Calcium in PDB 3t5h: Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt

All present enzymatic activity of Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt:
2.7.7.7;

The structure of Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt, PDB code: 3t5h was solved by S.Banerjee, P.P.Christov, A.Kozekova, C.J.Rizzo, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.27 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.815, 102.861, 53.148, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.7

The binding sites of Calcium atom in the Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt (pdb code 3t5h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt, PDB code: 3t5h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:35.0 occ:1.00 O A:PHE8 2.5 29.6 1.0 OD1 A:ASP7 2.5 36.6 1.0 OD2 A:ASP105 2.5 36.5 1.0 O3A A:DGT600 2.7 52.9 1.0 O2B A:DGT600 2.7 45.0 1.0 O2G A:DGT600 3.0 61.4 1.0 O A:HOH2104 3.0 86.9 1.0 O A:HOH2079 3.1 71.7 1.0 O5' A:DGT600 3.3 53.7 1.0 CA A:CA2002 3.4 59.3 1.0 CG A:ASP7 3.4 35.2 1.0 PB A:DGT600 3.4 44.2 1.0 C A:PHE8 3.6 29.4 1.0 OD2 A:ASP7 3.7 38.3 1.0 PA A:DGT600 3.7 51.8 1.0 O2A A:DGT600 3.7 58.0 1.0 O A:HOH2020 3.7 36.2 1.0 CG A:ASP105 3.7 37.9 1.0 PG A:DGT600 3.7 57.8 1.0 O3B A:DGT600 3.8 52.3 1.0 O1G A:DGT600 3.9 62.5 1.0 N A:PHE8 4.2 29.0 1.0 OD1 A:ASP105 4.4 38.5 1.0 C A:ASP7 4.4 29.8 1.0 CA A:PHE8 4.5 29.6 1.0 N A:TYR10 4.5 24.5 1.0 NZ A:LYS159 4.5 50.7 1.0 N A:ASP9 4.6 30.0 1.0 C5' A:DGT600 4.6 50.2 1.0 CA A:ASP9 4.6 27.9 1.0 O A:ASP7 4.6 29.5 1.0 CB A:ASP7 4.7 33.7 1.0 O1B A:DGT600 4.8 46.2 1.0 C A:ASP9 4.8 27.9 1.0 CB A:ASP105 4.8 34.8 1.0 O A:HOH2038 4.8 57.8 1.0 N A:PHE11 4.9 27.8 1.0 CA A:ASP7 4.9 30.5 1.0 O1A A:DGT600 4.9 59.0 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:59.3 occ:1.00 O2A A:DGT600 2.8 58.0 1.0 O A:HOH2038 2.8 57.8 1.0 OE1 A:GLU106 2.9 49.0 1.0 OD2 A:ASP7 2.9 38.3 1.0 O A:HOH2104 3.0 86.9 1.0 OD1 A:ASP105 3.0 38.5 1.0 O A:HOH2080 3.1 69.5 1.0 CG A:GLU106 3.1 42.4 1.0 OD2 A:ASP105 3.2 36.5 1.0 CA A:CA2001 3.4 35.0 1.0 CD A:GLU106 3.4 45.1 1.0 CG A:ASP105 3.4 37.9 1.0 O5' A:DGT600 3.5 53.7 1.0 CG A:ASP7 3.6 35.2 1.0 O A:HOH2079 3.7 71.7 1.0 OD1 A:ASP7 3.8 36.6 1.0 PA A:DGT600 3.9 51.8 1.0 O A:HOH2039 4.2 52.2 1.0 O3A A:DGT600 4.3 52.9 1.0 C5' A:DGT600 4.3 50.2 1.0 CB A:GLU106 4.5 37.5 1.0 O A:ASP105 4.6 31.7 1.0 OE2 A:GLU106 4.6 47.9 1.0 CB A:ASP7 4.7 33.7 1.0 C A:ASP105 4.8 33.2 1.0 OG A:SER103 4.8 36.6 1.0 CB A:ASP105 4.9 34.8 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of Hne Adduct Modified Dna (5'-Cxg-3' Vs 13-Mer) with DPO4 and Incoming Ddgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:48.2 occ:1.00 O A:ALA181 2.6 39.9 1.0 O C:HOH2041 2.7 36.8 1.0 O A:HOH2040 2.7 44.2 1.0 O A:HOH2042 2.7 31.2 1.0 O A:ILE186 2.8 33.9 1.0 O A:HOH2173 3.0 62.7 1.0 C A:ALA181 3.7 39.5 1.0 C A:ILE186 4.0 33.2 1.0 CA A:GLY187 4.4 37.1 1.0 OP1 C:DC513 4.4 38.0 1.0 CA A:ALA181 4.5 38.9 1.0 CB A:ALA181 4.6 38.8 1.0 N A:ASP182 4.7 39.8 1.0 N A:GLY187 4.7 33.4 1.0 OP2 C:DC513 4.7 35.7 1.0 CA A:ASP182 4.7 39.2 1.0 O A:VAL183 4.8 30.6 1.0 O A:HOH2043 4.8 62.9 1.0 C A:GLY187 4.8 38.7 1.0 O A:GLY187 5.0 39.5 1.0

S.Banerjee, P.P.Christov, A.Kozekova, C.J.Rizzo, M.Egli, M.P.Stone. Replication Bypass of the Trans-4-Hydroxynonenal-Derived (6S,8R,11S)-1,N(2)-Deoxyguanosine Dna Adduct By the Sulfolobus Solfataricus Dna Polymerase IV. Chem.Res.Toxicol. V. 25 422 2012.
ISSN: ISSN 0893-228X
PubMed: 22313351
DOI: 10.1021/TX200460J