Calcium in PDB 3rb3: DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion:
2.7.7.7;

The structure of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rb3 was solved by O.Rechkoblit, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.188, 110.366, 51.874, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.4

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion (pdb code 3rb3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rb3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:49.0 occ:1.00 OE2 A:GLU106 2.3 59.0 1.0 OD2 A:ASP7 2.4 58.2 1.0 O2A A:DGT414 2.4 63.1 1.0 O A:HOH344 2.9 24.3 1.0 OD1 A:ASP7 2.9 52.3 1.0 CG A:ASP7 2.9 50.4 1.0 OD2 A:ASP105 3.1 49.3 1.0 OD1 A:ASP105 3.2 49.7 1.0 CD A:GLU106 3.2 56.6 1.0 PA A:DGT414 3.5 56.2 1.0 CG A:ASP105 3.5 47.8 1.0 O1A A:DGT414 3.6 57.8 1.0 CA A:CA416 3.6 40.7 1.0 OE1 A:GLU106 3.7 58.7 1.0 O5' A:DGT414 4.2 53.5 1.0 CB A:ASP7 4.3 49.3 1.0 CG A:GLU106 4.3 53.6 1.0 CB A:GLU106 4.4 50.5 1.0 NZ A:LYS159 4.5 52.1 1.0 O1G A:DGT414 4.6 66.0 1.0 O3' D:DG813 4.6 53.2 1.0 C5' A:DGT414 4.7 49.4 1.0 NZ A:LYS152 4.7 56.0 1.0 O3A A:DGT414 4.9 57.9 1.0 O A:HOH368 4.9 64.0 1.0 OG A:SER103 5.0 45.2 1.0

Calcium binding site 2 out of 3 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca416 b:40.7 occ:1.00 OD1 A:ASP7 2.3 52.3 1.0 OD2 A:ASP105 2.3 49.3 1.0 O A:PHE8 2.3 47.5 1.0 O1G A:DGT414 2.3 66.0 1.0 O2A A:DGT414 2.3 63.1 1.0 O1B A:DGT414 2.3 59.2 1.0 PG A:DGT414 3.0 70.2 1.0 CG A:ASP7 3.0 50.4 1.0 OD2 A:ASP7 3.4 58.2 1.0 PB A:DGT414 3.4 57.5 1.0 C A:PHE8 3.4 46.0 1.0 PA A:DGT414 3.5 56.2 1.0 CG A:ASP105 3.5 47.8 1.0 O A:HOH353 3.6 39.4 1.0 CA A:CA415 3.6 49.0 1.0 O3B A:DGT414 3.8 64.2 1.0 O3A A:DGT414 3.8 57.9 1.0 N A:PHE8 3.9 46.5 1.0 O3G A:DGT414 4.1 71.2 1.0 C A:ASP7 4.1 47.7 1.0 NZ A:LYS159 4.1 52.1 1.0 O2G A:DGT414 4.2 71.2 1.0 C5' A:DGT414 4.2 49.4 1.0 CB A:ASP7 4.2 49.3 1.0 CA A:PHE8 4.2 46.5 1.0 O5' A:DGT414 4.3 53.5 1.0 OD1 A:ASP105 4.4 49.7 1.0 N A:ASP9 4.4 45.7 1.0 CB A:ASP105 4.4 46.0 1.0 O A:ASP7 4.5 48.9 1.0 CA A:ASP9 4.5 44.6 1.0 N A:TYR10 4.6 42.6 1.0 CA A:ASP7 4.6 48.6 1.0 O1A A:DGT414 4.6 57.8 1.0 C A:ASP9 4.7 43.6 1.0 O2B A:DGT414 4.7 57.5 1.0 N A:PHE11 4.8 40.6 1.0 CB A:PHE11 4.9 39.5 1.0 CB A:PHE8 4.9 45.7 1.0

Calcium binding site 3 out of 3 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca417 b:50.3 occ:1.00 O A:ALA181 2.3 74.6 1.0 O A:ILE186 2.4 73.5 1.0 O A:HOH343 2.4 18.1 1.0 C A:ILE186 3.5 71.6 1.0 C A:ALA181 3.5 75.2 1.0 OP2 D:DG813 3.6 62.1 1.0 CA A:GLY187 3.8 69.0 1.0 N A:GLY187 4.1 71.1 1.0 OP1 D:DG813 4.2 61.5 1.0 CA A:ALA181 4.2 78.0 1.0 C A:GLY187 4.4 71.0 1.0 P D:DG813 4.4 60.7 1.0 N A:ASP182 4.5 74.8 1.0 O D:HOH1 4.5 24.4 1.0 O A:GLY187 4.6 73.6 1.0 CB A:ALA181 4.6 78.0 1.0 O A:VAL183 4.7 68.6 1.0 CA A:ILE186 4.7 72.8 1.0 CA A:ASP182 4.8 71.4 1.0

O.Rechkoblit, J.C.Delaney, J.M.Essigmann, D.J.Patel. Implications For Damage Recognition During DPO4-Mediated Mutagenic Bypass of M1G and M3C Lesions. Structure V. 19 821 2011.
ISSN: ISSN 0969-2126
PubMed: 21645853
DOI: 10.1016/J.STR.2011.03.020