Magnesium in PDB 4b20: Structural Basis of Dna Loop Recognition By Endonuclease V

All present enzymatic activity of Structural Basis of Dna Loop Recognition By Endonuclease V:
3.1.21.7;

The structure of Structural Basis of Dna Loop Recognition By Endonuclease V, PDB code: 4b20 was solved by I.Rosnes, A.D.Rowe, R.J.Forstrom, I.Alseth, M.Bjoras, B.Dalhus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.0 / 2.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.231, 135.370, 194.993, 90.00, 90.00, 90.00
R / Rfree (%)	22.74 / 29.06

The binding sites of Magnesium atom in the Structural Basis of Dna Loop Recognition By Endonuclease V (pdb code 4b20). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis of Dna Loop Recognition By Endonuclease V, PDB code: 4b20:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Basis of Dna Loop Recognition By Endonuclease V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis of Dna Loop Recognition By Endonuclease V within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1224 b:37.6 occ:1.00 O3' C:DG7 2.1 41.3 1.0 OD2 A:ASP110 2.2 34.8 1.0 OD1 A:ASP43 2.3 39.6 1.0 OP2 D:DA8 3.1 58.8 1.0 C3' C:DG7 3.1 36.6 1.0 CG A:ASP43 3.2 39.1 1.0 OD2 A:ASP43 3.4 40.2 1.0 CG A:ASP110 3.4 37.4 1.0 C5' D:DA8 3.6 48.6 1.0 O A:LEU44 3.8 36.0 1.0 CB A:ASP110 4.2 36.8 1.0 C2' C:DG7 4.2 33.5 1.0 C4' C:DG7 4.3 35.0 1.0 OD1 A:ASP110 4.4 37.0 1.0 P D:DA8 4.4 59.2 1.0 O5' D:DA8 4.4 54.1 1.0 O A:HOH2007 4.4 26.9 1.0 N A:LEU44 4.4 37.4 1.0 OE2 A:GLU89 4.5 38.5 1.0 NZ A:LYS139 4.6 23.9 1.0 CB A:ASP43 4.6 37.2 1.0 C4' D:DA8 4.8 45.5 1.0 C A:LEU44 4.8 36.1 1.0 O A:HOH2013 4.9 27.8 1.0 CD2 A:HIS214 4.9 40.1 1.0 C5' C:DG7 4.9 32.3 1.0

Magnesium binding site 2 out of 2 in the Structural Basis of Dna Loop Recognition By Endonuclease V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis of Dna Loop Recognition By Endonuclease V within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1224 b:45.7 occ:1.00 OD2 B:ASP110 2.0 35.8 1.0 OD1 B:ASP43 2.0 40.0 1.0 O3' F:DG7 2.0 36.4 1.0 CG B:ASP43 3.0 36.4 1.0 CG B:ASP110 3.1 35.9 1.0 C3' F:DG7 3.4 28.6 1.0 OD2 B:ASP43 3.4 35.3 1.0 O B:LEU44 3.7 26.6 1.0 CB B:ASP110 3.9 31.5 1.0 OD1 B:ASP110 3.9 36.2 1.0 OP2 G:DA8 3.9 46.6 1.0 OE2 B:GLU89 4.0 49.6 1.0 N B:LEU44 4.1 29.6 1.0 C5' G:DA8 4.2 43.3 1.0 C4' F:DG7 4.2 29.8 1.0 CB B:ASP43 4.3 34.3 1.0 C2' F:DG7 4.4 28.6 1.0 O B:HOH2018 4.5 37.1 1.0 CA B:ASP43 4.6 32.2 1.0 O B:ASP110 4.6 29.4 1.0 NZ B:LYS139 4.7 19.1 1.0 C B:LEU44 4.7 28.7 1.0 OE1 B:GLU89 4.7 50.2 1.0 CD B:GLU89 4.8 48.0 1.0 C B:ASP43 4.9 30.6 1.0 P G:DA8 4.9 48.2 1.0 CA B:LEU44 4.9 29.1 1.0 C5' F:DG7 5.0 25.2 1.0

I.Rosnes, A.D.Rowe, E.S.Vik, R.J.Forstrom, I.Alseth, M.Bjoras, B.Dalhus. Structural Basis of Dna Loop Recognition By Endonuclease V. Structure V. 21 257 2013.
ISSN: ISSN 0969-2126
PubMed: 23313664
DOI: 10.1016/J.STR.2012.12.007