Sodium in PDB 3hbz: Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution

The structure of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution, PDB code: 3hbz 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)	29.75 / 2.05
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.551, 94.551, 107.812, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.1

The structure of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution also contains other interesting chemical elements:

Arsenic	(As)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution (pdb code 3hbz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution, PDB code: 3hbz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 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 A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:43.9 occ:1.00 O A:HOH555 2.2 42.9 1.0 O A:ILE118 2.4 26.6 1.0 OE1 A:GLU135 2.4 29.4 1.0 O A:HOH454 2.6 35.8 1.0 O A:HOH590 2.8 47.6 1.0 O A:HOH395 2.8 27.3 1.0 CD A:GLU135 3.6 30.0 1.0 C A:ILE118 3.6 25.9 1.0 O A:HOH581 3.6 44.1 1.0 CB A:GLU135 4.1 23.2 1.0 O A:HOH577 4.2 39.5 1.0 O A:HOH406 4.3 38.2 1.0 CG A:GLU135 4.3 25.4 1.0 CA A:ILE118 4.4 28.8 1.0 CB A:ILE118 4.4 29.6 1.0 OE2 A:GLU135 4.5 31.4 1.0 O A:HOH603 4.5 37.9 1.0 N A:ILE118 4.5 23.8 1.0 N A:TYR119 4.5 25.9 1.0 CA A:GLU135 4.6 26.4 1.0 CB A:ALA116 4.6 27.0 1.0 CA A:TYR119 4.6 24.4 1.0 O A:ARG136 4.7 35.6 1.0 N A:ARG136 4.9 31.1 1.0 CD1 A:TYR119 4.9 25.6 1.0 CG2 A:ILE118 5.0 30.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 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 A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:56.2 occ:1.00 O A:HOH436 2.1 35.5 1.0 OD1 A:ASP30 2.5 31.0 1.0 OD1 A:ASN26 2.6 87.5 1.0 O A:HOH528 2.7 43.6 1.0 OD2 A:ASP30 2.7 31.1 1.0 CG A:ASP30 3.0 32.2 1.0 O A:GLU28 3.0 54.7 1.0 CG A:ASN26 3.8 89.7 1.0 C A:GLU28 3.8 54.8 1.0 CB A:GLU28 4.0 58.9 1.0 NZ A:LYS104 4.0 33.1 1.0 O A:ASN26 4.2 91.5 1.0 CA A:GLU28 4.4 59.5 1.0 CB A:ASP30 4.5 30.0 1.0 CE A:LYS104 4.5 33.7 1.0 ND2 A:ASN26 4.6 89.1 1.0 CB A:ASN26 4.7 90.3 1.0 N A:ALA29 4.7 45.3 1.0 N A:GLU28 4.8 63.8 1.0 N A:ASP30 4.8 29.4 1.0 C A:ALA29 4.9 33.9 1.0 CA A:ALA29 4.9 39.0 1.0

A.P.Yeh, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.Mcmullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.Van Den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Structure of Bacteroides Thetaiotaomicron BT2081 at 2.05 A Resolution: the First Structural Representative of A New Protein Family That May Play A Role in Carbohydrate Metabolism. Acta Crystallogr.,Sect.F V. 66 1287 2010.
ISSN: ESSN 1744-3091
PubMed: 20944224
DOI: 10.1107/S1744309110028228