Manganese in PDB 3dsd: Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese

The structure of Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese, PDB code: 3dsd was solved by R.S.Williams, D.Moiani, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.157, 88.128, 137.410, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.6

The binding sites of Manganese atom in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese (pdb code 3dsd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese, PDB code: 3dsd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:44.1 occ:1.00 OD1 A:ASP8 2.0 29.4 1.0 NE2 A:HIS208 2.2 48.5 1.0 NE2 A:HIS10 2.4 27.8 1.0 OD1 A:ASP49 2.4 32.5 1.0 CG A:ASP8 3.0 29.7 1.0 CE1 A:HIS208 3.1 47.6 1.0 MN A:MN404 3.1 48.0 1.0 CD2 A:HIS208 3.3 47.3 1.0 CG A:ASP49 3.3 29.1 1.0 CE1 A:HIS10 3.3 28.2 1.0 CD2 A:HIS10 3.4 30.2 1.0 CB A:ASP49 3.5 26.6 1.0 O A:HOH463 3.5 57.3 1.0 CB A:ASP8 3.6 28.1 1.0 CA A:ASP8 4.0 28.0 1.0 OD2 A:ASP8 4.0 31.3 1.0 CE1 A:HIS173 4.2 25.9 1.0 O A:HIS206 4.2 42.5 1.0 ND1 A:HIS208 4.2 47.9 1.0 CG A:HIS208 4.4 45.4 1.0 NE2 A:HIS173 4.4 26.7 1.0 ND1 A:HIS10 4.5 27.6 1.0 OD2 A:ASP49 4.5 28.5 1.0 CG A:HIS10 4.5 29.7 1.0 CA A:HIS206 4.6 39.3 1.0 OD1 A:ASN84 4.7 39.5 1.0 OG A:SER85 4.7 36.0 1.0 C A:HIS206 4.8 40.5 1.0 ND1 A:HIS206 4.8 41.6 1.0 C A:ASP8 4.9 28.4 1.0 N A:ASP8 5.0 27.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:48.0 occ:1.00 OD1 A:ASN84 2.0 39.5 1.0 NE2 A:HIS173 2.1 26.7 1.0 OD1 A:ASP49 2.3 32.5 1.0 ND1 A:HIS206 2.3 41.6 1.0 CE1 A:HIS173 2.8 25.9 1.0 MN A:MN403 3.1 44.1 1.0 CE1 A:HIS206 3.2 43.2 1.0 CG A:ASN84 3.2 36.5 1.0 CG A:ASP49 3.2 29.1 1.0 CD2 A:HIS173 3.3 23.4 1.0 CG A:HIS206 3.4 41.7 1.0 O A:HOH463 3.5 57.3 1.0 CA A:HIS206 3.6 39.3 1.0 OD1 A:ASP8 3.7 29.4 1.0 OD2 A:ASP49 3.7 28.5 1.0 CB A:HIS206 3.8 39.5 1.0 ND2 A:ASN84 3.9 40.5 1.0 ND1 A:HIS173 4.0 23.5 1.0 O A:HIS206 4.1 42.5 1.0 N A:ASN84 4.2 30.9 1.0 CG A:HIS173 4.3 26.1 1.0 CB A:ASN84 4.3 33.0 1.0 CB A:ASP49 4.3 26.6 1.0 C A:HIS206 4.3 40.5 1.0 NE2 A:HIS206 4.4 44.6 1.0 CD2 A:HIS206 4.5 43.2 1.0 N A:HIS206 4.5 36.1 1.0 NE2 A:HIS208 4.6 48.5 1.0 OG A:SER85 4.6 36.0 1.0 CA A:ASN84 4.8 32.3 1.0 CG A:ASP8 4.8 29.7 1.0 N A:SER85 4.9 31.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn405 b:58.1 occ:1.00 OD1 B:ASN84 1.9 42.0 1.0 NE2 B:HIS173 2.2 27.9 1.0 ND1 B:HIS206 2.3 47.3 1.0 OD2 B:ASP49 2.6 32.8 1.0 CE1 B:HIS173 2.9 27.4 1.0 CG B:ASN84 3.0 36.6 1.0 CE1 B:HIS206 3.1 47.8 1.0 O B:HOH444 3.1 59.4 1.0 MN B:MN406 3.2 43.3 1.0 CD2 B:HIS173 3.3 28.0 1.0 CG B:ASP49 3.4 30.3 1.0 CG B:HIS206 3.5 44.4 1.0 ND2 B:ASN84 3.6 41.2 1.0 CA B:HIS206 3.7 39.2 1.0 OD1 B:ASP8 3.7 29.2 1.0 OD1 B:ASP49 3.9 30.5 1.0 CB B:HIS206 3.9 40.1 1.0 N B:ASN84 4.1 29.5 1.0 O B:HIS206 4.1 41.1 1.0 ND1 B:HIS173 4.1 27.3 1.0 CB B:ASN84 4.2 32.6 1.0 NE2 B:HIS206 4.3 49.4 1.0 CG B:HIS173 4.4 25.8 1.0 C B:HIS206 4.4 40.0 1.0 CD2 B:HIS206 4.5 47.1 1.0 CB B:ASP49 4.5 27.7 1.0 N B:HIS206 4.7 35.9 1.0 CA B:ASN84 4.7 31.0 1.0 N B:SER85 4.8 31.0 1.0 CG B:ASP8 4.9 29.2 1.0 NE2 B:HIS208 5.0 44.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of P. Furiosus MRE11-H85S Bound to A Branched Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn406 b:43.3 occ:1.00 OD1 B:ASP8 2.2 29.2 1.0 NE2 B:HIS208 2.3 44.7 1.0 NE2 B:HIS10 2.3 33.7 1.0 OD2 B:ASP49 2.5 32.8 1.0 CG B:ASP8 3.1 29.2 1.0 CE1 B:HIS208 3.2 44.6 1.0 MN B:MN405 3.2 58.1 1.0 CE1 B:HIS10 3.2 33.5 1.0 CD2 B:HIS208 3.3 43.7 1.0 O B:HOH444 3.4 59.4 1.0 CD2 B:HIS10 3.4 32.3 1.0 CG B:ASP49 3.4 30.3 1.0 CB B:ASP8 3.5 27.2 1.0 CB B:ASP49 3.6 27.7 1.0 CA B:ASP8 4.0 28.3 1.0 OD2 B:ASP8 4.2 28.0 1.0 CE1 B:HIS173 4.3 27.4 1.0 ND1 B:HIS208 4.3 44.4 1.0 O B:HIS206 4.3 41.1 1.0 ND1 B:HIS10 4.4 32.6 1.0 CG B:HIS208 4.4 40.3 1.0 CG B:HIS10 4.5 31.3 1.0 NE2 B:HIS173 4.6 27.9 1.0 OD1 B:ASP49 4.6 30.5 1.0 OD1 B:ASN84 4.6 42.0 1.0 CA B:HIS206 4.7 39.2 1.0 C B:HIS206 4.8 40.0 1.0 ND1 B:HIS206 4.9 47.3 1.0 C B:ASP8 4.9 28.1 1.0 OG B:SER85 4.9 35.1 1.0 N B:ASP8 5.0 27.8 1.0

R.S.Williams, G.Moncalian, J.S.Williams, Y.Yamada, O.Limbo, D.S.Shin, L.M.Groocock, D.Cahill, C.Hitomi, G.Guenther, D.Moiani, J.P.Carney, P.Russell, J.A.Tainer. MRE11 Dimers Coordinate Dna End Bridging and Nuclease Processing in Double-Strand-Break Repair. Cell(Cambridge,Mass.) V. 135 97 2008.
ISSN: ISSN 0092-8674
PubMed: 18854158
DOI: 10.1016/J.CELL.2008.08.017