Calcium in PDB 7t19: REV1 Ternary Complex with Dgtp and CA2+

The structure of REV1 Ternary Complex with Dgtp and CA2+, PDB code: 7t19 was solved by B.D.Freudenthal, T.M.Weaver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.59 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.183, 73.599, 117.098, 90, 90, 90
R / Rfree (%)	18.1 / 24.2

The binding sites of Calcium atom in the REV1 Ternary Complex with Dgtp and CA2+ (pdb code 7t19). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the REV1 Ternary Complex with Dgtp and CA2+, PDB code: 7t19:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the REV1 Ternary Complex with Dgtp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of REV1 Ternary Complex with Dgtp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca101 b:66.7 occ:1.00 O A:HOH904 2.7 52.2 1.0 C5' P:DG12 3.0 59.0 1.0 O3' P:DA11 3.6 72.4 1.0 C3' P:DA11 3.6 50.6 1.0 OP2 P:DG12 3.7 65.2 1.0 C2' P:DA11 3.7 48.7 1.0 O5' P:DG12 3.9 78.4 1.0 NH2 A:ARG518 3.9 56.6 1.0 O2A A:DGT802 4.0 47.2 0.7 P P:DG12 4.0 101.0 1.0 C4' P:DG12 4.0 58.1 1.0 C8 P:DG12 4.1 50.5 1.0 C3' P:DG12 4.3 59.2 1.0 O4' P:DG12 4.3 65.1 1.0 C2' P:DG12 4.4 52.5 1.0 CZ A:ARG518 4.7 51.0 1.0 C1' P:DG12 4.8 52.1 1.0 N2 A:DGT802 4.8 49.1 0.7 N9 P:DG12 4.8 45.2 1.0

Calcium binding site 2 out of 2 in the REV1 Ternary Complex with Dgtp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of REV1 Ternary Complex with Dgtp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:31.4 occ:0.42 O A:PHE363 2.3 26.2 1.0 O2B A:DGT802 2.4 39.3 0.7 OD2 A:ASP467 2.5 39.8 1.0 O1A A:DGT802 2.5 47.4 0.7 O3G A:DGT802 2.7 45.0 0.7 OD2 A:ASP362 3.0 38.9 1.0 C A:PHE363 3.3 25.0 1.0 CG A:ASP362 3.6 37.7 1.0 O A:HOH903 3.6 50.4 1.0 OD1 A:ASP362 3.6 41.2 1.0 PB A:DGT802 3.6 48.9 0.7 CG A:ASP467 3.6 30.4 1.0 PA A:DGT802 3.8 47.9 0.7 N A:PHE366 3.8 25.9 1.0 PG A:DGT802 3.8 50.2 0.7 O3B A:DGT802 4.0 40.2 0.7 CB A:PHE366 4.0 28.5 1.0 O3A A:DGT802 4.1 46.2 0.7 CA A:PHE363 4.1 27.0 1.0 N A:CYS365 4.1 25.9 1.0 CB A:PHE363 4.1 22.9 1.0 N A:PHE363 4.1 24.7 1.0 C5' A:DGT802 4.2 39.1 0.7 C A:ASP364 4.2 30.7 1.0 N A:ASP364 4.3 28.9 1.0 O2G A:DGT802 4.4 33.2 0.7 CA A:ASP364 4.4 26.9 1.0 OD1 A:ASP467 4.4 26.4 1.0 O5' A:DGT802 4.5 52.3 0.7 CA A:PHE366 4.5 21.9 1.0 NZ A:LYS525 4.5 42.2 1.0 CB A:ASP467 4.5 24.2 1.0 CA A:CYS365 4.7 22.8 1.0 C A:ASP362 4.7 23.9 1.0 C3' A:DGT802 4.7 30.5 0.7 C A:CYS365 4.7 21.2 1.0 O1B A:DGT802 4.8 31.1 0.7 CB A:ASP362 4.8 27.7 1.0 O A:ASP364 4.9 28.3 1.0 O2A A:DGT802 4.9 47.2 0.7 C4' A:DGT802 4.9 28.3 0.7 O A:ASP467 5.0 29.2 1.0

T.M.Weaver, T.H.Click, T.H.Khoang, M.Todd Washington, P.K.Agarwal, B.D.Freudenthal. Mechanism of Nucleotide Discrimination By the Translesion Synthesis Polymerase REV1. Nat Commun V. 13 2876 2022.
ISSN: ESSN 2041-1723
PubMed: 35610266
DOI: 10.1038/S41467-022-30577-0