Manganese in PDB 4o24: Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities

The structure of Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities, PDB code: 4o24 was solved by A.Shibata, D.Moiani, A.S.Arvai, J.Perry, S.M.Harding, M.Genois, R.Maity, S.Rossum-Fikkert, A.Kertokalio, F.Romoli, A.Ismail, E.Ismalaj, E.Petricci, M.J.Neale, R.G.Bristow, J.Masson, C.Wyman, P.A.Jeggo, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.48 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.183, 113.534, 81.563, 90.00, 100.64, 90.00
R / Rfree (%)	20.1 / 25.9

The binding sites of Manganese atom in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities (pdb code 4o24). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities, PDB code: 4o24:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:60.1 occ:0.27 NE2 A:HIS180 1.9 52.7 1.0 OD1 A:ASP58 2.5 55.4 1.0 CE1 A:HIS180 2.6 60.2 1.0 ND1 A:HIS216 2.6 81.2 1.0 CB A:HIS216 2.7 54.3 1.0 CD2 A:HIS180 3.0 59.1 1.0 CG A:HIS216 3.0 70.0 1.0 CA A:HIS216 3.1 37.2 1.0 CG A:ASP58 3.6 52.0 1.0 ND1 A:HIS180 3.7 53.4 1.0 CA A:GLY57 3.8 32.5 1.0 CE1 A:HIS216 3.9 84.2 1.0 N A:HIS216 3.9 29.7 1.0 CG A:HIS180 3.9 51.2 1.0 N A:ASP58 3.9 27.8 1.0 C A:GLY57 4.0 37.0 1.0 OD1 A:ASP14 4.2 35.9 1.0 OD2 A:ASP58 4.3 56.5 1.0 CD2 A:HIS216 4.3 66.5 1.0 C A:HIS216 4.3 35.4 1.0 O A:HIS216 4.5 36.5 1.0 MN A:MN403 4.5 54.9 0.3 CB A:ASP58 4.6 46.7 1.0 NE2 A:HIS216 4.7 75.0 1.0 C A:GLY215 4.7 30.3 1.0 CA A:ASP58 4.7 30.1 1.0 O A:GLY57 4.8 29.8 1.0 N A:GLY57 4.9 32.9 1.0 CA A:GLY92 5.0 70.6 1.0 O A:GLY215 5.0 35.5 1.0

Manganese binding site 2 out of 4 in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:54.9 occ:0.30 OD1 A:ASP14 2.2 35.9 1.0 NE2 A:HIS16 2.5 33.6 1.0 NE2 A:HIS218 3.2 47.0 1.0 CG A:ASP14 3.2 33.5 1.0 CD2 A:HIS218 3.3 35.5 1.0 CE1 A:HIS16 3.4 37.2 1.0 O A:HIS216 3.5 36.5 1.0 CD2 A:HIS16 3.6 26.8 1.0 CB A:ASP14 3.8 19.7 1.0 CB A:ASP58 3.8 46.7 1.0 CG A:ASP58 3.9 52.0 1.0 C A:HIS216 4.0 35.4 1.0 OD1 A:ASP58 4.2 55.4 1.0 CA A:HIS216 4.2 37.2 1.0 OD2 A:ASP14 4.3 29.3 1.0 N A:ASP58 4.3 27.8 1.0 OD2 A:ASP58 4.3 56.5 1.0 ND1 A:HIS216 4.5 81.2 1.0 CE1 A:HIS218 4.5 39.1 1.0 MN A:MN402 4.5 60.1 0.3 ND1 A:HIS16 4.5 34.8 1.0 CA A:ASP14 4.6 23.6 1.0 CG A:HIS16 4.6 34.4 1.0 CG A:HIS218 4.6 38.5 1.0 CA A:ASP58 4.7 30.1 1.0

Manganese binding site 3 out of 4 in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:60.7 occ:0.09 NE2 B:HIS180 2.0 40.3 1.0 OD1 B:ASP58 2.1 49.0 1.0 ND1 B:HIS216 2.4 72.5 1.0 CE1 B:HIS180 2.4 49.5 1.0 CB B:HIS216 2.8 45.5 1.0 CG B:HIS216 3.0 57.8 1.0 CA B:HIS216 3.1 32.1 1.0 CG B:ASP58 3.1 45.8 1.0 CD2 B:HIS180 3.2 53.3 1.0 CE1 B:HIS216 3.6 76.5 1.0 ND1 B:HIS180 3.6 47.2 1.0 OD2 B:ASP58 3.7 54.1 1.0 N B:HIS216 3.9 26.8 1.0 N B:ASP58 3.9 28.9 1.0 CG B:HIS180 4.0 49.8 1.0 CA B:GLY57 4.1 27.1 1.0 C B:GLY57 4.1 26.1 1.0 CD2 B:HIS216 4.2 55.4 1.0 C B:HIS216 4.3 34.9 1.0 OD1 B:ASP14 4.3 37.3 1.0 CB B:ASP58 4.4 30.7 1.0 O B:HIS216 4.4 42.2 1.0 NE2 B:HIS216 4.5 65.9 1.0 CA B:ASP58 4.6 22.1 1.0 O B:GLY57 4.8 28.3 1.0 MN B:MN403 4.8 46.4 0.3 C B:GLY215 4.9 27.7 1.0

Manganese binding site 4 out of 4 in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:46.4 occ:0.35 NE2 B:HIS16 2.3 32.3 1.0 OD1 B:ASP14 2.4 37.3 1.0 CE1 B:HIS16 3.1 35.2 1.0 CD2 B:HIS218 3.1 30.6 1.0 NE2 B:HIS218 3.2 45.6 1.0 CG B:ASP14 3.4 26.0 1.0 CD2 B:HIS16 3.4 24.4 1.0 O B:HIS216 3.7 42.2 1.0 CB B:ASP14 3.8 22.2 1.0 C B:HIS216 4.0 34.9 1.0 CG B:ASP58 4.0 45.8 1.0 CB B:ASP58 4.1 30.7 1.0 ND1 B:HIS16 4.3 31.5 1.0 OD2 B:ASP58 4.3 54.1 1.0 OD1 B:ASP58 4.3 49.0 1.0 CA B:HIS216 4.3 32.1 1.0 CG B:HIS218 4.4 36.9 1.0 OD2 B:ASP14 4.4 31.7 1.0 CG B:HIS16 4.5 29.7 1.0 CE1 B:HIS218 4.5 35.1 1.0 N B:ASP58 4.6 28.9 1.0 N B:ILE217 4.6 40.2 1.0 CA B:ASP14 4.7 27.5 1.0 N B:HIS218 4.8 27.8 1.0 C B:ILE217 4.8 40.6 1.0 MN B:MN402 4.8 60.7 0.1 ND1 B:HIS216 4.9 72.5 1.0 CA B:ASP58 5.0 22.1 1.0

A.Shibata, D.Moiani, A.S.Arvai, J.Perry, S.M.Harding, M.M.Genois, R.Maity, S.Van Rossum-Fikkert, A.Kertokalio, F.Romoli, A.Ismail, E.Ismalaj, E.Petricci, M.J.Neale, R.G.Bristow, J.Y.Masson, C.Wyman, P.A.Jeggo, J.A.Tainer. Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities. Mol.Cell V. 53 7 2014.
ISSN: ISSN 1097-2765
PubMed: 24316220
DOI: 10.1016/J.MOLCEL.2013.11.003