Manganese in PDB 3o3h: T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions

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

The structure of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions, PDB code: 3o3h 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)	41.20 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.658, 48.571, 77.910, 90.00, 131.97, 90.00
R / Rfree (%)	18.2 / 25.3

The binding sites of Manganese atom in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions (pdb code 3o3h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions, PDB code: 3o3h:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:51.0 occ:1.00 OD2 A:ASP124 2.4 40.0 1.0 O A:HOH246 2.5 36.9 1.0 OD1 A:ASP124 2.7 42.1 1.0 CG A:ASP124 2.9 40.3 1.0 OP2 D:C6 3.4 39.0 1.0 O A:HOH257 3.7 27.9 1.0 NZ A:LYS47 4.0 42.5 1.0 NE2 A:GLN125 4.2 44.6 1.0 OD1 A:ASP45 4.3 47.5 1.0 OP1 D:C6 4.3 43.6 1.0 P D:C6 4.3 44.2 1.0 CA A:LYS122 4.4 35.0 1.0 CB A:ASP124 4.4 36.6 1.0 MN A:MN224 4.7 41.8 1.0 ND2 A:ASN107 4.7 34.6 1.0 OD1 A:ASN107 4.7 30.5 1.0 CG A:ASP45 4.8 48.1 1.0 OP1 D:DC5 4.8 35.8 1.0 CE A:LYS47 4.8 39.9 1.0 C A:LYS122 4.9 35.5 1.0 OP2 D:DC5 5.0 32.8 1.0

Manganese binding site 2 out of 3 in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn224 b:41.8 occ:1.00 OP1 D:C6 2.4 43.6 1.0 O A:HOH253 2.5 36.5 1.0 OD1 A:ASP18 2.8 32.6 1.0 OD2 A:ASP124 3.0 40.0 1.0 OD2 A:ASP18 3.4 31.6 1.0 OD1 A:ASP45 3.4 47.5 1.0 OP2 D:DT7 3.4 39.8 1.0 CG A:ASP18 3.4 31.5 1.0 P D:C6 3.7 44.2 1.0 CG A:ASP124 3.8 40.3 1.0 OG A:SER134 3.9 33.7 1.0 CB A:ASP124 4.0 36.6 1.0 ND2 A:ASN107 4.0 34.6 1.0 CB A:SER134 4.1 32.2 1.0 O5' D:C6 4.3 36.0 1.0 OP2 D:C6 4.3 39.0 1.0 NZ A:LYS47 4.5 42.5 1.0 O A:GLU19 4.6 30.0 1.0 CG A:ASP45 4.6 48.1 1.0 CE A:LYS47 4.7 39.9 1.0 MN A:MN1 4.7 51.0 1.0 C5' D:C6 4.7 32.9 1.0 OG A:SER46 4.7 40.9 1.0 OD1 A:ASP124 4.8 42.1 1.0 P D:DT7 4.8 43.6 1.0 CB A:ASP18 4.9 30.1 1.0 O3' D:DC5 4.9 34.7 1.0 CG A:ASN107 4.9 32.0 1.0 CA A:SER134 4.9 31.5 1.0

Manganese binding site 3 out of 3 in the T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of T. Maritima Rnase H2 D107N in Complex with Nucleic Acid Substrate and Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn13 b:54.7 occ:1.00 OP2 C:DG10 3.7 27.3 1.0 O C:HOH17 4.1 23.8 1.0 O A:HOH232 4.3 22.8 1.0 C3' C:DT9 4.6 23.8 1.0 C2' C:DT9 4.7 24.5 1.0 P C:DG10 5.0 25.4 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