Manganese in PDB 3tho: Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State

The structure of Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State, PDB code: 3tho was solved by C.Moeckel, K.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 2.61
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.772, 121.772, 135.126, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.2

The structure of Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State (pdb code 3tho). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State, PDB code: 3tho:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1 b:49.3 occ:0.39 OD2 B:ASP58 2.5 44.4 1.0 OD2 B:ASP14 2.6 53.1 1.0 NE2 B:HIS16 2.8 52.8 1.0 NE2 B:HIS218 2.8 55.5 1.0 O B:HOH408 3.2 55.4 1.0 CD2 B:HIS218 3.4 49.4 1.0 CG B:ASP58 3.4 46.9 1.0 O B:HIS216 3.4 49.6 1.0 CE1 B:HIS16 3.5 49.5 1.0 NE2 B:GLN94 3.5 59.0 1.0 CB B:ASP58 3.6 42.8 1.0 CG B:ASP14 3.7 52.0 1.0 MN B:MN2 3.8 38.3 1.0 CD2 B:HIS16 3.8 51.7 1.0 C B:HIS216 3.9 46.9 1.0 CE1 B:HIS218 4.0 48.5 1.0 CA B:HIS216 4.0 42.7 1.0 CB B:ASP14 4.1 44.0 1.0 CD B:GLN94 4.5 61.3 1.0 OD1 B:ASP58 4.5 50.8 1.0 ND1 B:HIS216 4.5 43.0 1.0 CG B:HIS218 4.7 49.4 1.0 CA B:ASP14 4.7 48.1 1.0 ND1 B:HIS16 4.7 48.9 1.0 N B:HIS216 4.8 46.7 1.0 OE1 B:GLN94 4.8 62.3 1.0 OD1 B:ASP14 4.8 50.5 1.0 N B:ILE217 4.9 47.4 1.0 CG B:HIS16 4.9 48.5 1.0 ND1 B:HIS218 4.9 49.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of MRE11:RAD50 in Its Atp/Adp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2 b:38.3 occ:1.00 ND1 B:HIS216 1.9 43.0 1.0 NE2 B:HIS180 2.2 44.6 1.0 OD2 B:ASP58 2.2 44.4 1.0 OD1 B:ASN93 2.2 53.4 1.0 CE1 B:HIS216 2.9 44.7 1.0 CG B:HIS216 2.9 43.4 1.0 CG B:ASP58 3.0 46.9 1.0 CE1 B:HIS180 3.1 43.6 1.0 CD2 B:HIS180 3.2 40.5 1.0 OD1 B:ASP58 3.3 50.8 1.0 CB B:HIS216 3.3 41.3 1.0 CG B:ASN93 3.3 51.1 1.0 CA B:HIS216 3.4 42.7 1.0 NE2 B:GLN94 3.7 59.0 1.0 MN B:MN1 3.8 49.3 0.4 ND2 B:ASN93 3.8 49.2 1.0 NE2 B:HIS216 4.0 44.2 1.0 CD2 B:HIS216 4.0 47.3 1.0 O B:HOH408 4.1 55.4 1.0 O B:HIS216 4.2 49.6 1.0 ND1 B:HIS180 4.2 46.4 1.0 N B:ASN93 4.3 42.4 1.0 CG B:HIS180 4.3 47.3 1.0 C B:HIS216 4.3 46.9 1.0 CB B:ASP58 4.4 42.8 1.0 N B:HIS216 4.5 46.7 1.0 OD2 B:ASP14 4.6 53.1 1.0 CB B:ASN93 4.6 43.7 1.0 N B:GLN94 4.8 47.0 1.0 CA B:GLY92 4.9 41.8 1.0 CD B:GLN94 4.9 61.3 1.0 CA B:ASN93 5.0 47.0 1.0

C.Mockel, K.Lammens, A.Schele, K.P.Hopfner. Atp Driven Structural Changes of the Bacterial MRE11:RAD50 Catalytic Head Complex. Nucleic Acids Res. V. 40 914 2012.
ISSN: ISSN 0305-1048
PubMed: 21937514
DOI: 10.1093/NAR/GKR749