Calcium in PDB 7t1a: REV1 Ternary Complex with Datp and CA2+

The structure of REV1 Ternary Complex with Datp and CA2+, PDB code: 7t1a 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)	24.65 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.136, 73.336, 115.446, 90, 90, 90
R / Rfree (%)	19.3 / 23

The binding sites of Calcium atom in the REV1 Ternary Complex with Datp and CA2+ (pdb code 7t1a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the REV1 Ternary Complex with Datp and CA2+, PDB code: 7t1a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the REV1 Ternary Complex with Datp 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 Datp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:25.9 occ:0.34 O A:LEU550 2.5 15.2 1.0 O A:VAL553 3.0 17.6 1.0 O A:ASP548 3.0 19.1 1.0 OP2 P:DA11 3.0 29.9 1.0 OP1 P:DA11 3.1 22.0 1.0 C A:LEU550 3.4 17.1 1.0 P P:DA11 3.5 25.2 1.0 C A:VAL553 3.7 18.1 1.0 N A:VAL553 3.8 14.5 1.0 C A:ASP548 3.8 17.8 1.0 CA A:PRO551 3.9 18.3 1.0 N A:PRO551 4.0 16.6 1.0 N A:GLY552 4.0 18.9 1.0 C A:ASP549 4.2 18.5 1.0 CA A:VAL553 4.2 16.1 1.0 N A:LEU550 4.3 19.3 1.0 C A:PRO551 4.3 19.3 1.0 O A:HOH927 4.4 34.3 1.0 O A:ASP549 4.4 20.6 1.0 CA A:ASP548 4.4 18.8 1.0 CA A:LEU550 4.5 16.9 1.0 CB A:VAL553 4.6 18.3 1.0 N A:GLY554 4.6 17.6 1.0 CA A:ASP549 4.7 15.4 1.0 N A:ASP549 4.7 18.1 1.0 O5' P:DA11 4.7 26.1 1.0 C A:GLY552 4.7 15.2 1.0 O3' P:DT10 4.8 17.9 1.0 CB A:ASP548 4.8 21.1 1.0 CA A:GLY552 4.9 15.0 1.0

Calcium binding site 2 out of 3 in the REV1 Ternary Complex with Datp 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 Datp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:27.2 occ:0.80 O2B A:DTP802 2.1 22.2 0.4 OD2 A:ASP467 2.4 30.0 1.0 O2A A:DTP802 2.4 25.7 0.4 O A:PHE363 2.4 17.4 1.0 O2B A:DTP802 2.4 22.0 0.3 O2A A:DTP802 2.4 23.9 0.3 O3G A:DTP802 2.6 20.6 0.3 OD2 A:ASP362 2.7 28.8 1.0 OD1 A:ASP362 2.8 30.6 1.0 O3G A:DTP802 2.8 25.0 0.4 CG A:ASP362 3.0 27.9 1.0 CA A:CA805 3.3 22.0 0.3 PB A:DTP802 3.4 24.5 0.4 CG A:ASP467 3.5 22.6 1.0 PB A:DTP802 3.6 24.5 0.3 C A:PHE363 3.6 20.6 1.0 PA A:DTP802 3.6 33.2 0.4 PA A:DTP802 3.6 29.2 0.3 O3A A:DTP802 3.7 25.6 0.4 PG A:DTP802 3.7 26.6 0.4 PG A:DTP802 3.8 23.7 0.3 O3A A:DTP802 3.8 25.3 0.3 O3B A:DTP802 3.9 24.0 0.4 C5' A:DTP802 3.9 27.6 0.3 O3B A:DTP802 4.0 22.1 0.3 O2G A:DTP802 4.0 18.1 0.4 OD1 A:ASP467 4.1 19.6 1.0 N A:PHE363 4.1 19.1 1.0 CA A:PHE363 4.2 20.4 1.0 C5' A:DTP802 4.2 25.3 0.4 O5' A:DTP802 4.3 31.1 0.3 CB A:PHE363 4.3 18.1 1.0 O2G A:DTP802 4.3 16.4 0.3 CB A:PHE366 4.4 18.8 1.0 O5' A:DTP802 4.4 31.4 0.4 N A:PHE366 4.4 14.1 1.0 CB A:ASP362 4.4 22.8 1.0 C A:ASP362 4.5 22.9 1.0 CB A:ASP467 4.6 14.7 1.0 O A:ASP467 4.6 17.6 1.0 N A:CYS365 4.6 18.5 1.0 N A:ASP364 4.6 16.6 1.0 O1B A:DTP802 4.7 17.6 0.4 O1A A:DTP802 4.8 31.1 0.4 CA A:ASP364 4.8 17.8 1.0 C A:ASP364 4.8 24.4 1.0 O1A A:DTP802 4.9 30.2 0.3 CA A:ASP362 4.9 18.3 1.0 O3' A:DTP802 4.9 19.5 0.3 O1B A:DTP802 4.9 17.9 0.3 O A:ASP362 5.0 29.3 1.0 C4' A:DTP802 5.0 25.6 0.3 C3' A:DTP802 5.0 23.7 0.4 O1G A:DTP802 5.0 29.4 0.3

Calcium binding site 3 out of 3 in the REV1 Ternary Complex with Datp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of REV1 Ternary Complex with Datp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:22.0 occ:0.29 O2A A:DTP802 2.1 25.7 0.4 OD1 A:ASP467 2.4 19.6 1.0 O2A A:DTP802 2.5 23.9 0.3 OE2 A:GLU468 2.6 27.9 1.0 OD1 A:ASP362 2.7 30.6 1.0 O3' P:DG12 2.9 32.0 1.0 OD2 A:ASP467 3.0 30.0 1.0 C3' P:DG12 3.0 34.9 1.0 CG A:ASP467 3.1 22.6 1.0 PA A:DTP802 3.2 33.2 0.4 C5' A:DTP802 3.3 27.6 0.3 CA A:CA804 3.3 27.2 0.8 C5' A:DTP802 3.5 25.3 0.4 PA A:DTP802 3.5 29.2 0.3 O5' A:DTP802 3.6 31.4 0.4 OG A:SER465 3.7 22.3 1.0 O5' A:DTP802 3.7 31.1 0.3 CG A:ASP362 3.7 27.9 1.0 CB A:GLU468 3.7 18.6 1.0 CD A:GLU468 3.8 22.8 1.0 C4' P:DG12 3.9 38.3 1.0 O1A A:DTP802 3.9 31.1 0.4 OD2 A:ASP362 4.0 28.8 1.0 C5' P:DG12 4.1 36.5 1.0 O1A A:DTP802 4.3 30.2 0.3 CG A:GLU468 4.3 17.8 1.0 O A:ASP467 4.3 17.6 1.0 C2' P:DG12 4.3 31.7 1.0 C A:ASP467 4.5 15.4 1.0 CB A:ASP467 4.5 14.7 1.0 O3G A:DTP802 4.6 25.0 0.4 O3A A:DTP802 4.6 25.6 0.4 O2B A:DTP802 4.7 22.2 0.4 C4' A:DTP802 4.7 25.6 0.3 OE1 A:GLU468 4.8 22.4 1.0 O2B A:DTP802 4.8 22.0 0.3 CB A:SER465 4.8 14.6 1.0 O3G A:DTP802 4.8 20.6 0.3 CA A:GLU468 4.9 14.0 1.0 O3A A:DTP802 4.9 25.3 0.3 N A:GLU468 4.9 12.2 1.0 CB A:ASP362 4.9 22.8 1.0 C4' A:DTP802 5.0 25.0 0.4 CA A:ASP467 5.0 13.0 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