Manganese in PDB 4o43: 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: 4o43 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)	37.88 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.060, 113.943, 81.566, 90.00, 100.31, 90.00
R / Rfree (%)	19.5 / 25.6

The binding sites of Manganese atom in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities (pdb code 4o43). 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: 4o43:
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:Mn401 b:57.8 occ:0.30 NE2 A:HIS180 1.9 45.0 1.0 CE1 A:HIS180 2.3 54.8 1.0 OD1 A:ASP58 2.5 78.9 1.0 ND1 A:HIS216 2.5 74.2 1.0 CB A:HIS216 2.6 49.7 1.0 CG A:HIS216 2.9 63.7 1.0 CD2 A:HIS180 2.9 49.8 1.0 CA A:HIS216 3.0 37.6 1.0 ND1 A:HIS180 3.4 60.2 1.0 CG A:ASP58 3.6 76.3 1.0 N A:HIS216 3.7 30.9 1.0 CE1 A:HIS216 3.7 79.6 1.0 CG A:HIS180 3.7 51.7 1.0 CA A:GLY57 4.0 47.4 1.0 N A:ASP58 4.0 36.0 1.0 C A:HIS216 4.2 29.1 1.0 CD2 A:HIS216 4.2 62.0 1.0 OD2 A:ASP58 4.2 81.3 1.0 C A:GLY57 4.2 43.9 1.0 O A:HIS216 4.3 56.1 1.0 NE2 A:HIS216 4.5 77.1 1.0 OD1 A:ASP14 4.6 48.4 1.0 MN A:MN402 4.6 52.9 0.3 C A:GLY215 4.7 33.8 1.0 CB A:ASP58 4.7 64.0 1.0 CA A:GLY92 4.8 70.8 1.0 CA A:ASP58 4.8 45.1 1.0 O A:GLY57 5.0 43.7 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:Mn402 b:52.9 occ:0.30 OD1 A:ASP14 2.2 48.4 1.0 NE2 A:HIS16 2.6 37.5 1.0 O A:HOH529 2.7 58.6 1.0 O A:HIS216 3.1 56.1 1.0 NE2 A:HIS218 3.2 57.9 1.0 CG A:ASP14 3.3 39.0 1.0 CD2 A:HIS218 3.4 55.7 1.0 CE1 A:HIS16 3.4 34.3 1.0 CD2 A:HIS16 3.6 44.1 1.0 C A:HIS216 3.8 29.1 1.0 CB A:ASP14 3.9 22.9 1.0 CB A:ASP58 4.0 64.0 1.0 CG A:ASP58 4.1 76.3 1.0 CA A:HIS216 4.1 37.6 1.0 OD1 A:ASP58 4.2 78.9 1.0 N A:ASP58 4.3 36.0 1.0 OD2 A:ASP14 4.3 39.0 1.0 CE1 A:HIS218 4.5 52.5 1.0 ND1 A:HIS216 4.5 74.2 1.0 OD2 A:ASP58 4.6 81.3 1.0 ND1 A:HIS16 4.6 36.8 1.0 MN A:MN401 4.6 57.8 0.3 CG A:HIS218 4.7 53.6 1.0 CA A:ASP14 4.7 25.8 1.0 CG A:HIS16 4.7 36.0 1.0 CA A:ASP58 4.7 45.1 1.0 N A:ILE217 4.8 32.0 1.0 N A:HIS216 4.9 30.9 1.0 O A:ASP58 5.0 30.3 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:Mn401 b:73.7 occ:0.34 NE2 B:HIS180 2.1 60.2 1.0 OD2 B:ASP58 2.2 60.3 1.0 CE1 B:HIS180 2.4 62.1 1.0 ND1 B:HIS216 2.6 72.3 1.0 CB B:HIS216 3.0 37.3 1.0 CG B:HIS216 3.2 59.0 1.0 CG B:ASP58 3.3 45.9 1.0 CD2 B:HIS180 3.3 59.9 1.0 CA B:HIS216 3.4 32.6 1.0 ND1 B:HIS180 3.6 64.5 1.0 OD1 B:ASP58 3.6 58.8 1.0 O B:HOH546 3.7 58.6 1.0 CE1 B:HIS216 3.8 77.0 1.0 CG B:HIS180 4.0 56.4 1.0 N B:HIS216 4.1 36.0 1.0 N B:ASP58 4.3 31.8 1.0 C B:GLY57 4.5 34.6 1.0 CD2 B:HIS216 4.5 66.9 1.0 CA B:GLY57 4.5 31.9 1.0 CB B:ASP58 4.6 33.4 1.0 C B:HIS216 4.6 29.5 1.0 O B:HIS216 4.7 43.5 1.0 NE2 B:HIS216 4.7 76.8 1.0 OD1 B:ASP14 4.9 41.6 1.0 CA B:ASP58 4.9 17.4 1.0 MN B:MN402 4.9 61.0 0.4

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:Mn402 b:61.0 occ:0.36 NE2 B:HIS16 2.6 42.7 1.0 OD1 B:ASP14 2.7 41.6 1.0 CE1 B:HIS16 3.0 35.5 1.0 NE2 B:HIS218 3.0 60.0 1.0 CD2 B:HIS218 3.1 58.1 1.0 O B:HIS216 3.4 43.5 1.0 CG B:ASP14 3.8 37.6 1.0 CD2 B:HIS16 3.8 30.6 1.0 CG B:ASP58 3.9 45.9 1.0 C B:HIS216 4.0 29.5 1.0 OD2 B:ASP58 4.0 60.3 1.0 CB B:ASP58 4.1 33.4 1.0 OD1 B:ASP58 4.2 58.8 1.0 ND1 B:HIS16 4.2 27.9 1.0 CA B:HIS216 4.3 32.6 1.0 CE1 B:HIS218 4.3 52.2 1.0 CB B:ASP14 4.4 29.1 1.0 CG B:HIS218 4.5 46.0 1.0 CG B:HIS16 4.7 33.1 1.0 ND1 B:HIS216 4.7 72.3 1.0 N B:ASP58 4.8 31.8 1.0 OD2 B:ASP14 4.8 31.5 1.0 N B:ILE217 4.8 34.5 1.0 MN B:MN401 4.9 73.7 0.3

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