A:HOH975 3.9 20.2 1.0 O1G A:DCP804 4.0 13.8 1.0 N A:PHE363 4.0 11.1 1.0 NZ A:LYS525 4.0 15.2 1.0 CA A:PHE363 4.1 11.4 1.0 C5' A:DCP804 4.2 12.7 1.0 O5' A:DCP804 4.4 12.0 1.0 CB A:ASP362 4.4 8.3 1.0 CB A:PHE363 4.4 9.8 1.0 C A:ASP362 4.4 7.9 1.0 N A:ASP364 4.5 9.7 1.0 N A:PHE366 4.5 7.7 1.0 O2A A:DCP804 4.5 17.1 1.0 CB A:PHE366 4.5 6.0 1.0 O1B A:DCP804 4.6 12.1 1.0 N A:CYS365 4.6 10.7 1.0 O P:HOH207 4.6 12.5 1.0 CB A:ASP467 4.6 10.9 1.0 CE A:LYS525 4.6 14.2 1.0 CA A:ASP364 4.6 10.6 1.0 O2G A:DCP804 4.7 18.2 1.0 C A:ASP364 4.7 8.4 1.0 O A:ASP467 4.9 8.9 1.0 CA A:ASP362 4.9 10.3 1.0 O A:ASP362 4.9 11.8 1.0

Manganese binding site 4 out of 4 in the REV1 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 MN2+-Facilitated Product Complex with Second Dctp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn803 b:30.1 occ:1.00 O A:VAL553 2.1 18.9 1.0 O P:HOH212 2.3 19.8 1.0 OD2 A:ASP548 2.3 25.0 1.0 O A:ASP548 2.3 26.4 1.0 O A:HOH1130 2.4 33.3 1.0 O P:HOH203 2.7 30.4 1.0 C A:VAL553 3.3 24.4 1.0 C A:ASP548 3.3 22.4 1.0 CG A:ASP548 3.4 34.3 1.0 CA A:ASP548 3.7 22.6 1.0 CA A:GLY554 4.0 21.7 1.0 N A:GLY554 4.0 22.3 1.0 CB A:ASP548 4.1 23.1 1.0 O A:LEU550 4.1 25.4 1.0 OP1 P:DA11 4.2 37.5 1.0 OP2 P:DA11 4.3 31.6 1.0 OD1 A:ASP548 4.3 37.1 1.0 CA A:VAL553 4.4 21.0 1.0 O A:HOH953 4.5 39.2 1.0 N A:ASP549 4.5 16.1 1.0 N A:VAL553 4.6 30.9 1.0 CB A:VAL553 4.7 27.4 1.0 P P:DA11 4.8 36.1 1.0 N4 P:DC13 4.9 58.1 1.0 CA A:ASP549 4.9 18.8 1.0 C A:GLY554 5.0 25.1 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