Sodium in PDB 3imm: Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution

The structure of Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution, PDB code: 3imm was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.11 / 2.00
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	45.404, 45.404, 241.069, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 22.2

The structure of Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution (pdb code 3imm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution, PDB code: 3imm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution


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 Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:39.6 occ:1.00 OE1 A:GLN104 2.4 33.3 1.0 O A:SER84 2.5 28.2 1.0 OD1 A:ASN83 2.7 43.6 1.0 OE2 A:GLU102 2.7 36.2 1.0 O A:HOH9 3.1 38.2 1.0 C A:SER84 3.3 30.0 1.0 CD A:GLN104 3.3 32.8 1.0 CD A:GLU102 3.7 35.7 1.0 NE2 A:GLN104 3.7 29.6 1.0 N A:SER84 3.7 29.8 1.0 CA A:SER84 3.8 31.8 1.0 CG A:ASN83 3.9 41.0 1.0 NE2 A:GLN204 3.9 47.6 0.5 N A:GLY85 4.2 32.9 1.0 C A:ASN83 4.2 31.1 1.0 OE1 A:GLU102 4.2 33.4 1.0 O A:HOH378 4.3 38.6 1.0 CA A:GLY85 4.4 31.4 1.0 O A:ASN83 4.5 33.5 1.0 ND2 A:ASN83 4.6 46.2 1.0 CG A:GLN104 4.6 29.3 1.0 OE1 A:GLN204 4.6 42.7 0.5 OE1 A:GLN204 4.6 50.4 0.5 NE2 A:GLN204 4.7 38.4 0.5 O A:ILE105 4.7 33.3 1.0 CA A:GLN104 4.7 28.4 1.0 CD1 A:TYR126 4.7 30.0 1.0 CG A:GLU102 4.7 30.3 1.0 CD A:GLN204 4.7 47.1 0.5 N A:ILE105 4.8 30.2 1.0 CG A:TYR126 4.9 28.1 1.0 CA A:ASN83 4.9 31.9 1.0 CB A:GLN104 5.0 28.1 1.0 CB A:ASN83 5.0 34.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution


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 Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:30.7 occ:1.00 O B:HOH251 2.3 33.1 1.0 O B:HOH10 2.3 33.7 1.0 OE1 B:GLN104 2.4 31.1 1.0 OE2 B:GLU102 2.4 36.7 1.0 OD1 B:ASN83 2.5 47.1 1.0 O B:SER84 2.5 30.3 1.0 C B:SER84 3.3 27.7 1.0 CD B:GLN104 3.3 30.6 1.0 CD B:GLU102 3.5 32.9 1.0 CG B:ASN83 3.7 44.8 1.0 NE2 B:GLN104 3.7 29.0 1.0 N B:SER84 3.7 32.3 1.0 CA B:SER84 3.9 31.4 1.0 OE1 B:GLU102 3.9 31.8 1.0 OE1 B:GLN204 4.0 38.9 0.5 C B:ASN83 4.1 35.1 1.0 NE2 B:GLN204 4.2 41.3 0.5 N B:GLY85 4.3 30.1 1.0 CD B:GLN204 4.3 37.1 0.5 O B:ASN83 4.4 37.8 1.0 ND2 B:ASN83 4.4 48.7 1.0 NE2 B:GLN204 4.5 45.2 0.5 CA B:GLY85 4.5 29.8 1.0 CG B:GLU102 4.6 28.3 1.0 CG B:GLN104 4.6 27.5 1.0 CD1 B:TYR126 4.7 30.7 1.0 O B:ILE105 4.7 30.5 1.0 CA B:ASN83 4.7 34.9 1.0 CA B:GLN104 4.8 28.4 1.0 CB B:ASN83 4.8 38.0 1.0 N B:ILE105 4.9 27.2 1.0 CG B:TYR126 4.9 28.8 1.0 CD B:GLN204 5.0 39.0 0.5

Sodium binding site 3 out of 3 in the Crystal Structure of Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution


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 Putative Glycosyl Hydrolase (YP_001301887.1) From Parabacteroides Distasonis Atcc 8503 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3 b:37.6 occ:1.00 OE1 C:GLN104 2.2 36.0 1.0 O C:HOH383 2.2 35.2 1.0 OE2 C:GLU102 2.4 35.8 1.0 O C:SER84 2.4 32.5 1.0 OD1 C:ASN83 2.7 45.7 1.0 CD C:GLN104 3.3 33.4 1.0 C C:SER84 3.4 32.0 1.0 CD C:GLU102 3.5 33.5 1.0 OE1 C:GLN204 3.6 43.3 1.0 NE2 C:GLN204 3.7 37.7 1.0 NE2 C:GLN104 3.8 33.4 1.0 CG C:ASN83 3.9 42.5 1.0 CD C:GLN204 4.0 35.0 1.0 O C:ASN83 4.0 35.9 1.0 CA C:SER84 4.2 33.4 1.0 C C:ASN83 4.2 34.5 1.0 O3 C:TRS5 4.2 42.8 1.0 N C:GLY85 4.2 31.8 1.0 N C:SER84 4.2 32.3 1.0 CG C:GLU102 4.2 30.1 1.0 CA C:GLY85 4.3 32.1 1.0 OE1 C:GLU102 4.4 32.0 1.0 CG C:GLN104 4.5 32.9 1.0 ND2 C:ASN83 4.6 45.8 1.0 CA C:GLN104 4.6 30.1 1.0 N C:TRS5 4.6 36.5 1.0 C3 C:TRS5 4.8 39.0 1.0 N C:ILE105 4.9 30.3 1.0 O C:ILE105 4.9 31.9 1.0 CA C:ASN83 4.9 34.4 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.