Manganese in PDB 6asc: MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04

The structure of MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04, PDB code: 6asc was solved by D.Moiani, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.04 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.053, 112.682, 81.162, 90.00, 100.26, 90.00
R / Rfree (%)	19.7 / 23.2

The binding sites of Manganese atom in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04 (pdb code 6asc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04, PDB code: 6asc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:81.5 occ:0.35 ND1 A:HIS216 1.9 92.9 1.0 OD2 A:ASP58 2.7 72.3 1.0 CG A:HIS216 2.8 88.4 1.0 CE1 A:HIS180 2.9 69.1 1.0 CE1 A:HIS216 3.0 97.6 1.0 NE2 A:HIS180 3.0 63.2 1.0 CB A:HIS216 3.1 66.5 1.0 CG A:ASP58 3.3 68.3 1.0 OD1 A:ASP58 3.4 63.4 1.0 CA A:HIS216 3.4 52.4 1.0 O A:HIS216 3.9 52.9 1.0 CD2 A:HIS216 3.9 92.6 1.0 NE2 A:HIS216 4.0 93.8 1.0 ND1 A:HIS180 4.0 71.6 1.0 C A:HIS216 4.2 50.9 1.0 CD2 A:HIS180 4.2 69.0 1.0 MN A:MN402 4.3 60.2 0.3 N A:HIS216 4.6 44.8 1.0 CG A:HIS180 4.7 66.6 1.0 CB A:ASP58 4.7 65.1 1.0 N A:ASP58 4.8 42.7 1.0 OD1 A:ASP14 4.8 46.9 1.0

Manganese binding site 2 out of 4 in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:60.2 occ:0.35 OD1 A:ASP14 2.5 46.9 1.0 NE2 A:HIS16 2.8 49.4 1.0 OD2 A:ASP58 3.0 72.3 1.0 O A:HIS216 3.0 52.9 1.0 CD2 A:HIS218 3.2 60.1 1.0 NE2 A:HIS218 3.2 63.1 1.0 CG A:ASP14 3.4 51.1 1.0 CE1 A:HIS16 3.6 51.6 1.0 C A:HIS216 3.6 50.9 1.0 CD2 A:HIS16 3.9 47.8 1.0 CG A:ASP58 4.0 68.3 1.0 CA A:HIS216 4.0 52.4 1.0 CB A:ASP14 4.1 36.5 1.0 CB A:ASP58 4.2 65.1 1.0 OD2 A:ASP14 4.3 45.8 1.0 MN A:MN401 4.3 81.5 0.3 N A:ILE217 4.5 57.5 1.0 CG A:HIS218 4.5 58.9 1.0 CE1 A:HIS218 4.6 62.9 1.0 N A:ASP58 4.6 42.7 1.0 ND1 A:HIS216 4.7 92.9 1.0 C A:ILE217 4.8 57.9 1.0 ND1 A:HIS16 4.8 49.0 1.0 CA A:ILE217 4.8 60.6 1.0 N A:HIS218 4.9 52.0 1.0 N A:HIS216 4.9 44.8 1.0 CA A:ASP14 4.9 37.5 1.0 CG A:HIS16 5.0 41.5 1.0

Manganese binding site 3 out of 4 in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:75.8 occ:0.35 ND1 B:HIS216 2.0 91.1 1.0 OD1 B:ASP58 2.6 74.5 1.0 OD2 B:ASP58 2.9 75.0 1.0 CE1 B:HIS180 2.9 69.2 1.0 CE1 B:HIS216 3.0 94.2 1.0 CG B:HIS216 3.0 85.2 1.0 CG B:ASP58 3.1 65.8 1.0 NE2 B:HIS180 3.1 73.2 1.0 CB B:HIS216 3.4 58.9 1.0 CA B:HIS216 3.8 52.4 1.0 NE2 B:HIS216 4.1 93.5 1.0 ND1 B:HIS180 4.1 77.4 1.0 CD2 B:HIS216 4.1 90.6 1.0 O B:HIS216 4.3 51.8 1.0 MN B:MN402 4.4 51.0 0.3 CD2 B:HIS180 4.4 73.5 1.0 CB B:ASP58 4.6 48.7 1.0 C B:HIS216 4.6 51.2 1.0 N B:ASP58 4.8 45.4 1.0 CG B:HIS180 4.9 73.9 1.0 OD1 B:ASP14 5.0 45.8 1.0 N B:HIS216 5.0 50.2 1.0

Manganese binding site 4 out of 4 in the MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of MRE11 Dimer in Complex with Endonuclease Inhibitor PFM04 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:51.0 occ:0.35 OD1 B:ASP58 2.6 74.5 1.0 OD1 B:ASP14 2.7 45.8 1.0 NE2 B:HIS16 2.9 54.8 1.0 O B:HIS216 3.1 51.8 1.0 CD2 B:HIS218 3.2 59.6 1.0 NE2 B:HIS218 3.3 61.1 1.0 CE1 B:HIS16 3.5 47.6 1.0 C B:HIS216 3.6 51.2 1.0 CG B:ASP14 3.6 43.9 1.0 CG B:ASP58 3.7 65.8 1.0 CA B:HIS216 4.0 52.4 1.0 CD2 B:HIS16 4.0 41.6 1.0 CB B:ASP58 4.1 48.7 1.0 CB B:ASP14 4.2 39.1 1.0 MN B:MN401 4.4 75.8 0.3 N B:ILE217 4.4 55.1 1.0 ND1 B:HIS216 4.5 91.1 1.0 OD2 B:ASP14 4.5 42.8 1.0 CG B:HIS218 4.6 55.9 1.0 N B:ASP58 4.6 45.4 1.0 CE1 B:HIS218 4.6 55.7 1.0 C B:ILE217 4.7 53.5 1.0 ND1 B:HIS16 4.7 47.6 1.0 OD2 B:ASP58 4.8 75.0 1.0 CA B:ILE217 4.8 54.9 1.0 N B:HIS218 4.8 43.8 1.0 N B:HIS216 4.9 50.2 1.0 O B:ILE217 5.0 64.6 1.0 CG B:HIS216 5.0 85.2 1.0

D.Moiani, D.A.Ronato, C.A.Brosey, A.S.Arvai, A.Syed, J.Y.Masson, E.Petricci, J.A.Tainer. Targeting Allostery with Avatars to Design Inhibitors Assessed By Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities. Meth. Enzymol. V. 601 205 2018.
ISSN: ISSN 1557-7988
PubMed: 29523233
DOI: 10.1016/BS.MIE.2017.11.030