Manganese in PDB 3w5w: MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis

The structure of MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis, PDB code: 3w5w was solved by Y.Uemura, N.Nakagawa, T.Wakamatsu, G.T.Montelione, J.F.Hunt, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.828, 90.828, 107.878, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 27

The binding sites of Manganese atom in the MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis (pdb code 3w5w). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis, PDB code: 3w5w:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:51.2 occ:1.00 OD1 A:ASP33 2.2 40.6 1.0 OD2 A:ASP99 2.3 39.6 1.0 NE2 A:HIS29 2.6 39.4 1.0 CG A:ASP33 2.9 38.8 1.0 OD2 A:ASP33 3.0 45.2 1.0 O A:HOH544 3.3 53.8 1.0 CG A:ASP99 3.3 37.8 1.0 MN A:MN403 3.5 41.7 1.0 CD2 A:HIS29 3.5 39.4 1.0 CE1 A:HIS29 3.5 39.1 1.0 OD1 A:ASP99 3.8 38.9 1.0 CB A:ASP35 4.3 33.2 1.0 NE2 A:HIS126 4.4 55.9 1.0 CB A:ASP33 4.4 38.3 1.0 OD1 A:ASP177 4.4 51.6 1.0 N A:ALA36 4.4 35.7 1.0 O A:ASP99 4.5 40.1 1.0 CB A:ASP99 4.6 37.5 1.0 CB A:ALA36 4.6 36.0 1.0 ND1 A:HIS29 4.6 39.7 1.0 CG A:HIS29 4.7 40.2 1.0 OD2 A:ASP177 4.8 49.8 1.0 OD2 A:ASP35 4.8 31.1 1.0 CE1 A:HIS126 4.8 55.9 1.0 CA A:ALA36 5.0 36.1 1.0

Manganese binding site 2 out of 2 in the MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of MN2+-Gmp Complex of Nanornase (Nrn) From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:41.7 occ:1.00 OD2 A:ASP35 2.2 31.1 1.0 OD1 A:ASP99 2.2 38.9 1.0 OD2 A:ASP177 2.2 49.8 1.0 NE2 A:HIS125 2.3 52.0 1.0 CG A:ASP99 3.1 37.8 1.0 CG A:ASP35 3.1 32.7 1.0 CE1 A:HIS125 3.2 52.7 1.0 O A:HOH544 3.2 53.8 1.0 CG A:ASP177 3.2 49.6 1.0 OD2 A:ASP99 3.3 39.6 1.0 CD2 A:HIS125 3.3 49.9 1.0 CB A:ASP35 3.4 33.2 1.0 MN A:MN402 3.5 51.2 1.0 OD1 A:ASP177 3.6 51.6 1.0 NE2 A:HIS126 3.7 55.9 1.0 OG1 A:THR145 4.0 41.1 1.0 N A:THR145 4.1 39.9 1.0 OD1 A:ASP35 4.3 32.8 1.0 ND1 A:HIS125 4.3 50.5 1.0 CG A:HIS125 4.4 49.3 1.0 CE1 A:HIS126 4.5 55.9 1.0 CB A:ASP99 4.5 37.5 1.0 CB A:ASP177 4.5 46.6 1.0 CB A:THR145 4.6 40.0 1.0 CA A:SER144 4.6 40.6 1.0 CD2 A:HIS126 4.6 53.4 1.0 C A:SER144 4.8 39.9 1.0 OD2 A:ASP33 4.8 45.2 1.0 CA A:ASP35 4.9 34.4 1.0 CA A:THR145 5.0 38.8 1.0

Y.Uemura, N.Nakagawa, T.Wakamatsu, K.Kim, G.T.Montelione, J.F.Hunt, S.Kuramitsu, R.Masui. Crystal Structure of the Ligand-Binding Form of Nanornase From Bacteroides Fragilis, A Member of the Dhh/DHHA1 Phosphoesterase Family of Proteins To Be Published.