Magnesium in PDB 8un9: Crystal Structure of the Mrfb Exonuclease Catalytic Core

The structure of Crystal Structure of the Mrfb Exonuclease Catalytic Core, PDB code: 8un9 was solved by K.A.Manthei, J.Nandakumar, L.A.Simmons, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.74 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.874, 37.928, 92.616, 90, 99.15, 90
R / Rfree (%)	17.5 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of the Mrfb Exonuclease Catalytic Core (pdb code 8un9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Mrfb Exonuclease Catalytic Core, PDB code: 8un9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Mrfb Exonuclease Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mrfb Exonuclease Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.6 occ:1.00 O A:HOH419 2.0 41.3 1.0 OD2 A:ASP262 2.0 36.1 1.0 O A:HOH406 2.0 38.9 1.0 O A:HOH457 2.0 51.9 1.0 OE2 A:GLU109 2.3 40.2 1.0 OD2 A:ASP107 2.5 51.7 1.0 HE2 A:HIS258 3.0 30.0 0.0 CG A:ASP262 3.1 33.0 1.0 CG A:ASP107 3.2 47.7 1.0 CD A:GLU109 3.2 40.6 1.0 OD1 A:ASP107 3.3 43.8 1.0 OE1 A:GLU109 3.5 37.8 1.0 NE2 A:HIS258 3.7 34.1 1.0 HB3 A:ASP262 3.8 30.0 1.0 O A:THR108 3.8 41.1 1.0 O A:HOH524 3.9 55.6 1.0 HD21 A:ASN259 3.9 33.2 1.0 CB A:ASP262 3.9 29.3 1.0 HD2 A:HIS258 3.9 31.5 1.0 OD1 A:ASP262 4.0 31.6 1.0 HB2 A:ASP262 4.0 30.0 1.0 CD2 A:HIS258 4.2 30.4 1.0 HA A:ASN259 4.2 29.5 1.0 O A:HOH432 4.3 60.7 1.0 CG A:GLU109 4.6 37.2 1.0 HG2 A:GLU109 4.7 36.8 1.0 CB A:ASP107 4.7 34.5 1.0 H A:THR108 4.7 34.3 1.0 ND2 A:ASN259 4.7 34.4 1.0 CE1 A:HIS258 4.8 35.0 1.0 C A:THR108 4.8 41.1 1.0 HB3 A:ASP107 4.9 36.2 1.0 O A:HOH414 5.0 49.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mrfb Exonuclease Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mrfb Exonuclease Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:49.2 occ:1.00 O B:HOH407 1.9 42.9 1.0 O B:HOH442 2.0 57.7 1.0 OD2 B:ASP262 2.0 38.7 1.0 O B:HOH410 2.0 47.6 1.0 OE2 B:GLU109 2.3 45.6 1.0 OD2 B:ASP107 2.4 53.5 1.0 HE2 B:HIS258 3.1 30.0 0.0 CG B:ASP262 3.1 37.1 1.0 CG B:ASP107 3.1 47.1 1.0 OD1 B:ASP107 3.2 45.0 1.0 CD B:GLU109 3.3 47.5 1.0 OE1 B:GLU109 3.5 44.8 1.0 HB3 B:ASP262 3.7 33.6 1.0 O B:THR108 3.8 45.4 1.0 NE2 B:HIS258 3.8 37.5 1.0 HD21 B:ASN259 3.8 38.5 1.0 CB B:ASP262 3.9 32.9 1.0 HB2 B:ASP262 4.0 33.5 1.0 OD1 B:ASP262 4.0 33.2 1.0 HD2 B:HIS258 4.0 34.7 1.0 HA B:ASN259 4.2 34.6 1.0 CD2 B:HIS258 4.3 33.9 1.0 CB B:ASP107 4.6 36.3 1.0 CG B:GLU109 4.6 41.5 1.0 H B:THR108 4.7 39.6 1.0 ND2 B:ASN259 4.7 39.3 1.0 HG2 B:GLU109 4.7 42.1 1.0 C B:THR108 4.7 42.3 1.0 HB3 B:ASP107 4.8 37.6 1.0 CE1 B:HIS258 4.9 36.0 1.0 O B:HOH402 4.9 62.5 1.0 HA B:GLU109 5.0 42.7 1.0 N B:THR108 5.0 39.0 1.0

K.A.Manthei, L.M.Munson, J.Nandakumar, L.A.Simmons. Structural and Biochemical Characterization of the Mitomycin C Repair Exonuclease Mrfb. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38661211
DOI: 10.1093/NAR/GKAE308