Calcium in PDB 3gik: DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair

All present enzymatic activity of DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair:
2.7.7.7;

The structure of DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair, PDB code: 3gik was solved by O.Rechkoblit, L.Malinina, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.855, 112.399, 52.834, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.7

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair (pdb code 3gik). 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 the Oxog(Anti)-C(Anti) Pair, PDB code: 3gik:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair


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 the Oxog(Anti)-C(Anti) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:44.9 occ:1.00 O A:HOH502 2.3 2.0 1.0 OE2 A:GLU106 2.3 43.8 1.0 CD A:GLU106 2.3 43.8 1.0 OD2 A:ASP7 2.3 42.7 1.0 O D:HOH503 2.6 2.0 1.0 OE1 A:GLU106 2.9 42.2 1.0 CG A:GLU106 3.0 42.1 1.0 CG A:ASP7 3.0 43.2 1.0 OP1 D:DOC13 3.1 21.9 1.0 OD1 A:ASP7 3.3 45.7 1.0 C5' D:DOC13 3.5 29.8 1.0 OD1 A:ASP105 3.5 42.7 1.0 OD2 A:ASP105 3.7 44.0 1.0 O5' D:DOC13 3.7 29.4 1.0 O2A A:DGT414 3.8 41.8 1.0 P D:DOC13 3.9 27.0 1.0 CG A:ASP105 4.1 42.2 1.0 O1A A:DGT414 4.2 37.4 1.0 CA A:CA416 4.3 46.5 1.0 CB A:ASP7 4.3 42.3 1.0 CB A:GLU106 4.4 42.4 1.0 C3' D:DOC13 4.5 30.0 1.0 C4' D:DOC13 4.5 30.0 1.0 PA A:DGT414 4.6 38.1 1.0 OP2 D:DOC13 4.6 26.6 1.0 O D:HOH537 4.8 21.7 1.0 NZ A:LYS152 4.9 43.7 1.0

Calcium binding site 2 out of 3 in the DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair


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 the Oxog(Anti)-C(Anti) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca416 b:46.5 occ:1.00 OD1 A:ASP7 2.3 45.7 1.0 O2A A:DGT414 2.3 41.8 1.0 O1B A:DGT414 2.3 44.2 1.0 O A:PHE8 2.3 43.3 1.0 OD2 A:ASP105 2.3 44.0 1.0 O1G A:DGT414 2.3 48.3 1.0 CG A:ASP7 3.2 43.2 1.0 O3G A:DGT414 3.2 50.4 1.0 NZ A:LYS159 3.4 47.2 1.0 CG A:ASP105 3.5 42.2 1.0 OD2 A:ASP7 3.5 42.7 1.0 C A:PHE8 3.5 42.4 1.0 PG A:DGT414 3.6 50.5 1.0 PB A:DGT414 3.6 39.1 1.0 PA A:DGT414 3.7 38.1 1.0 N A:PHE8 4.0 42.2 1.0 C A:ASP7 4.0 42.0 1.0 O A:ASP7 4.0 43.1 1.0 O3B A:DGT414 4.1 44.0 1.0 OD1 A:ASP105 4.3 42.7 1.0 CA A:CA415 4.3 44.9 1.0 O3A A:DGT414 4.3 38.6 1.0 CB A:ASP105 4.3 42.0 1.0 O A:HOH502 4.3 2.0 1.0 CA A:PHE8 4.3 42.2 1.0 CB A:ASP7 4.4 42.3 1.0 N A:ASP9 4.5 42.2 1.0 O1A A:DGT414 4.5 37.4 1.0 CE A:LYS159 4.5 48.0 1.0 CA A:ASP9 4.5 42.4 1.0 C5' A:DGT414 4.5 32.7 1.0 CA A:ASP7 4.7 41.9 1.0 O2G A:DGT414 4.7 48.1 1.0 O2B A:DGT414 4.7 40.8 1.0 O5' A:DGT414 4.7 35.8 1.0 N A:TYR10 4.8 42.6 1.0 C A:ASP9 4.9 42.4 1.0 N A:PHE11 4.9 43.5 1.0

Calcium binding site 3 out of 3 in the DPO4 Extension Ternary Complex with the Oxog(Anti)-C(Anti) Pair


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 the Oxog(Anti)-C(Anti) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca417 b:51.2 occ:1.00 O A:HOH505 2.3 2.0 1.0 O A:ILE186 2.3 45.1 1.0 O A:ALA181 2.3 47.6 1.0 O A:HOH504 2.6 6.9 1.0 O A:HOH506 3.2 36.4 1.0 C A:ALA181 3.4 46.9 1.0 C A:ILE186 3.5 43.4 1.0 CA A:ALA181 4.1 46.6 1.0 CB A:ALA181 4.2 46.4 1.0 N A:ASP182 4.3 46.9 1.0 OP2 D:DG12 4.4 32.4 1.0 CB A:ILE186 4.4 42.8 1.0 N A:GLY187 4.4 43.4 1.0 CA A:GLY187 4.4 43.0 1.0 CA A:ILE186 4.4 43.1 1.0 CA A:ASP182 4.6 46.6 1.0 CG2 A:ILE186 4.7 41.8 1.0 C A:GLY187 4.7 42.9 1.0 O A:VAL183 4.8 45.7 1.0 O A:GLY187 4.9 42.7 1.0

O.Rechkoblit, L.Malinina, Y.Cheng, N.E.Geacintov, S.Broyde, D.J.Patel. Impact of Conformational Heterogeneity of Oxog Lesions and Their Pairing Partners on Bypass Fidelity By Y Family Polymerases. Structure V. 17 725 2009.
ISSN: ISSN 0969-2126
PubMed: 19446528
DOI: 10.1016/J.STR.2009.03.011