Sodium in PDB 4py9: Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192

The structure of Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192, PDB code: 4py9 was solved by J.Seetharaman, M.Abashidze, H.Wang, H.Janjua, E.L.Foote, R.Xiao, R.Nair, J.K.Everett, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.45 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.892, 90.892, 107.684, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 26.4

The binding sites of Sodium atom in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 (pdb code 4py9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192, PDB code: 4py9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:49.9 occ:1.00 OD1 A:ASN184 3.5 43.6 1.0 O A:HOH572 3.6 38.5 1.0 O3 A:PO4404 3.7 51.6 1.0 N A:ASN186 4.0 34.9 1.0 CB A:ASN186 4.0 37.2 1.0 CA A:ASN184 4.1 37.3 1.0 C A:ASN184 4.1 36.1 1.0 N A:SER185 4.3 34.9 1.0 ND2 A:ASN186 4.5 38.5 1.0 O A:ASN184 4.5 34.3 1.0 CG A:ASN184 4.5 41.5 1.0 CA A:ASN186 4.5 36.2 1.0 O1 A:PO4404 4.7 54.1 1.0 CG A:ASN186 4.8 38.4 1.0 P A:PO4404 4.9 52.8 1.0 CB A:ASN184 4.9 39.3 1.0 N A:ASN187 4.9 36.6 1.0 C A:SER185 5.0 34.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:44.3 occ:1.00 OD2 A:ASP33 2.9 38.0 1.0 OD1 A:ASP177 3.1 37.8 1.0 OG1 A:THR176 3.1 30.1 1.0 CG A:ASP33 3.4 34.0 1.0 O A:HOH571 3.4 50.9 1.0 N A:ASP35 3.6 29.9 1.0 N A:ASP177 3.6 33.0 1.0 CB A:THR176 3.7 30.2 1.0 CB A:ASP35 3.7 30.3 1.0 C A:THR176 3.7 32.1 1.0 CA A:ASP177 3.7 33.5 1.0 OD1 A:ASP33 3.8 34.4 1.0 O A:HOH563 3.9 60.1 1.0 CG A:ASP177 4.0 36.9 1.0 CB A:ASP177 4.0 35.1 1.0 O A:THR176 4.0 32.8 1.0 O A:HOH564 4.1 59.9 1.0 N A:GLY34 4.1 29.2 1.0 CB A:ASP33 4.2 32.5 1.0 CA A:ASP35 4.3 30.2 1.0 CA A:THR176 4.3 31.1 1.0 CA A:GLY34 4.4 29.3 1.0 C A:GLY34 4.5 29.6 1.0 O A:HOH555 4.5 41.6 1.0 C A:ASP33 4.8 30.5 1.0 O A:GLY173 4.9 29.4 1.0 CG2 A:THR176 5.0 29.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:25.5 occ:1.00 NH1 A:ARG155 3.4 41.2 1.0 N A:VAL5 3.4 42.3 1.0 N A:ILE6 3.5 37.0 1.0 NH2 A:ARG151 3.7 34.7 1.0 CB A:ARG151 3.7 32.6 1.0 O A:THR3 3.8 49.9 1.0 CG A:ARG155 3.8 41.3 1.0 CD A:ARG151 3.9 33.2 1.0 CG A:ARG151 3.9 32.7 1.0 CG1 A:ILE6 3.9 36.3 1.0 CB A:ILE6 4.1 36.4 1.0 CB A:VAL5 4.1 39.9 1.0 CA A:VAL5 4.1 40.0 1.0 CD1 A:ILE6 4.1 35.7 1.0 CD A:ARG155 4.2 40.7 1.0 CA A:LYS4 4.2 47.2 1.0 C A:LYS4 4.2 44.6 1.0 C A:VAL5 4.3 38.6 1.0 CA A:ILE6 4.3 36.1 1.0 CZ A:ARG155 4.5 41.8 1.0 CA A:ARG151 4.6 32.8 1.0 O A:ARG151 4.6 33.8 1.0 CZ A:ARG151 4.6 34.6 1.0 C A:ARG151 4.7 34.1 1.0 NE A:ARG151 4.7 33.9 1.0 CG2 A:VAL5 4.7 39.8 1.0 NE A:ARG155 4.8 41.0 1.0 O A:ILE6 4.8 35.6 1.0 C A:THR3 4.8 50.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:57.6 occ:1.00 OG A:SER138 2.4 37.1 1.0 O A:HIS126 2.4 31.9 1.0 OD2 A:ASP124 3.0 35.6 1.0 C A:HIS126 3.5 33.6 1.0 ND2 A:ASN101 3.5 39.0 1.0 CB A:SER138 3.5 38.3 1.0 N A:HIS126 3.6 34.9 1.0 CG A:ASP124 3.8 35.3 1.0 CB A:PRO129 3.9 38.1 1.0 CB A:ASN101 3.9 38.2 1.0 CE A:MSE122 3.9 47.2 1.0 CB A:ASP124 3.9 34.8 1.0 CA A:SER138 4.0 38.5 1.0 CA A:HIS126 4.0 35.6 1.0 O A:ASP124 4.1 32.6 1.0 CG A:PRO129 4.1 37.0 1.0 C A:ASP124 4.2 33.5 1.0 CG A:ASN101 4.2 38.2 1.0 CD A:PRO129 4.3 36.4 1.0 C A:HIS125 4.3 34.5 1.0 N A:HIS125 4.4 33.9 1.0 CB A:HIS126 4.5 36.5 1.0 SE A:MSE122 4.5 45.3 0.8 CA A:HIS125 4.6 34.8 1.0 N A:LEU127 4.6 33.3 1.0 C A:SER138 4.6 38.5 1.0 CA A:PRO129 4.6 38.2 1.0 N A:PRO129 4.6 36.7 1.0 CA A:ASP124 4.7 34.3 1.0 N A:HIS139 4.7 38.0 1.0 CG A:PRO140 4.8 35.2 1.0 OD1 A:ASP124 4.9 35.5 1.0 C A:LEU127 5.0 34.8 1.0 CA A:LEU127 5.0 34.2 1.0

J.Seetharaman, M.Abashidze, H.Wang, H.Janjua, E.L.Foote, R.Xiao, R.Nair, J.K.Everett, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg). Crystal Structure of An Exopolyphosphatase-Related Protein From Bacteroides Fragilis. Northeast Structural Genomics Target BFR192 To Be Published.