Calcium in PDB 3t5j: Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 13-Mer) with DPO4 and Incoming Ddtp

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

The structure of Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 13-Mer) with DPO4 and Incoming Ddtp, PDB code: 3t5j 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)	29.20 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.009, 103.057, 53.217, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.9

The binding sites of Calcium atom in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 13-Mer) with DPO4 and Incoming Ddtp (pdb code 3t5j). 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 13-Mer) with DPO4 and Incoming Ddtp, PDB code: 3t5j:
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 13-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 13-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:37.1 occ:1.00 OD1 A:ASP7 2.4 31.7 1.0 OD2 A:ASP105 2.5 32.6 1.0 O A:PHE8 2.6 29.3 1.0 O3A A:DTP600 2.7 63.2 1.0 O2B A:DTP600 2.8 56.4 1.0 O A:HOH2002 2.8 58.0 1.0 O2G A:DTP600 3.0 72.6 1.0 O5' A:DTP600 3.2 64.5 1.0 CA A:CA1002 3.3 64.6 1.0 CG A:ASP7 3.3 30.5 1.0 PB A:DTP600 3.4 56.1 1.0 PA A:DTP600 3.6 62.9 1.0 O2A A:DTP600 3.6 67.5 1.0 CG A:ASP105 3.6 33.1 1.0 OD2 A:ASP7 3.6 32.6 1.0 C A:PHE8 3.7 29.1 1.0 PG A:DTP600 3.7 69.2 1.0 O3B A:DTP600 3.7 64.4 1.0 O A:HOH2001 3.8 37.3 1.0 O1G A:DTP600 3.9 71.3 1.0 OD1 A:ASP105 4.1 33.0 1.0 N A:PHE8 4.3 28.4 1.0 NZ A:LYS159 4.4 52.5 1.0 C A:ASP7 4.5 29.3 1.0 C5' A:DTP600 4.6 62.0 1.0 CA A:PHE8 4.6 27.9 1.0 N A:ASP9 4.6 28.9 1.0 CB A:ASP7 4.6 30.5 1.0 CA A:ASP9 4.6 27.9 1.0 N A:TYR10 4.6 25.0 1.0 O1B A:DTP600 4.8 56.7 1.0 CB A:ASP105 4.8 30.7 1.0 O A:ASP105 4.8 30.0 1.0 O A:ASP7 4.8 30.5 1.0 C A:ASP9 4.9 27.1 1.0 O1A A:DTP600 4.9 67.7 1.0 CA A:ASP7 4.9 29.1 1.0 CE A:LYS159 4.9 52.0 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 13-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 13-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:64.6 occ:1.00 O2A A:DTP600 2.7 67.5 1.0 OD1 A:ASP105 3.0 33.0 1.0 OE1 A:GLU106 3.1 54.7 1.0 CD A:GLU106 3.1 47.7 1.0 OD2 A:ASP7 3.1 32.6 1.0 CG A:GLU106 3.1 44.0 1.0 OD1 A:ASP7 3.1 31.7 1.0 O A:HOH2095 3.3 52.1 1.0 CA A:CA1001 3.3 37.1 1.0 O5' A:DTP600 3.4 64.5 1.0 CG A:ASP7 3.4 30.5 1.0 OD2 A:ASP105 3.4 32.6 1.0 CG A:ASP105 3.6 33.1 1.0 O A:HOH2002 3.7 58.0 1.0 OE2 A:GLU106 3.8 50.8 1.0 PA A:DTP600 3.9 62.9 1.0 O A:HOH2096 4.1 46.6 1.0 O3A A:DTP600 4.2 63.2 1.0 C5' A:DTP600 4.3 62.0 1.0 CB A:GLU106 4.3 37.9 1.0 O A:ASP105 4.4 30.0 1.0 OG A:SER103 4.7 39.5 1.0 C A:ASP105 4.7 30.9 1.0 CB A:ASP7 4.7 30.5 1.0 N A:GLU106 4.9 33.6 1.0 CB A:ASP105 5.0 30.7 1.0 CA A:GLU106 5.0 34.2 1.0 O1A A:DTP600 5.0 67.7 1.0 NZ A:LYS152 5.0 48.7 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Hne Adduct Modified Dna (5'-Txg-3' Vs 13-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 13-Mer) with DPO4 and Incoming Ddtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:47.4 occ:1.00 O A:HOH2006 2.7 28.1 1.0 O A:ALA181 2.7 44.2 1.0 O A:HOH2005 2.7 49.1 1.0 O C:HOH2004 2.7 42.9 1.0 O A:ILE186 2.8 33.8 1.0 O A:HOH2104 2.8 49.7 1.0 C A:ALA181 3.8 42.8 1.0 C A:ILE186 4.0 34.2 1.0 OP1 C:DC513 4.4 35.0 1.0 CA A:GLY187 4.5 36.5 1.0 CA A:ALA181 4.5 42.3 1.0 OP2 C:DC513 4.6 37.9 1.0 N A:ASP182 4.7 43.2 1.0 CB A:ALA181 4.7 40.2 1.0 N A:GLY187 4.7 33.0 1.0 CA A:ASP182 4.7 43.1 1.0 C A:GLY187 4.8 38.0 1.0 O A:VAL183 4.9 35.4 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