Magnesium in PDB 3o3f: T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions

All present enzymatic activity of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions:
3.1.26.4;

The structure of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions, PDB code: 3o3f was solved by M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.062, 48.570, 78.391, 90.00, 131.80, 90.00
R / Rfree (%)	19.1 / 24.4

The binding sites of Magnesium atom in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions (pdb code 3o3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions, PDB code: 3o3f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg224 b:32.3 occ:1.00 OP2 D:DT7 2.4 28.3 1.0 O A:GLU19 2.5 26.9 1.0 O A:HOH257 2.5 38.4 1.0 OP1 D:C6 2.5 44.9 1.0 OD2 A:ASP18 2.6 25.7 0.5 O A:HOH269 2.7 40.2 1.0 OD1 A:ASP18 3.2 32.0 0.5 CG A:ASP18 3.2 30.1 0.5 OD2 A:ASP18 3.3 29.6 0.5 OD1 A:ASP18 3.3 32.6 0.5 CG A:ASP18 3.4 30.9 0.5 C A:GLU19 3.6 25.2 1.0 P D:DT7 3.7 31.0 1.0 P D:C6 3.8 37.8 1.0 C5' D:C6 3.8 30.7 1.0 O5' D:C6 3.9 31.8 1.0 N A:GLU19 4.3 21.7 1.0 OE2 A:GLU19 4.3 27.9 0.5 OP1 D:DT7 4.3 28.8 1.0 CB A:SER134 4.4 30.3 1.0 N A:ALA20 4.4 19.1 1.0 CA A:ALA20 4.5 19.3 1.0 ND2 A:ASN107 4.5 32.0 1.0 O3' D:C6 4.5 28.1 1.0 OD2 A:ASP124 4.5 47.0 1.0 OG A:SER46 4.5 45.2 1.0 CA A:GLU19 4.6 25.2 0.5 CA A:GLU19 4.6 24.8 0.5 CB A:ASP18 4.6 27.4 0.5 CB A:ASP18 4.7 27.3 0.5 O3' D:DC5 4.8 31.1 1.0 CA A:SER134 4.8 28.9 1.0 OP2 D:C6 4.8 42.0 1.0 C4' D:C6 4.8 30.4 1.0 O5' D:DT7 4.8 37.0 1.0 CB A:ALA20 4.9 24.9 1.0 OE1 A:GLU19 5.0 25.3 0.5 C3' D:C6 5.0 26.2 1.0

Magnesium binding site 2 out of 2 in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg13 b:56.6 occ:1.00 O D:HOH100 2.5 37.5 1.0 O A:HOH318 2.6 50.7 1.0 O A:HOH300 2.8 45.9 1.0 O A:HOH304 2.8 56.7 1.0 OP2 D:C6 3.1 42.0 1.0 O A:HOH303 3.3 52.4 1.0 OD1 A:ASP124 3.5 45.8 1.0 OD2 A:ASP124 3.5 47.0 1.0 O A:HOH299 3.8 46.5 1.0 CG A:ASP124 3.9 49.8 1.0 O D:HOH152 4.1 46.3 1.0 O5' D:DC5 4.2 33.9 1.0 NZ A:LYS47 4.2 48.6 1.0 OP2 D:DC5 4.2 28.6 1.0 OP1 D:DC5 4.2 33.4 1.0 P D:C6 4.3 37.8 1.0 P D:DC5 4.4 31.6 1.0 CA A:LYS122 4.4 36.9 1.0 OP1 D:C6 4.7 44.9 1.0 CG A:LYS122 4.8 41.3 1.0 OD1 A:ASN107 4.8 29.0 1.0 O3' D:DC5 4.8 31.1 1.0 ND2 A:ASN107 4.8 32.0 1.0 N A:LYS122 5.0 27.5 1.0

M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, M.Nowotny. Crystal Structures of Rnase H2 in Complex with Nucleic Acid Reveal the Mechanism of Rna-Dna Junction Recognition and Cleavage. Mol.Cell V. 40 658 2010.
ISSN: ISSN 1097-2765
PubMed: 21095591
DOI: 10.1016/J.MOLCEL.2010.11.001