Calcium in PDB 3gim: DPO4 Extension Ternary Complex with Oxog(Anti)-G(Syn) Pair

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

The structure of DPO4 Extension Ternary Complex with Oxog(Anti)-G(Syn) Pair, PDB code: 3gim 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.668, 111.924, 53.158, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.7

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

Calcium binding site 1 out of 3 in the DPO4 Extension Ternary Complex with Oxog(Anti)-G(Syn) 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 Oxog(Anti)-G(Syn) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:46.5 occ:1.00 O2A A:DGT414 2.3 44.1 1.0 OD1 A:ASP105 2.3 47.2 1.0 OD2 A:ASP7 2.3 49.1 1.0 OE2 A:GLU106 2.3 48.7 1.0 OD1 A:ASP7 2.5 48.0 1.0 O D:HOH373 2.6 36.8 1.0 CG A:ASP7 2.7 50.4 1.0 C3' D:DDG814 3.3 87.0 1.0 CD A:GLU106 3.3 51.6 1.0 CG A:ASP105 3.3 49.1 1.0 CA A:CA416 3.4 44.3 1.0 OD2 A:ASP105 3.5 48.6 1.0 C5' D:DDG814 3.7 83.3 1.0 PA A:DGT414 3.7 41.8 1.0 OE1 A:GLU106 3.9 55.5 1.0 C4' D:DDG814 3.9 86.6 1.0 O1A A:DGT414 4.0 41.4 1.0 CB A:GLU106 4.0 51.8 1.0 O A:HOH375 4.1 55.7 1.0 O5' D:DDG814 4.1 79.9 1.0 CB A:ASP7 4.1 48.5 1.0 OG A:SER103 4.1 54.6 1.0 CG A:GLU106 4.2 50.8 1.0 O5' A:DGT414 4.4 41.7 1.0 C5' A:DGT414 4.6 43.6 1.0 C2' D:DDG814 4.6 87.8 1.0 CB A:ASP105 4.7 50.6 1.0 O1G A:DGT414 4.7 44.0 1.0 C A:ASP105 4.7 51.7 1.0 NZ A:LYS159 4.7 60.0 1.0 O A:ASP105 4.8 52.6 1.0 CA A:ASP7 4.9 48.5 1.0 N A:GLU106 4.9 51.6 1.0 O3A A:DGT414 4.9 40.6 1.0

Calcium binding site 2 out of 3 in the DPO4 Extension Ternary Complex with Oxog(Anti)-G(Syn) 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 Oxog(Anti)-G(Syn) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca416 b:44.3 occ:1.00 O A:PHE8 2.3 48.0 1.0 OD1 A:ASP7 2.3 48.0 1.0 O1B A:DGT414 2.3 42.0 1.0 O2A A:DGT414 2.3 44.1 1.0 O1G A:DGT414 2.3 44.0 1.0 OD2 A:ASP105 2.3 48.6 1.0 CG A:ASP7 3.1 50.4 1.0 PG A:DGT414 3.3 41.4 1.0 PB A:DGT414 3.3 40.2 1.0 CG A:ASP105 3.4 49.1 1.0 PA A:DGT414 3.4 41.8 1.0 CA A:CA415 3.4 46.5 1.0 O3A A:DGT414 3.5 40.6 1.0 OD2 A:ASP7 3.5 49.1 1.0 C A:PHE8 3.5 49.1 1.0 NZ A:LYS159 3.7 60.0 1.0 OD1 A:ASP105 3.7 47.2 1.0 O3B A:DGT414 4.0 41.9 1.0 N A:PHE8 4.1 48.3 1.0 C5' A:DGT414 4.1 43.6 1.0 O3G A:DGT414 4.2 41.4 1.0 O5' A:DGT414 4.3 41.7 1.0 CB A:ASP7 4.3 48.5 1.0 C A:ASP7 4.3 48.4 1.0 CA A:PHE8 4.4 48.6 1.0 N A:ASP9 4.5 49.6 1.0 N A:TYR10 4.5 50.0 1.0 O2G A:DGT414 4.6 40.5 1.0 CA A:ASP9 4.6 50.4 1.0 O1A A:DGT414 4.6 41.4 1.0 O2B A:DGT414 4.6 35.8 1.0 O A:HOH375 4.6 55.7 1.0 CB A:ASP105 4.7 50.6 1.0 O A:ASP7 4.7 48.5 1.0 O D:HOH373 4.7 36.8 1.0 CA A:ASP7 4.7 48.5 1.0 C A:ASP9 4.8 50.5 1.0 O A:ASP105 5.0 52.6 1.0

Calcium binding site 3 out of 3 in the DPO4 Extension Ternary Complex with Oxog(Anti)-G(Syn) 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 Oxog(Anti)-G(Syn) Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca417 b:68.6 occ:1.00 O A:HOH342 2.1 49.3 1.0 O A:ALA181 2.3 67.7 1.0 O A:ILE186 2.3 66.6 1.0 O A:HOH346 2.9 73.3 1.0 C A:ALA181 3.4 67.5 1.0 C A:ILE186 3.5 65.8 1.0 CA A:GLY187 3.9 66.0 1.0 CA A:ALA181 4.1 67.5 1.0 OP2 D:DG813 4.1 54.3 1.0 N A:GLY187 4.1 66.0 1.0 CB A:ALA181 4.2 67.6 1.0 C A:GLY187 4.5 66.2 1.0 N A:ASP182 4.6 67.3 1.0 O A:HOH368 4.7 57.9 1.0 CA A:ILE186 4.7 65.5 1.0 CA A:ASP182 4.8 67.1 1.0 O A:VAL183 4.8 65.8 1.0 CB A:ILE186 4.8 65.5 1.0 N A:ASN188 4.9 66.5 1.0 OP1 D:DG813 5.0 55.0 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