Magnesium in PDB 2w35: Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair

All present enzymatic activity of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair:
3.1.21.7;

The structure of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair, PDB code: 2w35 was solved by B.Dalhus, A.S.Arvai, I.Rosnes, O.E.Olsen, P.H.Backe, I.Alseth, H.Gao, W.Cao, J.A.Tainer, M.Bjoras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.064, 134.292, 194.450, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 28.8

The binding sites of Magnesium atom in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair (pdb code 2w35). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair, PDB code: 2w35:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1224 b:33.5 occ:1.00 OD1 A:ASP43 1.9 40.3 1.0 O3' C:DG9 2.0 39.5 1.0 O C:HOH2009 2.0 39.4 1.0 O C:HOH2007 2.2 33.2 1.0 OD1 A:ASP110 2.2 42.2 1.0 O A:HOH2024 2.2 33.4 1.0 CG A:ASP43 3.0 41.5 1.0 CG A:ASP110 3.3 41.7 1.0 C3' C:DG9 3.3 34.1 1.0 OD2 A:ASP43 3.4 41.5 1.0 CB A:ASP110 3.7 38.7 1.0 O A:LEU44 3.9 37.5 1.0 C5' D:DA10 4.0 56.5 1.0 C4' C:DG9 4.1 36.2 1.0 N A:LEU44 4.1 36.7 1.0 OP2 D:DA10 4.2 55.5 1.0 CB A:ASP43 4.3 41.3 1.0 OD2 A:ASP110 4.3 47.2 1.0 C2' C:DG9 4.4 35.0 1.0 O A:ASP110 4.5 39.8 1.0 OE2 A:GLU89 4.5 45.5 1.0 CA A:ASP43 4.5 38.7 1.0 OE1 A:GLU89 4.6 46.3 1.0 O A:HOH2119 4.7 43.7 1.0 C A:LEU44 4.9 36.2 1.0 C A:ASP43 4.9 37.8 1.0 C5' C:DG9 4.9 30.9 1.0 NZ A:LYS139 5.0 39.4 1.0

Magnesium binding site 2 out of 2 in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1224 b:38.6 occ:1.00 O B:HOH2041 1.9 34.6 1.0 OD1 B:ASP43 1.9 46.1 1.0 O3' F:DG9 1.9 40.2 1.0 O F:HOH2004 2.2 35.4 1.0 OD2 B:ASP110 2.2 42.5 1.0 O F:HOH2005 2.4 35.4 1.0 CG B:ASP43 3.0 45.0 1.0 C3' F:DG9 3.3 34.9 1.0 CG B:ASP110 3.3 42.0 1.0 OD2 B:ASP43 3.4 46.7 1.0 CB B:ASP110 3.8 37.9 1.0 O B:LEU44 3.8 41.9 1.0 C5' G:DA10 4.0 51.1 1.0 N B:LEU44 4.0 41.4 1.0 C4' F:DG9 4.2 35.6 1.0 CB B:ASP43 4.2 44.4 1.0 C2' F:DG9 4.3 37.8 1.0 OP2 G:DA10 4.4 54.1 1.0 OD1 B:ASP110 4.4 45.5 1.0 OE2 B:GLU89 4.4 45.2 1.0 CA B:ASP43 4.5 41.3 1.0 OE1 B:GLU89 4.5 47.2 1.0 O B:ASP110 4.5 35.0 1.0 C B:LEU44 4.8 41.0 1.0 C B:ASP43 4.8 41.0 1.0 CD B:GLU89 4.9 44.6 1.0 CA B:LEU44 4.9 40.6 1.0 C4' G:DA10 5.0 48.4 1.0

B.Dalhus, A.S.Arvai, I.Rosnes, O.E.Olsen, P.H.Backe, I.Alseth, H.Gao, W.Cao, J.A.Tainer, M.Bjoras. Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair. Nat.Struct.Mol.Biol. V. 16 138 2009.
ISSN: ISSN 1545-9993
PubMed: 19136958
DOI: 10.1038/NSMB.1538