Calcium in PDB 1n48: Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion

All present enzymatic activity of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion:
2.7.7.7;

The structure of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n48 was solved by H.Ling, F.Boudsocq, R.Woodgate, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.40 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.546, 88.458, 92.389, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23

The binding sites of Calcium atom in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion (pdb code 1n48). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n48:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:30.0 occ:1.00 O B:HOH214 2.1 28.4 1.0 O A:HOH638 2.1 35.4 1.0 O1A B:ATP1814 2.2 29.5 1.0 OP1 B:DA1813 2.4 28.1 1.0 O2B B:ATP1814 2.4 31.4 1.0 O B:HOH223 2.4 41.8 1.0 O B:HOH239 2.5 51.4 1.0 PB B:ATP1814 3.4 28.9 1.0 PA B:ATP1814 3.5 30.5 1.0 O3A B:ATP1814 3.6 29.4 1.0 P B:DA1813 3.6 31.5 1.0 C3' B:DT1812 3.8 26.3 1.0 O B:HOH17 3.9 27.2 1.0 O3' B:DT1812 3.9 31.1 1.0 O1B B:ATP1814 4.2 25.7 1.0 O2A B:ATP1814 4.2 32.4 1.0 C2' B:DT1812 4.3 24.8 1.0 O A:HOH526 4.3 35.0 1.0 O B:HOH238 4.3 51.1 1.0 OP2 B:DA1813 4.3 30.2 1.0 O B:HOH82 4.6 38.0 1.0 NZ A:LYS152 4.7 23.6 1.0 O5' B:ATP1814 4.7 32.8 1.0 O B:HOH172 4.8 43.4 1.0 O A:HOH543 4.8 38.6 1.0 O3B B:ATP1814 4.9 31.0 1.0 O5' B:DA1813 4.9 34.2 1.0 OD1 A:ASP156 5.0 31.4 1.0

Calcium binding site 2 out of 3 in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:22.1 occ:1.00 OE1 A:GLU106 2.1 27.7 1.0 OP2 B:DA1813 2.2 30.2 1.0 O B:HOH17 2.2 27.2 1.0 OD2 A:ASP7 2.3 32.5 1.0 OD1 A:ASP105 2.3 29.4 1.0 O1B B:ATP1814 2.4 25.7 1.0 OD2 A:ASP105 2.5 30.2 1.0 CG A:ASP105 2.7 25.8 1.0 P B:DA1813 3.3 31.5 1.0 CD A:GLU106 3.3 28.3 1.0 CG A:ASP7 3.4 27.1 1.0 OP1 B:DA1813 3.7 28.1 1.0 CA A:CA502 3.7 26.8 1.0 PB B:ATP1814 3.7 28.9 1.0 O5' B:DA1813 3.8 34.2 1.0 O A:HOH512 4.0 29.4 1.0 CG A:GLU106 4.1 28.9 1.0 O2B B:ATP1814 4.2 31.4 1.0 OD1 A:ASP7 4.2 28.9 1.0 CB A:GLU106 4.2 27.7 1.0 OE2 A:GLU106 4.2 31.6 1.0 CB A:ASP105 4.3 27.1 1.0 NZ A:LYS152 4.3 23.6 1.0 CB A:ASP7 4.4 25.9 1.0 O3A B:ATP1814 4.4 29.4 1.0 C5' B:DA1813 4.5 35.8 1.0 O3B B:ATP1814 4.6 31.0 1.0 O A:ASP105 4.6 27.1 1.0 OG A:SER103 4.6 33.7 1.0 C A:ASP105 4.6 28.6 1.0 O A:HOH520 4.6 30.2 1.0 O3' B:DT1812 4.7 31.1 1.0 O A:HOH514 4.8 28.7 1.0 N A:GLU106 4.9 27.8 1.0

Calcium binding site 3 out of 3 in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:26.8 occ:1.00 O A:HOH514 2.2 28.7 1.0 OD1 A:ASP7 2.2 28.9 1.0 OD2 A:ASP105 2.3 30.2 1.0 O A:PHE8 2.3 26.4 1.0 OD2 A:ASP7 2.6 32.5 1.0 O1B B:ATP1814 2.6 25.7 1.0 O3G B:ATP1814 2.7 23.5 1.0 CG A:ASP7 2.7 27.1 1.0 O3B B:ATP1814 2.9 31.0 1.0 CG A:ASP105 3.4 25.8 1.0 C A:PHE8 3.4 24.6 1.0 PB B:ATP1814 3.6 28.9 1.0 PG B:ATP1814 3.6 28.1 1.0 CA A:CA501 3.7 22.1 1.0 N A:PHE8 4.1 26.8 1.0 N A:TYR10 4.1 22.9 1.0 CB A:ASP105 4.1 27.1 1.0 O2G B:ATP1814 4.2 28.3 1.0 N A:ASP9 4.2 24.7 1.0 CB A:ASP7 4.2 25.9 1.0 CA A:ASP9 4.3 24.9 1.0 OD1 A:ASP105 4.3 29.4 1.0 O3A B:ATP1814 4.4 29.4 1.0 O A:HOH504 4.4 24.3 1.0 CA A:PHE8 4.4 27.1 1.0 C A:ASP9 4.4 24.3 1.0 N A:PHE11 4.5 25.2 1.0 C A:ASP7 4.6 26.7 1.0 O A:HOH569 4.6 40.9 1.0 O B:HOH17 4.6 27.2 1.0 O2B B:ATP1814 4.7 31.4 1.0 CB A:PHE11 4.8 28.8 1.0 O A:ASP105 4.8 27.1 1.0 O1G B:ATP1814 4.8 28.5 1.0 CA A:TYR10 4.9 24.5 1.0 CA A:ASP7 4.9 26.2 1.0

H.Ling, F.Boudsocq, R.Woodgate, W.Yang. A Y-Family Polymerase Complexed with Abasic Lesions: Catching Dna with A Loaded Nucleoside Triphosphate To Be Published.