Calcium in PDB 6x77: REV1 R518A Ternary Complex with Dctp and CA2+

The structure of REV1 R518A Ternary Complex with Dctp and CA2+, PDB code: 6x77 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)	24.89 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.258, 73.771, 116.811, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.1

The binding sites of Calcium atom in the REV1 R518A Ternary Complex with Dctp and CA2+ (pdb code 6x77). 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 R518A Ternary Complex with Dctp and CA2+, PDB code: 6x77:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the REV1 R518A 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 R518A Ternary Complex with Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:9.7 occ:0.48 O1A A:DCP804 2.2 9.4 1.0 OD1 A:ASP467 2.4 10.0 1.0 OE2 A:GLU468 2.4 11.6 1.0 O3' P:DG12 2.4 18.0 1.0 OD1 A:ASP362 2.5 11.9 1.0 HB2 A:GLU468 2.8 10.5 1.0 HG A:SER465 3.0 14.2 0.6 CG A:ASP467 3.2 10.3 1.0 OD2 A:ASP467 3.3 9.8 1.0 C3' P:DG12 3.3 14.3 1.0 PA A:DCP804 3.4 9.7 1.0 CA A:CA803 3.4 10.5 1.0 CD A:GLU468 3.5 15.3 1.0 H5'2 A:DCP804 3.5 11.9 1.0 CB A:GLU468 3.6 8.7 1.0 HB3 A:GLU468 3.6 10.5 1.0 OG A:SER465 3.6 11.8 0.6 CG A:ASP362 3.7 13.1 1.0 HB3 A:SER465 3.7 13.8 0.4 H5'1 A:DCP804 3.7 11.9 1.0 O5' A:DCP804 3.8 10.1 1.0 C5' A:DCP804 3.9 9.8 1.0 O A:HOH1203 4.0 36.8 1.0 CG A:GLU468 4.1 9.9 1.0 O2A A:DCP804 4.1 9.3 1.0 HB2 A:SER465 4.3 13.8 0.4 C4' P:DG12 4.3 18.3 1.0 CB A:SER465 4.3 11.4 0.4 C5' P:DG12 4.4 14.9 1.0 OD2 A:ASP362 4.4 11.3 1.0 HG3 A:GLU468 4.4 12.0 1.0 C2' P:DG12 4.5 17.3 1.0 OE1 A:GLU468 4.5 13.7 1.0 OG A:SER465 4.5 6.6 0.4 HB2 A:ASP362 4.5 13.3 1.0 H A:ASP467 4.6 10.1 1.0 O A:HOH1112 4.6 21.5 1.0 C A:ASP467 4.6 9.9 1.0 O A:ASP467 4.6 8.8 1.0 CB A:ASP467 4.6 11.8 1.0 O3A A:DCP804 4.7 9.7 1.0 CB A:ASP362 4.7 11.0 1.0 CA A:GLU468 4.8 10.6 1.0 N A:GLU468 4.8 8.0 1.0 CB A:SER465 4.9 9.3 0.6 O1G A:DCP804 4.9 9.5 1.0 O1B A:DCP804 4.9 8.4 1.0 HG2 A:GLU468 4.9 12.0 1.0 HB3 A:SER465 4.9 11.3 0.6

Calcium binding site 2 out of 3 in the REV1 R518A 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 R518A Ternary Complex with Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:43.7 occ:1.00 OP1 P:DA11 2.6 16.6 1.0 O A:HOH1177 2.7 30.6 1.0 O P:HOH112 2.7 31.1 1.0 O A:ASP548 2.8 15.3 1.0 O A:VAL553 2.8 14.3 1.0 O A:LEU550 2.8 13.1 1.0 O A:HOH916 2.9 23.5 1.0 H A:VAL553 3.4 15.5 1.0 HA A:PRO551 3.5 21.6 1.0 P P:DA11 3.6 15.1 1.0 OP2 P:DA11 3.7 15.8 1.0 C A:LEU550 3.7 13.3 1.0 H A:GLY552 3.7 16.6 1.0 C A:ASP548 3.7 17.4 1.0 C A:VAL553 3.7 15.0 1.0 O P:HOH127 3.7 24.9 1.0 N A:VAL553 4.0 12.8 1.0 HA A:ASP548 4.0 22.5 1.0 HB2 A:ASP548 4.0 16.9 1.0 HB A:VAL553 4.0 15.2 1.0 CA A:PRO551 4.1 17.9 1.0 N A:GLY552 4.2 13.8 1.0 N A:PRO551 4.3 16.9 1.0 HA A:ASP549 4.3 15.7 1.0 C A:ASP549 4.3 13.6 1.0 CA A:ASP548 4.4 18.7 1.0 CA A:VAL553 4.4 13.9 1.0 N A:LEU550 4.5 13.9 1.0 HA2 A:GLY554 4.5 14.7 1.0 C A:PRO551 4.5 18.9 1.0 O A:ASP549 4.5 13.6 1.0 O3' P:DT10 4.6 14.6 1.0 N A:ASP549 4.6 14.9 1.0 CA A:ASP549 4.6 13.1 1.0 N A:GLY554 4.7 12.3 1.0 CB A:ASP548 4.7 14.0 1.0 CB A:VAL553 4.7 12.6 1.0 CA A:LEU550 4.7 15.5 1.0 O5' P:DA11 4.7 13.7 1.0 C A:GLY552 4.9 14.7 1.0

Calcium binding site 3 out of 3 in the REV1 R518A 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 R518A Ternary Complex with Dctp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:10.5 occ:1.00 O1B A:DCP804 2.3 8.4 1.0 O A:PHE363 2.3 10.8 1.0 OD2 A:ASP467 2.4 9.8 1.0 O1A A:DCP804 2.4 9.4 1.0 OD2 A:ASP362 2.4 11.3 1.0 O1G A:DCP804 2.5 9.5 1.0 OD1 A:ASP362 2.6 11.9 1.0 CG A:ASP362 2.8 13.1 1.0 H5'1 A:DCP804 3.3 11.9 1.0 PB A:DCP804 3.4 10.1 1.0 CA A:CA801 3.4 9.7 0.5 CG A:ASP467 3.5 10.3 1.0 PA A:DCP804 3.5 9.7 1.0 C A:PHE363 3.5 14.0 1.0 O3A A:DCP804 3.6 9.7 1.0 PG A:DCP804 3.6 10.7 1.0 HZ2 A:LYS525 3.6 18.7 1.0 HB2 A:PHE366 3.8 10.6 1.0 O3B A:DCP804 3.9 11.1 1.0 HZ3 A:LYS525 3.9 18.7 1.0 H A:PHE366 3.9 9.8 1.0 OD1 A:ASP467 3.9 10.0 1.0 HB2 A:PHE363 4.0 13.0 1.0 H A:PHE363 4.0 13.5 1.0 N A:PHE363 4.0 11.2 1.0 O2G A:DCP804 4.2 12.9 1.0 NZ A:LYS525 4.2 15.6 1.0 C5' A:DCP804 4.2 9.8 1.0 O A:HOH1112 4.2 21.5 1.0 CA A:PHE363 4.3 15.3 1.0 CB A:ASP362 4.3 11.0 1.0 HA A:ASP364 4.3 15.1 1.0 HE3 A:LYS525 4.4 15.1 1.0 O5' A:DCP804 4.4 10.1 1.0 C A:ASP362 4.4 10.5 1.0 H5'2 A:DCP804 4.5 11.9 1.0 H A:CYS365 4.5 16.6 1.0 CB A:PHE363 4.6 10.8 1.0 N A:ASP364 4.6 11.9 1.0 HB2 A:ASP467 4.6 14.2 1.0 CB A:PHE366 4.6 8.8 1.0 HB3 A:PHE366 4.6 10.6 1.0 N A:PHE366 4.6 8.1 1.0 N A:CYS365 4.7 13.8 1.0 O2A A:DCP804 4.7 9.3 1.0 CB A:ASP467 4.7 11.8 1.0 HB3 A:ASP362 4.7 13.3 1.0 O2B A:DCP804 4.8 7.9 1.0 HB2 A:ASP362 4.8 13.3 1.0 CA A:ASP364 4.8 12.5 1.0 HB3 A:PHE363 4.8 13.0 1.0 CA A:ASP362 4.8 8.1 1.0 HB2 A:GLU468 4.8 10.5 1.0 O A:ASP467 4.8 8.8 1.0 CE A:LYS525 4.9 12.5 1.0 HZ1 A:LYS525 4.9 18.7 1.0 HA A:ASP362 4.9 9.8 1.0 O3G A:DCP804 4.9 7.8 1.0 HA A:CYS365 4.9 9.7 1.0 O A:ASP362 5.0 11.7 1.0 C A:ASP364 5.0 15.9 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