Calcium in PDB 6x6z: REV1 Ternary Complex with Dctp and CA2+

The structure of REV1 Ternary Complex with Dctp and CA2+, PDB code: 6x6z 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)	35.26 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.376, 73.947, 117.290, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 20.7

The binding sites of Calcium atom in the REV1 Ternary Complex with Dctp and CA2+ (pdb code 6x6z). 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 Dctp and CA2+, PDB code: 6x6z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the REV1 Ternary Complex with Dctp 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 Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca101 b:12.0 occ:0.55 OE2 A:GLU468 2.2 14.4 1.0 OD1 A:ASP362 2.3 13.7 1.0 O2A A:DCP801 2.4 12.2 1.0 OD1 A:ASP467 2.4 12.2 1.0 O3' P:DG12 2.5 14.5 1.0 O A:HOH1197 3.0 28.1 1.0 CG A:ASP467 3.1 13.1 1.0 OD2 A:ASP467 3.2 12.8 1.0 CD A:GLU468 3.3 13.4 1.0 CA A:CA803 3.4 11.8 1.0 C3' P:DG12 3.5 13.1 1.0 CB A:GLU468 3.5 13.9 1.0 PA A:DCP801 3.5 12.2 1.0 CG A:ASP362 3.6 11.9 1.0 O5' A:DCP801 3.9 11.0 1.0 C5' A:DCP801 3.9 11.5 1.0 CG A:GLU468 3.9 14.6 1.0 O1A A:DCP801 4.2 13.8 1.0 OE1 A:GLU468 4.2 16.1 1.0 OD2 A:ASP362 4.3 13.1 1.0 C4' P:DG12 4.3 13.0 1.0 CB A:SER465 4.3 15.9 1.0 C5' P:DG12 4.4 14.6 1.0 O A:HOH1124 4.5 18.6 1.0 OG A:SER465 4.6 19.6 1.0 C A:ASP467 4.6 12.1 1.0 CB A:ASP467 4.6 12.9 1.0 O A:ASP467 4.6 11.6 1.0 C2' P:DG12 4.6 16.5 1.0 CB A:ASP362 4.6 12.8 1.0 O A:HOH1030 4.7 38.1 1.0 CA A:GLU468 4.7 12.1 1.0 N A:GLU468 4.8 11.4 1.0 O3G A:DCP801 4.9 12.7 1.0 O2B A:DCP801 4.9 11.2 1.0 O3A A:DCP801 4.9 12.6 1.0

Calcium binding site 2 out of 3 in the REV1 Ternary Complex with Dctp 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 Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca102 b:16.5 occ:0.56 O A:HOH1384 2.5 27.4 1.0 O A:ASP548 2.5 16.1 1.0 O A:VAL553 2.5 16.3 1.0 O A:LEU550 2.5 16.6 1.0 O P:HOH219 2.5 21.7 1.0 OP1 P:DA11 2.6 16.5 1.0 O A:HOH1035 3.3 32.4 1.0 C A:ASP548 3.5 17.7 1.0 C A:VAL553 3.5 15.8 1.0 C A:LEU550 3.5 16.1 1.0 P P:DA11 3.6 13.8 1.0 OP2 P:DA11 3.8 14.9 1.0 N A:VAL553 3.8 15.3 1.0 O P:HOH239 3.9 31.9 1.0 CA A:PRO551 4.1 16.5 1.0 CA A:VAL553 4.1 15.6 1.0 CA A:ASP548 4.1 20.1 1.0 N A:GLY552 4.1 15.6 1.0 C A:ASP549 4.2 15.5 1.0 N A:LEU550 4.2 15.8 1.0 N A:PRO551 4.2 16.4 1.0 CB A:ASP548 4.3 18.2 1.0 O A:ASP549 4.4 18.2 1.0 O A:HOH914 4.4 43.1 1.0 CB A:VAL553 4.4 17.3 1.0 N A:ASP549 4.5 14.3 1.0 CA A:LEU550 4.5 17.4 1.0 C A:PRO551 4.5 19.5 1.0 N A:GLY554 4.5 14.8 1.0 O3' P:DT10 4.6 13.5 1.0 CA A:ASP549 4.6 15.3 1.0 C A:GLY552 4.8 15.8 1.0 O A:HOH1251 4.8 27.5 1.0 O5' P:DA11 4.8 14.2 1.0 CA A:GLY554 4.9 15.6 1.0

Calcium binding site 3 out of 3 in the REV1 Ternary Complex with Dctp 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 Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:11.8 occ:1.00 O2B A:DCP801 2.3 11.2 1.0 O A:PHE363 2.3 12.2 1.0 O2A A:DCP801 2.3 12.2 1.0 OD2 A:ASP467 2.3 12.8 1.0 OD2 A:ASP362 2.4 13.1 1.0 O3G A:DCP801 2.4 12.7 1.0 OD1 A:ASP362 2.6 13.7 1.0 CG A:ASP362 2.8 11.9 1.0 CA P:CA101 3.4 12.0 0.6 PB A:DCP801 3.4 12.2 1.0 CG A:ASP467 3.5 13.1 1.0 C A:PHE363 3.5 11.7 1.0 PA A:DCP801 3.5 12.2 1.0 PG A:DCP801 3.6 12.8 1.0 O3A A:DCP801 3.7 12.6 1.0 O3B A:DCP801 3.9 11.8 1.0 N A:PHE363 4.0 11.2 1.0 OD1 A:ASP467 4.0 12.2 1.0 O A:HOH1124 4.0 18.6 1.0 NZ A:LYS525 4.1 12.7 1.0 C5' A:DCP801 4.2 11.5 1.0 O1G A:DCP801 4.2 13.5 1.0 CA A:PHE363 4.2 12.1 1.0 CB A:ASP362 4.2 12.8 1.0 C A:ASP362 4.4 11.5 1.0 O5' A:DCP801 4.4 11.0 1.0 CB A:PHE363 4.5 12.2 1.0 N A:ASP364 4.6 12.4 1.0 CB A:PHE366 4.6 12.6 1.0 N A:PHE366 4.7 11.7 1.0 O A:HOH1197 4.7 28.1 1.0 CB A:ASP467 4.7 12.9 1.0 N A:CYS365 4.7 11.8 1.0 O1A A:DCP801 4.7 13.8 1.0 O1B A:DCP801 4.8 11.4 1.0 CA A:ASP364 4.8 12.5 1.0 CA A:ASP362 4.8 12.8 1.0 CE A:LYS525 4.8 14.0 1.0 C A:ASP364 4.8 11.9 1.0 O A:ASP467 4.9 11.6 1.0 O2G A:DCP801 4.9 13.6 1.0 O A:ASP362 4.9 13.6 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