Magnesium in PDB 1n56: Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion

The structure of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n56 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)	29.90 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.016, 102.358, 105.660, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.3

The structure of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion (pdb code 1n56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n56:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium 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 Magnesium with other atoms in the Mg 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 A:Mg401 b:95.4 occ:1.00 OE2 A:GLU106 1.8 61.3 1.0 O1A A:ATP1803 2.2 0.2 1.0 O A:HOH648 2.3 54.8 1.0 O A:HOH1023 2.4 82.7 1.0 OD1 A:ASP7 2.7 54.8 1.0 CD A:GLU106 2.8 56.3 1.0 PA A:ATP1803 3.3 0.8 1.0 CG A:GLU106 3.4 52.5 1.0 CG A:ASP7 3.5 48.5 1.0 MG A:MG402 3.6 48.9 1.0 OD2 A:ASP7 3.7 52.7 1.0 O2A A:ATP1803 3.7 0.8 1.0 OD1 A:ASP105 3.8 48.7 1.0 OE1 A:GLU106 3.9 59.2 1.0 OD2 A:ASP105 3.9 53.3 1.0 O5' A:ATP1803 3.9 0.4 1.0 O1G A:ATP1803 3.9 0.7 1.0 NZ A:LYS152 4.2 42.6 1.0 CG A:ASP105 4.3 49.0 1.0 O C:HOH804 4.5 52.7 1.0 NZ A:LYS159 4.5 61.3 1.0 OP1 C:DA1814 4.5 94.7 1.0 C5' A:ATP1803 4.6 0.6 1.0 O3A A:ATP1803 4.6 0.2 1.0 CB A:ASP7 4.6 45.5 1.0 O A:HOH965 4.8 52.8 1.0 CB A:GLU106 4.8 45.4 1.0 OP2 C:DA1814 4.9 93.9 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402 b:48.9 occ:1.00 O1G A:ATP1803 2.2 0.7 1.0 O A:PHE8 2.2 42.0 1.0 O1A A:ATP1803 2.3 0.2 1.0 OD1 A:ASP7 2.3 54.8 1.0 OD2 A:ASP105 2.5 53.3 1.0 OD2 A:ASP7 2.5 52.7 1.0 O A:HOH666 2.6 95.7 1.0 CG A:ASP7 2.7 48.5 1.0 O3A A:ATP1803 3.3 0.2 1.0 O A:HOH514 3.3 41.1 1.0 C A:PHE8 3.4 40.6 1.0 PG A:ATP1803 3.4 0.1 1.0 PA A:ATP1803 3.4 0.8 1.0 MG A:MG401 3.6 95.4 1.0 CG A:ASP105 3.7 49.0 1.0 O2B A:ATP1803 3.8 0.6 1.0 O3G A:ATP1803 3.8 0.3 1.0 PB A:ATP1803 3.9 0.4 1.0 N A:PHE8 3.9 41.1 1.0 O3B A:ATP1803 4.0 0.9 1.0 CB A:ASP7 4.0 45.5 1.0 C A:ASP7 4.0 42.4 1.0 O A:HOH1023 4.1 82.7 1.0 CA A:PHE8 4.3 40.0 1.0 OD1 A:ASP105 4.3 48.7 1.0 O5' A:ATP1803 4.3 0.4 1.0 N A:ASP9 4.4 41.3 1.0 NZ A:LYS159 4.4 61.3 1.0 O A:ASP7 4.4 43.2 1.0 CA A:ASP7 4.4 42.4 1.0 CA A:ASP9 4.5 40.6 1.0 C5' A:ATP1803 4.5 0.6 1.0 O2A A:ATP1803 4.5 0.8 1.0 O2G A:ATP1803 4.6 0.1 1.0 O A:ASP105 4.7 37.6 1.0 N A:TYR10 4.7 40.8 1.0 CB A:ASP105 4.8 43.3 1.0 C A:ASP9 4.9 39.8 1.0 CB A:PHE8 5.0 40.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 B:Mg404 b:33.2 occ:1.00 O B:PHE8 2.2 39.4 1.0 OD2 B:ASP105 2.3 44.5 1.0 OD1 B:ASP7 2.4 53.9 1.0 O1G B:ATP1804 2.5 76.5 1.0 O B:HOH812 2.5 0.6 1.0 O1A B:ATP1804 2.7 59.3 1.0 OD2 B:ASP7 2.8 56.3 1.0 O B:HOH822 2.8 68.1 1.0 CG B:ASP7 2.9 50.4 1.0 O3A B:ATP1804 3.1 67.7 1.0 O2B B:ATP1804 3.3 69.5 1.0 C B:PHE8 3.4 40.0 1.0 CA B:CA403 3.4 62.0 1.0 CG B:ASP105 3.5 43.0 1.0 PA B:ATP1804 3.6 64.1 1.0 PB B:ATP1804 3.6 67.4 1.0 PG B:ATP1804 3.7 76.7 1.0 O3B B:ATP1804 3.9 72.0 1.0 N B:PHE8 3.9 42.1 1.0 O B:HOH934 4.0 94.4 1.0 O3G B:ATP1804 4.1 73.7 1.0 OD1 B:ASP105 4.2 43.2 1.0 CA B:PHE8 4.2 40.5 1.0 C B:ASP7 4.2 44.6 1.0 CB B:ASP7 4.3 47.5 1.0 N B:ASP9 4.4 39.7 1.0 C5' B:ATP1804 4.4 58.0 1.0 O5' B:ATP1804 4.5 62.3 1.0 CA B:ASP9 4.5 39.0 1.0 NZ B:LYS159 4.5 63.5 1.0 N B:TYR10 4.6 36.0 1.0 O B:HOH947 4.6 90.2 1.0 CB B:ASP105 4.6 38.1 1.0 O B:HOH799 4.7 68.9 1.0 CA B:ASP7 4.7 44.6 1.0 O B:ASP7 4.7 44.4 1.0 O B:HOH915 4.7 44.1 1.0 O2A B:ATP1804 4.7 64.3 1.0 C B:ASP9 4.8 37.9 1.0 O E:HOH649 4.8 75.6 1.0 O B:ASP105 4.8 39.9 1.0 CB B:PHE8 4.9 39.5 1.0 O2G B:ATP1804 4.9 77.3 1.0 O1B B:ATP1804 5.0 65.9 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.