Calcium in PDB 7t18: REV1 Ternary Complex with Dttp and CA2+

The structure of REV1 Ternary Complex with Dttp and CA2+, PDB code: 7t18 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)	24.66 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.202, 73.639, 117.766, 90, 90, 90
R / Rfree (%)	18.2 / 22.5

The binding sites of Calcium atom in the REV1 Ternary Complex with Dttp and CA2+ (pdb code 7t18). 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 Dttp and CA2+, PDB code: 7t18:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the REV1 Ternary Complex with Dttp 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 Dttp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:11.0 occ:1.00 O1B A:TTP805 2.3 11.4 1.0 OD1 A:ASP362 2.3 18.1 1.0 O A:PHE363 2.4 11.0 1.0 OD2 A:ASP467 2.4 8.4 1.0 O1G A:TTP805 2.4 11.0 1.0 O1A A:TTP805 2.4 10.1 1.0 OD2 A:ASP362 2.7 15.7 1.0 CG A:ASP362 2.8 12.9 1.0 PB A:TTP805 3.5 10.8 1.0 CG A:ASP467 3.5 9.6 1.0 C A:PHE363 3.5 12.4 1.0 CA A:CA802 3.6 12.4 0.4 PA A:TTP805 3.6 11.7 1.0 PG A:TTP805 3.6 12.1 1.0 O3A A:TTP805 3.8 11.3 1.0 O3B A:TTP805 3.9 8.5 1.0 OD1 A:ASP467 3.9 10.7 1.0 N A:PHE363 4.0 8.9 1.0 O A:HOH1204 4.1 25.1 1.0 C5' A:TTP805 4.2 11.7 1.0 NZ A:LYS525 4.2 17.8 1.0 O2G A:TTP805 4.2 15.0 1.0 CA A:PHE363 4.2 8.9 1.0 CB A:ASP362 4.3 11.7 1.0 O5' A:TTP805 4.4 11.6 1.0 C A:ASP362 4.4 9.4 1.0 CB A:PHE363 4.5 11.7 1.0 N A:ASP364 4.6 8.3 1.0 N A:PHE366 4.6 7.8 1.0 CB A:PHE366 4.7 9.5 1.0 CB A:ASP467 4.7 9.1 1.0 CE A:LYS525 4.7 17.6 1.0 N A:CYS365 4.7 13.0 1.0 O2A A:TTP805 4.7 14.3 1.0 CA A:ASP364 4.8 11.0 1.0 CA A:ASP362 4.8 8.8 1.0 O A:ASP467 4.8 8.4 1.0 O2B A:TTP805 4.8 9.7 1.0 C A:ASP364 4.9 9.7 1.0 O3G A:TTP805 4.9 13.4 1.0

Calcium binding site 2 out of 3 in the REV1 Ternary Complex with Dttp 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 Dttp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:12.4 occ:0.38 OD1 A:ASP467 2.4 10.7 1.0 O3' P:DG12 2.5 33.2 1.0 OD2 A:ASP362 2.5 15.7 1.0 O1A A:TTP805 2.6 10.1 1.0 OE2 A:GLU468 2.6 20.0 1.0 CG A:ASP467 3.3 9.6 1.0 OD2 A:ASP467 3.4 8.4 1.0 CB A:GLU468 3.6 9.2 1.0 CA A:CA801 3.6 11.0 1.0 O A:HOH1304 3.6 31.1 1.0 OG A:SER465 3.6 13.1 0.7 PA A:TTP805 3.7 11.7 1.0 CD A:GLU468 3.7 18.3 1.0 C3' P:DG12 3.7 37.7 1.0 CG A:ASP362 3.7 12.9 1.0 O5' A:TTP805 3.9 11.6 1.0 C5' A:TTP805 3.9 11.7 1.0 CG A:GLU468 4.2 10.4 1.0 O2A A:TTP805 4.2 14.3 1.0 OD1 A:ASP362 4.4 18.1 1.0 CB A:SER465 4.5 13.8 0.3 O A:HOH1204 4.6 25.1 1.0 C A:ASP467 4.6 9.0 1.0 O A:ASP467 4.6 8.4 1.0 C4' P:DG12 4.6 33.2 1.0 CB A:SER465 4.6 13.9 0.7 CB A:ASP467 4.7 9.1 1.0 OE1 A:GLU468 4.7 14.2 1.0 CA A:GLU468 4.7 8.2 1.0 OG A:SER465 4.7 14.6 0.3 N A:GLU468 4.8 7.8 1.0 C2' P:DG12 4.8 41.3 1.0 CB A:ASP362 4.8 11.7 1.0 C5' P:DG12 5.0 33.8 1.0

Calcium binding site 3 out of 3 in the REV1 Ternary Complex with Dttp 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 Dttp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:23.1 occ:0.39 O A:LEU550 2.5 13.8 1.0 O P:HOH125 2.5 37.9 1.0 OP1 P:DA11 2.6 23.4 1.0 O A:VAL553 2.8 17.2 1.0 O A:ASP548 2.8 20.6 1.0 O A:HOH943 2.9 35.4 1.0 C A:LEU550 3.5 21.8 1.0 O A:HOH1068 3.6 31.3 1.0 P P:DA11 3.6 18.1 1.0 C A:VAL553 3.7 21.9 1.0 C A:ASP548 3.7 19.9 1.0 OP2 P:DA11 3.8 22.3 1.0 N A:VAL553 3.8 15.1 1.0 CA A:PRO551 4.1 22.0 1.0 N A:GLY552 4.1 19.7 1.0 N A:PRO551 4.2 16.8 1.0 C A:ASP549 4.2 18.4 1.0 CA A:VAL553 4.2 18.1 1.0 N A:LEU550 4.3 14.9 1.0 O A:ASP549 4.3 20.1 1.0 CA A:ASP548 4.4 17.0 1.0 C A:PRO551 4.4 18.8 1.0 O3' P:DT10 4.5 17.8 1.0 CB A:VAL553 4.5 16.2 1.0 CA A:LEU550 4.5 19.7 1.0 N A:ASP549 4.6 16.2 1.0 CA A:ASP549 4.6 14.9 1.0 CB A:ASP548 4.7 21.0 1.0 N A:GLY554 4.7 14.9 1.0 C A:GLY552 4.8 15.8 1.0 O5' P:DA11 4.9 19.6 1.0 O A:HOH1303 4.9 42.9 1.0 CA A:GLY552 5.0 17.7 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