Manganese in PDB 4nzv: 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: 4nzv 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)	44.48 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.116, 109.949, 76.917, 90.00, 100.21, 90.00
R / Rfree (%)	23.1 / 26.6

The binding sites of Manganese atom in the Dna Double-Strand Break Repair Pathway Choice Is Directed By Distinct MRE11 Nuclease Activities (pdb code 4nzv). 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: 4nzv:
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:33.3 occ:0.64 ND1 A:HIS216 1.9 38.6 1.0 OD2 A:ASP58 2.0 34.7 1.0 CE1 A:HIS180 2.1 36.8 1.0 O A:HOH504 2.3 39.6 1.0 NE2 A:HIS180 2.4 40.1 1.0 CG A:ASP58 2.7 40.5 1.0 CE1 A:HIS216 2.8 43.2 1.0 CG A:HIS216 2.9 36.6 1.0 OD1 A:ASP58 2.9 39.4 1.0 CB A:HIS216 3.3 34.2 1.0 ND1 A:HIS180 3.3 44.8 1.0 CD2 A:HIS180 3.7 38.7 1.0 CA A:HIS216 3.7 34.5 1.0 NE2 A:HIS216 3.9 40.6 1.0 CD2 A:HIS216 4.0 39.6 1.0 CB A:ASP58 4.1 35.2 1.0 CG A:HIS180 4.1 41.3 1.0 MN A:MN402 4.4 39.2 0.3 O A:HIS216 4.5 32.6 1.0 C A:HIS216 4.7 32.0 1.0 N A:ASN93 4.7 69.1 1.0 OD1 A:ASP14 4.7 38.5 1.0 N A:HIS216 4.8 30.9 1.0 CE2 A:TYR139 4.8 60.2 1.0 CA A:GLY92 4.9 48.6 1.0 OH A:TYR139 4.9 68.8 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:39.2 occ:0.35 NE2 A:HIS16 2.6 32.9 1.0 OD1 A:ASP14 2.6 38.5 1.0 NE2 A:HIS218 2.8 38.7 1.0 OD2 A:ASP58 2.8 34.7 1.0 CD2 A:HIS218 3.2 38.5 1.0 O A:HIS216 3.4 32.6 1.0 CE1 A:HIS16 3.4 33.7 1.0 CB A:ASP58 3.5 35.2 1.0 CG A:ASP58 3.5 40.5 1.0 CD2 A:HIS16 3.6 33.1 1.0 CG A:ASP14 3.7 36.8 1.0 CE1 A:HIS218 4.0 38.8 1.0 CB A:ASP14 4.0 30.4 1.0 C A:HIS216 4.0 32.0 1.0 CA A:HIS216 4.2 34.5 1.0 MN A:MN401 4.4 33.3 0.6 ND1 A:HIS216 4.4 38.6 1.0 CG A:HIS218 4.5 35.8 1.0 ND1 A:HIS16 4.6 29.5 1.0 OD1 A:ASP58 4.7 39.4 1.0 CA A:ASP14 4.7 24.0 1.0 CG A:HIS16 4.7 30.3 1.0 OD2 A:ASP14 4.7 29.1 1.0 ND1 A:HIS218 4.8 40.0 1.0 CA A:ASP58 5.0 36.1 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:Mn401 b:28.4 occ:0.47 ND1 B:HIS216 1.7 38.4 1.0 NE2 B:HIS180 1.9 39.1 1.0 OD1 B:ASP58 2.0 35.0 1.0 CE1 B:HIS180 2.5 39.3 1.0 CE1 B:HIS216 2.5 43.0 1.0 OD1 B:ASN93 2.6 71.7 1.0 CG B:ASP58 2.7 37.3 1.0 OD2 B:ASP58 2.8 41.0 1.0 CG B:HIS216 2.8 36.8 1.0 CD2 B:HIS180 3.1 42.5 1.0 CB B:HIS216 3.4 35.4 1.0 CG B:ASN93 3.6 76.5 1.0 NE2 B:HIS216 3.7 43.2 1.0 ND1 B:HIS180 3.7 44.7 1.0 CA B:HIS216 3.7 37.5 1.0 CD2 B:HIS216 3.8 45.3 1.0 CG B:HIS180 4.0 42.2 1.0 ND2 B:ASN93 4.0 79.4 1.0 CB B:ASP58 4.1 32.6 1.0 MN B:MN402 4.3 43.2 0.4 N B:ASN93 4.5 63.7 1.0 O B:HIS216 4.6 39.6 1.0 O B:HOH507 4.6 41.1 1.0 C B:HIS216 4.7 34.0 1.0 OD1 B:ASP14 4.7 44.7 1.0 N B:HIS216 4.8 33.5 1.0 CB B:ASN93 4.9 77.7 1.0 O B:HOH620 4.9 63.2 1.0 CA B:GLY92 4.9 53.8 1.0 CE1 B:TYR139 5.0 67.3 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:43.2 occ:0.39 OD1 B:ASP14 2.6 44.7 1.0 NE2 B:HIS16 2.6 36.5 1.0 OD1 B:ASP58 2.8 35.0 1.0 NE2 B:HIS218 2.9 44.2 1.0 O B:HOH620 2.9 63.2 1.0 CD2 B:HIS218 3.2 41.2 1.0 O B:HIS216 3.4 39.6 1.0 CB B:ASP58 3.5 32.6 1.0 CE1 B:HIS16 3.5 39.0 1.0 CG B:ASP58 3.6 37.3 1.0 CG B:ASP14 3.6 37.0 1.0 CD2 B:HIS16 3.6 40.0 1.0 CB B:ASP14 3.9 32.1 1.0 C B:HIS216 4.0 34.0 1.0 CE1 B:HIS218 4.1 43.9 1.0 CA B:HIS216 4.2 37.5 1.0 MN B:MN401 4.3 28.4 0.5 ND1 B:HIS216 4.5 38.4 1.0 CG B:HIS218 4.5 39.5 1.0 CA B:ASP14 4.6 24.5 1.0 ND1 B:HIS16 4.7 38.0 1.0 OD2 B:ASP14 4.7 36.4 1.0 CG B:HIS16 4.8 32.5 1.0 OD2 B:ASP58 4.8 41.0 1.0 O B:HOH622 4.9 61.2 1.0 ND1 B:HIS218 4.9 42.6 1.0 N B:HIS216 5.0 33.5 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