Calcium in PDB 3t5k: Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp

All present enzymatic activity of Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp:
2.7.7.7;

The structure of Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp, PDB code: 3t5k 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)	29.15 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.372, 104.011, 52.831, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.3

The binding sites of Calcium atom in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp (pdb code 3t5k). 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'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp, PDB code: 3t5k:
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'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp


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'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:68.3 occ:1.00 O A:PHE8 2.6 36.9 1.0 OD2 A:ASP105 2.7 54.4 1.0 OD1 A:ASP7 2.8 47.8 1.0 O3A A:DTP600 2.9 0.6 1.0 O2G A:DTP600 3.0 0.7 1.0 O2B A:DTP600 3.0 0.7 1.0 CG A:ASP7 3.1 43.7 1.0 OD2 A:ASP7 3.2 44.5 1.0 CA A:CA1002 3.4 67.9 1.0 C A:PHE8 3.5 36.9 1.0 PB A:DTP600 3.6 0.9 1.0 O1G A:DTP600 3.6 0.5 1.0 PG A:DTP600 3.6 0.2 1.0 O3B A:DTP600 3.8 0.3 1.0 O A:ASP7 3.9 41.1 1.0 O5' A:DTP600 3.9 93.3 1.0 CG A:ASP105 3.9 50.8 1.0 C A:ASP7 3.9 39.7 1.0 PA A:DTP600 4.0 96.4 1.0 CB A:ASP7 4.1 41.5 1.0 O2A A:DTP600 4.2 97.2 1.0 N A:PHE8 4.2 37.4 1.0 N A:ASP9 4.3 38.1 1.0 CA A:PHE8 4.4 35.5 1.0 CA A:ASP9 4.4 37.2 1.0 CA A:ASP7 4.5 40.1 1.0 OD1 A:ASP105 4.7 51.4 1.0 NZ A:LYS159 4.7 63.9 1.0 N A:TYR10 4.7 36.8 1.0 O A:ASP105 4.8 40.6 1.0 CB A:ASP105 4.9 45.4 1.0 C A:ASP9 4.9 36.6 1.0 CE A:LYS159 5.0 63.7 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp


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'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:67.9 occ:1.00 OE1 A:GLU106 2.7 57.4 1.0 O2A A:DTP600 2.8 97.2 1.0 OD2 A:ASP7 3.0 44.5 1.0 CA A:CA1001 3.4 68.3 1.0 OD1 A:ASP7 3.5 47.8 1.0 CG A:ASP7 3.6 43.7 1.0 OP1 C:DC514 3.7 75.3 1.0 O5' C:DC514 3.7 75.2 1.0 PA A:DTP600 3.7 96.4 1.0 O3A A:DTP600 3.8 0.6 1.0 CD A:GLU106 3.8 56.7 1.0 NZ A:LYS159 4.1 63.9 1.0 P C:DC514 4.1 76.2 1.0 OD2 A:ASP105 4.2 54.4 1.0 O5' A:DTP600 4.3 93.3 1.0 CG A:GLU106 4.3 51.7 1.0 OP2 C:DC514 4.4 75.6 1.0 C3' C:DC514 4.7 71.9 1.0 OD1 A:ASP105 4.7 51.4 1.0 C5' C:DC514 4.7 73.2 1.0 O1G A:DTP600 4.8 0.5 1.0 OE2 A:GLU106 4.8 58.2 1.0 CG A:ASP105 4.9 50.8 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp


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'-Txg-3' Vs 14-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:53.2 occ:1.00 O A:ALA181 2.7 52.7 1.0 O A:HOH2047 2.7 53.7 1.0 O C:HOH2045 2.7 54.4 1.0 O A:HOH2044 2.8 40.8 1.0 O A:HOH2046 2.9 34.7 1.0 O A:ILE186 2.9 44.9 1.0 C A:ALA181 3.8 52.7 1.0 C A:ILE186 4.0 44.9 1.0 OP1 C:DC513 4.3 48.0 1.0 OP2 C:DC513 4.3 47.1 1.0 CA A:GLY187 4.6 47.4 1.0 CA A:ALA181 4.7 52.7 1.0 N A:ASP182 4.7 52.5 1.0 CA A:ASP182 4.7 51.9 1.0 N A:GLY187 4.8 45.1 1.0 O A:VAL183 4.8 42.3 1.0 P C:DC513 4.8 46.2 1.0 CB A:ALA181 4.9 53.6 1.0 O A:GLY187 4.9 49.4 1.0 CA A:ILE186 4.9 44.1 1.0 C A:GLY187 5.0 49.2 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