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

Protein crystallography data

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

Other elements in 3hbz:

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

Sodium Binding Sites:

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 3hbz

Go back to Sodium Binding Sites List in 3hbz
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 3hbz

Go back to Sodium Binding Sites List in 3hbz
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

Reference:

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
Page generated: Tue Dec 15 06:13:14 2020

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