Manganese in PDB 4o4k: 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: 4o4k 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)	37.41 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.769, 113.154, 80.891, 90.00, 101.47, 90.00
R / Rfree (%)	19.3 / 24

The binding sites of Manganese atom in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities (pdb code 4o4k). 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: 4o4k:
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:63.2 occ:0.64 ND1 A:HIS216 2.0 56.4 1.0 OD2 A:ASP58 2.3 71.6 1.0 CE1 A:HIS180 2.5 58.1 1.0 NE2 A:HIS180 2.6 45.4 1.0 OD1 A:ASP58 2.9 48.7 1.0 CE1 A:HIS216 2.9 54.7 1.0 CG A:ASP58 3.0 58.3 1.0 CG A:HIS216 3.0 53.4 1.0 CB A:HIS216 3.4 54.7 1.0 CA A:HIS216 3.7 43.7 1.0 ND1 A:HIS180 3.8 55.3 1.0 CD2 A:HIS180 3.8 42.8 1.0 NE2 A:HIS216 4.1 51.8 1.0 CD2 A:HIS216 4.1 49.0 1.0 MN A:MN402 4.3 52.4 0.3 O A:HIS216 4.3 53.4 1.0 CB A:ASP58 4.4 53.5 1.0 CG A:HIS180 4.4 49.5 1.0 C A:HIS216 4.6 46.4 1.0 OD1 A:ASP14 4.8 47.3 1.0 N A:HIS216 4.8 33.5 1.0 N A:ASN93 4.8 1.0 1.0 N A:ASP58 5.0 39.9 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:52.4 occ:0.35 OD1 A:ASP14 2.5 47.3 1.0 OD2 A:ASP58 2.7 71.6 1.0 NE2 A:HIS16 2.8 34.2 1.0 NE2 A:HIS218 2.9 64.9 1.0 CD2 A:HIS218 3.1 61.8 1.0 O A:HIS216 3.2 53.4 1.0 CG A:ASP14 3.5 45.7 1.0 CG A:ASP58 3.6 58.3 1.0 CE1 A:HIS16 3.6 31.5 1.0 CD2 A:HIS16 3.8 32.0 1.0 CB A:ASP58 3.8 53.5 1.0 C A:HIS216 3.9 46.4 1.0 CB A:ASP14 4.1 35.8 1.0 CE1 A:HIS218 4.2 68.5 1.0 CA A:HIS216 4.2 43.7 1.0 MN A:MN401 4.3 63.2 0.6 CG A:HIS218 4.4 61.3 1.0 OD2 A:ASP14 4.6 41.9 1.0 OD1 A:ASP58 4.7 48.7 1.0 ND1 A:HIS216 4.7 56.4 1.0 N A:ASP58 4.8 39.9 1.0 ND1 A:HIS16 4.8 36.0 1.0 CA A:ASP14 4.8 26.2 1.0 N A:ILE217 4.8 39.4 1.0 CG A:HIS16 4.9 32.0 1.0 CA A:ASP58 4.9 43.2 1.0 ND1 A:HIS218 4.9 71.0 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:70.0 occ:0.47 ND1 B:HIS216 2.1 58.2 1.0 OD1 B:ASP58 2.5 73.0 1.0 OD2 B:ASP58 2.6 59.5 1.0 CE1 B:HIS180 2.7 71.8 1.0 CE1 B:HIS216 2.8 60.2 1.0 NE2 B:HIS180 2.8 65.9 1.0 CG B:ASP58 2.9 62.7 1.0 CG B:HIS216 3.3 54.4 1.0 CB B:HIS216 3.8 46.2 1.0 ND1 B:HIS180 3.9 68.9 1.0 NE2 B:HIS216 4.0 71.2 1.0 CD2 B:HIS180 4.1 61.1 1.0 CA B:HIS216 4.1 44.3 1.0 CD2 B:HIS216 4.3 69.0 1.0 MN B:MN402 4.4 64.7 0.4 CB B:ASP58 4.4 45.6 1.0 O B:HIS216 4.6 54.3 1.0 NAI B:2PK403 4.6 74.2 0.4 CG B:HIS180 4.6 57.6 1.0 OAB B:2PK403 4.9 73.9 0.4 C B:HIS216 4.9 43.1 1.0 N B:ASP58 4.9 42.0 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:Mn402 b:64.7 occ:0.39 OD1 B:ASP58 2.5 73.0 1.0 OD1 B:ASP14 2.6 50.5 1.0 NE2 B:HIS16 2.7 46.0 1.0 NE2 B:HIS218 3.0 62.7 1.0 O B:HIS216 3.1 54.3 1.0 CD2 B:HIS218 3.1 56.7 1.0 CE1 B:HIS16 3.5 46.2 1.0 CG B:ASP58 3.6 62.7 1.0 CG B:ASP14 3.7 45.1 1.0 C B:HIS216 3.8 43.1 1.0 CD2 B:HIS16 3.9 41.8 1.0 CB B:ASP58 4.0 45.6 1.0 CA B:HIS216 4.2 44.3 1.0 CB B:ASP14 4.3 37.5 1.0 CE1 B:HIS218 4.3 55.8 1.0 MN B:MN401 4.4 70.0 0.5 CG B:HIS218 4.5 56.6 1.0 ND1 B:HIS216 4.6 58.2 1.0 ND1 B:HIS16 4.7 36.3 1.0 OD2 B:ASP58 4.7 59.5 1.0 N B:ASP58 4.7 42.0 1.0 N B:ILE217 4.7 43.3 1.0 OD2 B:ASP14 4.7 42.3 1.0 CG B:HIS16 4.9 36.9 1.0 CG B:HIS216 5.0 54.4 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