Manganese in PDB 2ygk: Crystal Structure of the Nura Nuclease From Sulfolobus Solfataricus

The structure of Crystal Structure of the Nura Nuclease From Sulfolobus Solfataricus, PDB code: 2ygk was solved by N.J.Rzechorzek, J.K.Blackwood, A.S.Abrams, J.D.Maman, N.P.Robinson, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.94 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.740, 80.280, 67.670, 90.00, 107.17, 90.00
R / Rfree (%)	23.176 / 27.089

The binding sites of Manganese atom in the Crystal Structure of the Nura Nuclease From Sulfolobus Solfataricus (pdb code 2ygk). 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 the Nura Nuclease From Sulfolobus Solfataricus, PDB code: 2ygk:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Nura Nuclease From Sulfolobus Solfataricus


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 the Nura Nuclease From Sulfolobus Solfataricus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1336 b:0.9 occ:1.00 OD1 A:ASP58 2.4 39.5 1.0 OD2 A:ASP133 2.5 47.8 1.0 O A:HOH2005 3.2 54.7 1.0 O A:HOH2016 3.3 65.5 1.0 CG A:ASP58 3.4 37.7 1.0 OD2 A:ASP58 3.6 48.6 1.0 CG A:ASP133 3.6 39.5 1.0 O A:GLY59 3.7 31.3 1.0 CB A:ASP133 4.2 38.1 1.0 N A:GLY59 4.2 32.5 1.0 O A:ASP133 4.3 39.1 1.0 O A:HOH2003 4.5 62.7 1.0 OE1 A:GLU116 4.6 39.4 1.0 OE2 A:GLU116 4.6 39.9 1.0 OD1 A:ASP133 4.6 45.1 1.0 C A:GLY59 4.7 31.6 1.0 CB A:ASP58 4.8 35.6 1.0 ND1 A:HIS306 4.9 47.8 1.0 CA A:GLY59 4.9 32.3 1.0 CD A:GLU116 4.9 36.9 1.0 C A:ASP133 5.0 37.7 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Nura Nuclease From Sulfolobus Solfataricus


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 the Nura Nuclease From Sulfolobus Solfataricus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1336 b:0.6 occ:1.00 OD1 B:ASP58 2.4 39.1 1.0 OD2 B:ASP133 2.5 48.3 1.0 CG B:ASP58 3.4 37.0 1.0 O B:HOH2031 3.5 47.2 1.0 CG B:ASP133 3.6 39.4 1.0 O B:HOH2030 3.6 59.1 1.0 OD2 B:ASP58 3.7 47.8 1.0 O B:GLY59 3.7 30.4 1.0 O B:HOH2013 3.7 62.4 1.0 CB B:ASP133 4.2 38.2 1.0 N B:GLY59 4.3 32.2 1.0 O B:ASP133 4.3 39.1 1.0 OE2 B:GLU116 4.6 40.2 1.0 OD1 B:ASP133 4.6 44.6 1.0 C B:GLY59 4.7 30.9 1.0 ND1 B:HIS306 4.7 47.2 1.0 OE1 B:GLU116 4.8 39.5 1.0 CB B:ASP58 4.8 35.3 1.0 CA B:GLY59 4.9 31.7 1.0 C B:ASP133 5.0 37.8 1.0

J.K.Blackwood, N.J.Rzechorzek, A.S.Abrams, J.D.Maman, L.Pellegrini, N.P.Robinson. Structural and Functional Insights Into Dna-End Processing By the Archaeal Hera Helicase-Nura Nuclease Complex. Nucleic Acids Res. V. 40 3183 2012.
ISSN: ISSN 0305-1048
PubMed: 22135300
DOI: 10.1093/NAR/GKR1157